BLASTP 2.2.21 [Jun-14-2009] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Reference for compositional score matrix adjustment: Altschul, Stephen F., John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis, Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109. Query= 0005.0312.p (556 letters) Database: COGmodified 192,987 sequences; 59,019,183 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value RSp1390 [K] COG1191 DNA-directed RNA polymerase specialized sigm... 302 1e-81 STM1956 [K] COG1191 DNA-directed RNA polymerase specialized sigm... 237 7e-62 fliA [K] COG1191 DNA-directed RNA polymerase specialized sigma s... 236 1e-61 ZfliA [K] COG1191 DNA-directed RNA polymerase specialized sigma ... 236 1e-61 ECs2661 [K] COG1191 DNA-directed RNA polymerase specialized sigm... 236 1e-61 >RSp1390 [K] COG1191 DNA-directed RNA polymerase specialized sigma subunit Rso Ralstonia solanacearum Length = 253 Score = 302 bits (774), Expect = 1e-81, Method: Compositional matrix adjust. Identities = 143/240 (59%), Positives = 186/240 (77%), Gaps = 2/240 (0%) Query: 285 MYNVKGKKGKNDLLEQHAPLVKKLAHQLKAKLPPSVEVDDLIQAGMMGLLDAVNRYEETH 344 MY G+K K+D + +APLV+++A+Q+ KLP SVE+DDLIQAGMMGLLDA++RYEET Sbjct: 11 MYTATGRKTKSDEMAAYAPLVRRIANQMMVKLPASVELDDLIQAGMMGLLDALSRYEETQ 70 Query: 345 GAQFETYAVQRIRGAMLDELRSSDWLPRSIRQNARKVEEAMQTLLQQLGRQPKEAELAQH 404 G QFE YA QRIRGA+LDELR SDWLPR +R+NAR +E+A+Q L QQ GR P E E+A Sbjct: 71 GVQFEFYAAQRIRGAILDELRGSDWLPRGLRRNARTIEQAIQKLQQQKGRAPTETEIAAA 130 Query: 405 MQISLEDYQSLLSECGGHQLIYYEDFHDDDGGHEHFLDRHQTSDSDDPLQNLINGGFREA 464 + +SL DYQ LL E G QL+YYEDF +D + F++ + PL L++ RE+ Sbjct: 131 LNMSLADYQKLLVELQGSQLLYYEDFDREDA--DAFIENRAPENDATPLDQLLDHDLRES 188 Query: 465 VVDSIKALPEREQILMALYYEQEMNLKEIGAVMGVSESRVCQLHSQAISRMRSYLREHSW 524 VV +I+ALPERE+++M+LYYEQ++NL+EIGAVMGVSESRVCQ+HSQAI+R+RS LRE +W Sbjct: 189 VVAAIEALPEREKLMMSLYYEQDLNLREIGAVMGVSESRVCQIHSQAIARIRSRLRERAW 248 >STM1956 [K] COG1191 DNA-directed RNA polymerase specialized sigma subunit Sty Salmonella typhimurium LT2 Length = 239 Score = 237 bits (604), Expect = 7e-62, Method: Compositional matrix adjust. Identities = 117/239 (48%), Positives = 171/239 (71%), Gaps = 4/239 (1%) Query: 282 VTCMYNVKGKKGKNDLLEQHAPLVKKLAHQLKAKLPPSVEVDDLIQAGMMGLLDAVNRYE 341 + +Y +G K+ L +++ PLV+ A +L+ +LP SVE+DDL+QAG +GLL+AV+RY+ Sbjct: 1 MNSLYTAEGVMDKHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVDRYD 60 Query: 342 ETHGAQFETYAVQRIRGAMLDELRSSDWLPRSIRQNARKVEEAMQTLLQQLGRQPKEAEL 401 G F TYAVQRIRGAMLDELRS DW+PRS+R+NAR+V +AM L Q+LGR E E+ Sbjct: 61 ALQGTAFTTYAVQRIRGAMLDELRSRDWVPRSVRRNAREVAQAMGQLEQELGRNATETEV 120 Query: 402 AQHMQISLEDYQSLLSECGGHQLIYYEDFHDDDGGH-EHFLDRHQTSDSDDPLQNLINGG 460 A+ + I + +Y+ +L + QL Y+++ ++ G E + HQ ++PL L+ G Sbjct: 121 AERLGIPVAEYRQMLLDTNNSQLFSYDEWREEHGDSIELVTEEHQ---QENPLHQLLEGD 177 Query: 461 FREAVVDSIKALPEREQILMALYYEQEMNLKEIGAVMGVSESRVCQLHSQAISRMRSYL 519 R+ V+D+I++LPEREQ+++ LYY++E+NLKEIGAV+ V ESRV QLHSQAI R+R+ L Sbjct: 178 LRQRVMDAIESLPEREQLVLTLYYQEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKL 236 >fliA [K] COG1191 DNA-directed RNA polymerase specialized sigma subunit Eco Escherichia coli K12 Length = 239 Score = 236 bits (601), Expect = 1e-61, Method: