BLASTP 2.2.18 [Mar-02-2008] 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= 0523.0012.p (422 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value Q8R962.1 Q8R962_THETN DNA-directed RNA polymerase specialized si... 233 2e-59 A1HTX7.1 A1HTX7_9FIRM RNA polymerase, sigma 54 subunit, RpoN 233 3e-59 A5CYP0.1 A5CYP0_PELTS DNA-directed RNA polymerase specialized si... 233 3e-59 B0K876.1 B0K876_THEP3 RNA polymerase, sigma 54 subunit, RpoN 231 8e-59 A8MFX6.1 A8MFX6_ALKOO RNA polymerase, sigma 54 subunit, RpoN 226 2e-57 >Q8R962.1 Q8R962_THETN DNA-directed RNA polymerase specialized sigma subunits, sigma54 homologs Length = 451 Score = 233 bits (595), Expect = 2e-59, Method: Compositional matrix adjust. Identities = 147/434 (33%), Positives = 232/434 (53%), Gaps = 17/434 (3%) Query: 1 MRQGLEILQLSITDLSTYLERQCEENPMLERLESLEQ-------------PEGLENAFET 47 ++Q +EILQL+ +L+ ++++ E NP+LER E E E + + Sbjct: 21 LKQAIEILQLNALELNELIQQELENNPLLEREEVEEDIYVVDVKELAKSIREMEKRMYYR 80 Query: 48 TSWAAKGNPFSGELKAVRQDTLEEVLLEQLNCLSGLPESVIAAARYLIGNINDRXXXXXX 107 S + + F+ E + L + LL QL+ ++ +P + Y+I ++ Sbjct: 81 DSDDEEMDEFNYENFVSAKPGLSDHLLFQLH-ITPVPTRIRKICEYIIFSLTPSGYLKED 139 Query: 108 XXXXXXXXXXXXXVLREALDVVQGFEPAGVGAATLSECLLLQLRRMVPRQPLAEALAAGY 167 + EAL VVQ F+P GVGA L ECL LQL + + + L + Sbjct: 140 VREIAQMLECTEEEVLEALAVVQSFDPPGVGARNLQECLKLQLLAQGNYKGIIKDLVENH 199 Query: 168 LEVXXXXXXXXXXXXXFVTNEEIACAYRTIQSLNPYPGACYGGGTDSYVIPDLYIRSGLR 227 LE V+ +E+ A I+ LNP PG+ + + Y++PD+ + Sbjct: 200 LEDIAEGRYSYLAKLYNVSAKEVQKAVDAIKKLNPKPGSVFAPEAEGYIVPDVEVIKRDG 259 Query: 228 GYEIFCNESALPAVTINRYYDGMMNSMSRTSPELQFLKGYHRSAKWLVKCIEERKKTLLL 287 Y + N+S +P + IN YY ++ S + +++ +SA WL+K IE RK+TL Sbjct: 260 EYLVLVNDSNIPRLRINSYYYSILESSDEEAK--KYITSKLQSAMWLIKSIESRKETLYK 317 Query: 288 VGRAMLEHQFDFVVKGKASLKPLTLRMVSDCIGLHESTVSRAVNGKYVQTPGGLYELKDL 347 V + +++ Q +F+ KG LKPLT + V+D +G+HESTVSRA+NGKYVQTP G +ELK Sbjct: 318 VVKTIVDLQKEFLDKGINYLKPLTQKQVADILGIHESTVSRAINGKYVQTPRGTFELKFF 377 Query: 348 LCSAVNSAGGEVSSVPYIQSRIRELIREEDPGKPLSDQRLSEQLAEEGLTVARRTVAKYR 407 S ++S G+ S +++ I++LI EEDP PLSDQ+++E L E+ + ++RRTVAKYR Sbjct: 378 FQSGLSSKNGKEFSAETVKNLIKKLIEEEDPANPLSDQKIAEILREKNINISRRTVAKYR 437 Query: 408 EELGLSSAALRRSR 421 EE + S L+R R Sbjct: 438 EECNIPS-TLKRKR 450 >A1HTX7.1 A1HTX7_9FIRM RNA polymerase, sigma 54 subunit, RpoN Length = 462 Score = 233 bits (593), Expect = 3e-59, Method: Compositional matrix adjust. Identities = 161/444 (36%), Positives = 231/444 (52%), Gaps = 29/444 (6%) Query: 1 MRQGLEILQLSITDLSTYLERQCEENPMLERLES-LEQPEG--------LENAFETTSW- 50 +RQ + ILQLS +L +E + ENP+LE ++ L + EG L+ A + W Sbjct: 21 LRQAIAILQLSSLELVEMVEAELLENPVLEVEDNRLGEAEGEAPADSGSLDLANDYLEWV 80 Query: 51 -------------AAKGNPFSGELKAVRQDTLEEVLLEQLNCLSGLPESVIAAARYLIGN 97 AA+ S E L E L QL+ L+ L S A YLIG Sbjct: 81 KYLDEGIDTGFVPAAEEEKSSAEFYGATMVPLHEHLEFQLH-LAALNASARRAGEYLIGC 139 Query: 98 INDRXXXXXXXXXXXXXXXXXXXVLREALDVVQGFEPAGVGAATLSECLLLQLRRMVPRQ 157 I+D ++ E L ++Q F+P GVGA L ECL +Q R+ Sbjct: 140 IDDNGYLRVSVEEAAAALAMPAALVEEVLTLIQTFDPPGVGARDLRECLSIQARQRGIAD 199 Query: 158 PLAEALAAGYLEVXXXXXXXXXXXXXFVTNEEIACAYRTIQSLNPYPGACYGGGTDS-YV 216 P+ A+ GYL T +++ A I++L+P PG +G G S Y+ Sbjct: 200 PIVWAVIDGYLPDIAAGRLRCIANKLGCTTQDVQRAVDIIRTLDPKPGRGFGQGKQSAYI 259 Query: 217 IPDLYI-RSGLRGYEIFCNESALPAVTINRYYDGMMNSMSRTSPELQFLKGYHRSAKWLV 275 +PD+ I R G R Y I N+S +P +TIN YY +M S +F++G +A WL+ Sbjct: 260 LPDVTIERVGGR-YVILVNDSIVPRLTINPYYRRLMREAD--SDARRFVEGRINAALWLM 316 Query: 276 KCIEERKKTLLLVGRAMLEHQFDFVVKGKASLKPLTLRMVSDCIGLHESTVSRAVNGKYV 335 + IE+R++TL V A+++ Q DF G L+PLT++ V++ +G+HESTVSRA KY Sbjct: 317 RSIEQRRQTLYNVVEAIVDLQRDFFDHGPKFLRPLTMKKVAERLGIHESTVSRATANKYA 376 Query: 336 QTPGGLYELKDLLCSAVNSAGGEVSSVPYIQSRIRELIREEDPGKPLSDQRLSEQLAEEG 395 TP GL L+ + V AGGE + ++ IREL+ EDP PLSDQ L+E L+ G Sbjct: 377 ATPHGLLALRAFFSAGVQGAGGEDVAACQVKREIRELVAREDPAHPLSDQALTELLSRRG 436 Query: 396 LTVARRTVAKYREELGLSSAALRR 419 + V+RRTVAKYREELG+ S+ R+ Sbjct: 437 IAVSRRTVAKYREELGIPSSCKRK 460 >A5CYP0.1 A5CYP0_PELTS DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog Length = 471 Score = 233 bits (593), Expect = 3e-59, Method: Compositional matrix adjust. Identities = 150/454 (33%), Positives = 241/454 (53%), Gaps = 36/454 (7%) Query: 1 MRQGLEILQLSITDLSTYLERQCEENPMLE-------RLESLE-----QPEG-------- 40 +RQ + +LQLS +LS Y+E+Q +ENPMLE R E E +P+G Sbjct: 21 LRQAITVLQLSSLELSMYIEQQLQENPMLELTDDDYGREEEFEPTVEPEPDGGGPEYDLD 80 Query: 41 ----LENA------FETTSWAAKGNPFSGELKAVRQDTLEEVLLEQLNCLSGLPESVIAA 90 L+ + F W + +S E + TL E L QLN LS Sbjct: 81 WEEYLQESSDDPGIFRQERWQDQ-QEYSYENFLYQMPTLTEHLTTQLN-LSPCRGKDKLI 138 Query: 91 ARYLIGNINDRXXXXXXXXXXXXXXXXXXXVLREALDVVQGFEPAGVGAATLSECLLLQL 150 YLIGNI++ + + L V+QGF+P GVGA +L ECLL+Q+ Sbjct: 139 GEYLIGNIDENGYLRVPLKEVAACLNVSTSRVFKVLKVIQGFDPPGVGARSLEECLLIQV 198 Query: 151 RRMVPRQPLAEALAAGYLEVXXXXXXXXXXXXXFVTNEEIACAYRTIQSLNPYPGACYGG 210 ++ + + L +L VT +E+ A +++L+P PG + Sbjct: 199 