Compositional matrix adjust. Identities = 116/239 (48%), Positives = 170/239 (71%), Gaps = 4/239 (1%) Query: 282 VTCMYNVKGKKGKNDLLEQHAPLVKKLAHQLKAKLPPSVEVDDLIQAGMMGLLDAVNRYE 341 + +Y +G K+ L +++ PLV+ A +L+ +LP SVE+DDL+QAG +GLL+AV RY+ Sbjct: 1 MNSLYTAEGVMDKHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYD 60 Query: 342 ETHGAQFETYAVQRIRGAMLDELRSSDWLPRSIRQNARKVEEAMQTLLQQLGRQPKEAEL 401 G F TYAVQRIRGAMLDELRS DW+PRS+R+NAR+V +A+ L Q+LGR E E+ Sbjct: 61 ALQGTAFTTYAVQRIRGAMLDELRSRDWVPRSVRRNAREVAQAIGQLEQELGRNATETEV 120 Query: 402 AQHMQISLEDYQSLLSECGGHQLIYYEDFHDDDGGH-EHFLDRHQTSDSDDPLQNLINGG 460 A+ + I + DY+ +L + QL Y+++ ++ G E D HQ ++PLQ L++ Sbjct: 121 AERLGIDIADYRQMLLDTNNSQLFSYDEWREEHGDSIELVTDDHQ---RENPLQQLLDSN 177 Query: 461 FREAVVDSIKALPEREQILMALYYEQEMNLKEIGAVMGVSESRVCQLHSQAISRMRSYL 519 R+ V+++I+ LPERE++++ LYY++E+NLKEIGAV+ V ESRV QLHSQAI R+R+ L Sbjct: 178 LRQRVMEAIETLPEREKLVLTLYYQEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKL 236 >ZfliA [K] COG1191 DNA-directed RNA polymerase specialized sigma subunit EcZ Escherichia coli O157:H7 EDL933 Length = 239 Score = 236 bits (601), Expect = 1e-61, Method: Compositional matrix adjust. Identities = 116/239 (48%), Positives = 170/239 (71%), Gaps = 4/239 (1%) Query: 282 VTCMYNVKGKKGKNDLLEQHAPLVKKLAHQLKAKLPPSVEVDDLIQAGMMGLLDAVNRYE 341 + +Y +G K+ L +++ PLV+ A +L+ +LP SVE+DDL+QAG +GLL+AV RY+ Sbjct: 1 MNSLYTAEGVMDKHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYD 60 Query: 342 ETHGAQFETYAVQRIRGAMLDELRSSDWLPRSIRQNARKVEEAMQTLLQQLGRQPKEAEL 401 G F TYAVQRIRGAMLDELRS DW+PRS+R+NAR+V +A+ L Q+LGR E E+ Sbjct: 61 ALQGTAFTTYAVQRIRGAMLDELRSRDWVPRSVRRNAREVAQAIGQLEQELGRNATETEV 120 Query: 402 AQHMQISLEDYQSLLSECGGHQLIYYEDFHDDDGGH-EHFLDRHQTSDSDDPLQNLINGG 460 A+ + I + DY+ +L + QL Y+++ ++ G E D HQ ++PLQ L++ Sbjct: 121 AERLGIDIADYRQMLLDTNNSQLFSYDEWREEHGDSIELVTDDHQ---RENPLQQLLDSN 177 Query: 461 FREAVVDSIKALPEREQILMALYYEQEMNLKEIGAVMGVSESRVCQLHSQAISRMRSYL 519 R+ V+++I+ LPERE++++ LYY++E+NLKEIGAV+ V ESRV QLHSQAI R+R+ L Sbjct: 178 LRQRVMEAIETLPEREKLVLTLYYQEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKL 236 >ECs2661 [K] COG1191 DNA-directed RNA polymerase specialized sigma subunit Ecs Escherichia coli O157:H7 Length = 239 Score = 236 bits (601), Expect = 1e-61, Method: Compositional matrix adjust. Identities = 116/239 (48%), Positives = 170/239 (71%), Gaps = 4/239 (1%) Query: 282 VTCMYNVKGKKGKNDLLEQHAPLVKKLAHQLKAKLPPSVEVDDLIQAGMMGLLDAVNRYE 341 + +Y +G K+ L +++ PLV+ A +L+ +LP SVE+DDL+QAG +GLL+AV RY+ Sbjct: 1 MNSLYTAEGVMDKHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYD 60 Query: 342 ETHGAQFETYAVQRIRGAMLDELRSSDWLPRSIRQNARKVEEAMQTLLQQLGRQPKEAEL 401 G F TYAVQRIRGAMLDELRS DW+PRS+R+NAR+V +A+ L Q+LGR E E+ Sbjct: 61 ALQGTAFTTYAVQRIRGAMLDELRSRDWVPRSVRRNAREVAQAIGQLEQELGRNATETEV 120 Query: 402 AQHMQISLEDYQSLLSECGGHQLIYYEDFHDDDGGH-EHFLDRHQTSDSDDPLQNLINGG 460 A+ + I + DY+ +L + QL Y+++ ++ G E D HQ ++PLQ L++ Sbjct: 121 AERLGIDIADYRQMLLDTNNSQLFSYDEWREEHGDSIELVTDDHQ---RENPLQQLLDSN 177 Query: 461 FREAVVDSIKALPEREQILMALYYEQEMNLKEIGAVMGVSESRVCQLHSQAISRMRSYL 519 R+ V+++I+ LPERE++++ LYY++E+NLKEIGAV+ V ESRV QLHSQAI R+R+ L Sbjct: 178 LRQRVMEAIETLPEREKLVLTLYYQEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKL 236