GQLGIKNEILNKLIKEHLSDLAKGKLNRIAQSLGVTVQEVQKAADVLRTLDPKPGRNFSN 258 Query: 211 GTDS-YVIPDLYIRSGLRGYEIFCNESALPAVTINRYYDGMMNSMSR-TSPELQFLKGYH 268 D+ Y++PD+ + Y I N+ A+P +TIN Y +++S + S +F++ Sbjct: 259 LNDTRYIVPDIVLEKVEGEYVILINDVAIPRLTINSTYRSVLSSNTNCDSGTRRFVESKL 318 Query: 269 RSAKWLVKCIEERKKTLLLVGRAMLEHQFDFVVKGKASLKPLTLRMVSDCIGLHESTVSR 328 +A WL++ IE+R+ TL V + +++ Q DF+ G LKPL L+ V++ +GLHESTVSR Sbjct: 319 NAAAWLIRSIEQRRLTLYKVAKCLVDLQRDFLDYGVKYLKPLNLKKVAEMVGLHESTVSR 378 Query: 329 AVNGKYVQTPGGLYELKDLLCSAVNSAGGEVSSVPYIQSRIRELIREEDPGKPLSDQRLS 388 A + KY+QTP G++E+K C+ +N+ G + S I+ ++E++ ED PL+DQ++S Sbjct: 379 ATSNKYIQTPQGVFEMKYFFCTGLNNTAGNMVSAECIKKMLQEIVAGEDARSPLNDQKIS 438 Query: 389 EQLAEEGLTVARRTVAKYREELGLSSAALRRSRQ 422 E + G+ ++RRTVAKYR+ELG+ AA+R+ ++ Sbjct: 439 ELFRQRGIKISRRTVAKYRDELGI--AAIRKRKR 470 >B0K876.1 B0K876_THEP3 RNA polymerase, sigma 54 subunit, RpoN Length = 454 Score = 231 bits (590), Expect = 8e-59, Method: Compositional matrix adjust. Identities = 144/447 (32%), Positives = 231/447 (51%), Gaps = 43/447 (9%) Query: 1 MRQGLEILQLSITDLSTYLERQCEENPMLERLESLEQPEGLENAFETTSWAAKGNPFSGE 60 ++Q +EILQL+ +L+ +E++ E NP+LE+ E +E E+ +E+ N F+ Sbjct: 21 LKQAIEILQLNSLELNALIEQELETNPLLEKEEVIE-----EDIYES-------NDFTEL 68 Query: 61 LKAVRQD---------------------------TLEEVLLEQLNCLSGLPESVIAAARY 93 K +R+ +L + LL QL+ P+ + Y Sbjct: 69 AKYIRETEERMYYDDSDDEEIEEVNYENFVSTKPSLTDHLLFQLHITPVSPK-IQKICEY 127 Query: 94 LIGNINDRXXXXXXXXXXXXXXXXXXXVLREALDVVQGFEPAGVGAATLSECLLLQLRRM 153 +I +++ + E L +VQ F+P G+ A L ECL LQL Sbjct: 128 IIFSLSPSGYLREDIKDIAEILECTEEEVLEGLSIVQSFDPPGIAARNLQECLKLQLLAQ 187 Query: 154 VPRQPLAEALAAGYLEVXXXXXXXXXXXXXFVTNEEIACAYRTIQSLNPYPGACYGGGTD 213 + + + L +LE ++ +E+ A I+ LNP PG+ + D Sbjct: 188 DSYKGIVKELVDYHLEEIAEGKYSYLAKLYNISLKEVQQAVDFIKKLNPKPGSSFSSTAD 247 Query: 214 -SYVIPDLYIRSGLRGYEIFCNESALPAVTINRYYDGMMNSMSRTSPELQFLKGYHRSAK 272 Y++PD+ + Y + N+S P + IN YY ++NS + +++ +SA Sbjct: 248 VRYIVPDVEVIKREGEYFVIVNDSVTPKLKINNYYHSILNSHDEEAK--KYINSKLQSAM 305 Query: 273 WLVKCIEERKKTLLLVGRAMLEHQFDFVVKGKASLKPLTLRMVSDCIGLHESTVSRAVNG 332 WL+K +E RK+TL V +A++E Q DF+ KG LKP+T + ++D +G+HESTVSRA+NG Sbjct: 306 WLIKSLESRKETLYKVVKAIVELQRDFLDKGINYLKPMTQKQIADIVGIHESTVSRAING 365 Query: 333 KYVQTPGGLYELKDLLCSAVNSAGGEVSSVPYIQSRIRELIREEDPGKPLSDQRLSEQLA 392 KYV TP GL+ELK S +++ G S I++ I++LI EEDP PLSDQ++++ L Sbjct: 366 KYVATPRGLFELKFFFQSGISNKNGNEFSAETIKNLIKKLIEEEDPTNPLSDQKIADILK 425 Query: 393 EEGLTVARRTVAKYREELGLSSAALRR 419 E+ + ++RRTVAKYREE + S RR Sbjct: 426 EKNINISRRTVAKYREECNIPSTIKRR 452 >A8MFX6.1 A8MFX6_ALKOO RNA polymerase, sigma 54 subunit, RpoN Length = 461 Score = 226 bits (577), Expect = 2e-57, Method: Compositional matrix adjust. Identities = 137/427 (32%), Positives = 217/427 (50%), Gaps = 22/427 (5%) Query: 14 DLSTYLERQCEENPMLE-----------------RLESLEQPEGLEN----AFETTSWAA 52 +L ++ Q E+NP+LE +++ + E +E+ ++ +++ Sbjct: 34 ELEEFIAEQLEKNPVLENDAEKEHNELWDSKIEDKIKEINWKEYIEDFNNYSYTKSNYQN 93 Query: 53 KGNPFSGELKAVRQDTLEEVLLEQLNCLSGLPESVIAAARYLIGNINDRXXXXXXXXXXX 112 + N F+ E + +L+E LL Q L+ L YLI +I+DR Sbjct: 94 EDNEFNYENIISNKSSLQEYLLFQY-SLTLLDRKYFEIGEYLINSIDDRGYLTVTIKDVT 152 Query: 113 XXXXXXXXVLREALDVVQGFEPAGVGAATLSECLLLQLRRMVPRQPLAEALAAGYLEVXX 172 ++ L ++Q F+P GVGA T+ ECLLLQLR + + L YL Sbjct: 153 EHFNEEENIVESILQIIQSFDPPGVGARTIEECLLLQLRFLDVKDEKIYQLIKEYLPEIA 212 Query: 173 XXXXXXXXXXXFVTNEEIACAYRTIQSLNPYPGACYGGGTDSYVIPDLYIRSGLRGYEIF 232 VT E++ I++L P PG + + Y+ PD+ ++ Y + Sbjct: 213 ANKYPLLAKKLGVTIEQLQGYCDFIKTLEPKPGRMFESNLNRYITPDITVKKLDEEYILL 272 Query: 233 CNESALPAVTINRYYDGMMNSMSRTSPELQFLKGYHRSAKWLVKCIEERKKTLLLVGRAM 292 N+ P + I Y M+ S S +FL SA WL++ IE+RK+T+ V + Sbjct: 273 TNDFDEPRLKIREDYRTMIISEDENSEVAKFLNNQFNSAAWLIRSIEQRKQTIYKVAEVI 332 Query: 293 LEHQFDFVVKGKASLKPLTLRMVSDCIGLHESTVSRAVNGKYVQTPGGLYELKDLLCSAV 352 +E Q F KGK L P+TL+ V++ I +HESTVSRA NGKY++TP G +ELK V Sbjct: 333 VEKQKGFFEKGKKFLVPMTLKEVAEEISVHESTVSRATNGKYMETPHGTFELKFFFTGGV 392 Query: 353 NSAGGEVSSVPYIQSRIRELIREEDPGKPLSDQRLSEQLAEEGLTVARRTVAKYREELGL 412 S G S I+S IR++I+ EDP KPLSD ++ +L +G++++RRTVAKYR+E+G+ Sbjct: 393 ESDEGMGISSESIKSFIRDIIKVEDPKKPLSDDKIVSELERKGISISRRTVAKYRDEMGI 452 Query: 413 SSAALRR 419 S++ R+ Sbjct: 453 LSSSKRK 459 Database: pfamseq Posted date: Aug 5, 2010 3:22 PM Number of letters in database: 3,060,696,203 Number of sequences in database: 9,421,015 Lambda K H 0.317 0.134 0.383 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 9421015 Number of Hits to DB: 2,246,320,773 Number of extensions: 85134112 Number of successful extensions: 214844 Number of sequences better than 1.0e-05: 1062 Number of HSP's gapped: 211801 Number of HSP's successfully gapped: 1062 Length of query: 422 Length of database: 3,060,696,203 Length adjustment: 138 Effective length of query: 284 Effective length of database: 1,760,596,133 Effective search space: 500009301772 Effective search space used: 500009301772 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 133 (55.8 bits)