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: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF 2,715,099 sequences; 757,237,578 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value ref|NP_623354.1| DNA-directed RNA polymerase specialized sigma s... 233 5e-60 ref|ZP_00034184.1| COG1508: DNA-directed RNA polymerase speciali... 224 3e-57 gb|EAJ36227.1| unknown [environmental sequence] 221 2e-56 ref|NP_834808.1| RNA polymerase sigma-54 factor rpoN [Bacillus c... 219 7e-56 ref|NP_981538.1| RNA polymerase sigma-54 factor [Bacillus cereus... 219 9e-56 >ref|NP_623354.1| DNA-directed RNA polymerase specialized sigma subunits, sigma54 homologs [Thermoanaerobacter tengcongensis] gb|AAM24958.1| DNA-directed RNA polymerase specialized sigma subunits, sigma54 homologs [Thermoanaerobacter tengcongensis] Length = 451 Score = 233 bits (595), Expect = 5e-60, 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 >ref|ZP_00034184.1| COG1508: DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Burkholderia fungorum] Length = 567 Score = 224 bits (571), Expect = 3e-57, Method: Compositional matrix adjust. Identities = 120/301 (39%), Positives = 182/301 (60%), Gaps = 3/301 (0%) Query: 122 LREALDVVQGFEPAGVGAATLSECLLLQLRRM--VPRQPLAEALAAGYLEVXXXXXXXXX 179 L AL ++ F+PAGVGA + SECL LQL R+ P + LA + A +LE+ Sbjct: 267 LNAALALLHSFDPAGVGARSASECLKLQLLRLDASPTRTLALEIVAHHLELLAARDFTRL 326 Query: 180 XXXXFVTNEEIACAYRTIQSLNPYPGACYGGGTDSYVIPDLYIRSGLRGYEIFCNESALP 239 +++++ A+ I+SL P+PGA YG YV+PD+ +R +G++ N +P Sbjct: 327 RKHLKASDDDLRDAHVLIRSLEPFPGAAYGKAEADYVVPDIMVRKTAQGWQAELNPEVVP 386 Query: 240 AVTINRYYDGMMNSMSRTSPELQFLKGYHRSAKWLVKCIEERKKTLLLVGRAMLEHQFDF 299 + IN Y ++ + +R P L+ + A+WL+K I++R +T+L V +A++E Q F Sbjct: 387 KLRINHLYANILRN-NRGDPGSGSLRQQLQEARWLIKNIQQRFETILRVAQAIVERQKSF 445 Query: 300 VVKGKASLKPLTLRMVSDCIGLHESTVSRAVNGKYVQTPGGLYELKDLLCSAVNSAGGEV 359 V G+ +++PL LR ++D +GLHESTVSR GKY+ TP G E K S V++ G Sbjct: 446 FVHGEIAMRPLVLREIADTLGLHESTVSRVTTGKYMLTPFGTLEFKYFFGSHVSTDTGGA 505 Query: 360 SSVPYIQSRIRELIREEDPGKPLSDQRLSEQLAEEGLTVARRTVAKYREELGLSSAALRR 419 +S I++ I++LI E+P PLSD R++E LAE+G VARRTVAKYRE L + + LR+ Sbjct: 506 ASSTAIRALIKQLIGAENPKSPLSDSRIAELLAEQGFVVARRTVAKYREALKIPAVNLRK 565 Query: 420 S 420 S Sbjct: 566 S 566 >gb|EAJ36227.1| unknown [environmental sequence] Length = 501 Score = 221 bits (564), Expect = 2e-56, Method: Compositional matrix adjust. Identities = 120/301 (39%), Positives = 179/301 (59%), Gaps = 3/301 (0%) Query: 122 LREALDVVQGFEPAGVGAATLSECLLLQLRRM--VPRQPLAEALAAGYLEVXXXXXXXXX 179 L AL ++ F+PAGVGA + SECL LQL R+ P + LA + + +LE+ Sbjct: 201 LNAALALLHSFDPAGVGARSASECLKLQLLRLDPSPTRTLALEIVSQHLELLAARDFTRL 260 Query: 180 XXXXFVTNEEIACAYRTIQSLNPYPGACYGGGTDSYVIPDLYIRSGLRGYEIFCNESALP 239 +++ + A+ I+SL P+PGA YG YV+PD+ ++ +G+ N +P Sbjct: 261 RKHLKASDDALRDAHALIRSLEPFPGAAYGKAEADYVVPDIIVKKAGQGWLAELNPEVVP 320 Query: 240 AVTINRYYDGMMNSMSRTSPELQFLKGYHRSAKWLVKCIEERKKTLLLVGRAMLEHQFDF 299 + IN Y ++ + SR P LK + A+WL+K I++R T+L V +A++E Q +F Sbjct: 321 RLRINNLYANILRN-SRGDPSAGSLKQQLQEARWLIKNIQQRFDTILRVAQAIVERQKNF 379 Query: 300 VVKGKASLKPLTLRMVSDCIGLHESTVSRAVNGKYVQTPGGLYELKDLLCSAVNSAGGEV 359 G+ +++PL LR ++D +GLHESTVSR GKY+ TP G E K S V++ G Sbjct: 380 FAHGEIAMRPLVLREIADTLGLHESTVSRVTTGKYMLTPFGTLEFKYFFGSHVSTDTGGA 439 Query: 360 SSVPYIQSRIRELIREEDPGKPLSDQRLSEQLAEEGLTVARRTVAKYREELGLSSAALRR 419 +S I++ I++LI EDP PLSD R++E LAE+G VARRTVAKYRE L + + LR+ Sbjct: 440 ASSTAIRALIKQLIGAEDPKSPLSDSRIAELLAEQGFVVARRTVAKYREALKIPAVNLRK 499 Query: 420 S 420 S Sbjct: 500 S 500 >ref|NP_834808.1| RNA polymerase sigma-54 factor rpoN [Bacillus cereus ATCC 14579] gb|AAP12009.1| RNA polymerase sigma-54 factor rpoN [Bacillus cereus ATCC 14579] Length = 435 Score = 219 bits (559), Expect = 7e-56, Method: Compositional matrix adjust. Identities = 131/421 (31%), Positives = 224/421 (53%), Gaps = 7/421 (1%) Query: 1 MRQGLEILQLSITDLSTYLERQCEENPMLERLESLEQPEGLENAFETTSWAAKGNPFSGE 60 +RQ + +LQ ++ +LS +L Q ENP++E L E+ + + ++ N E Sbjct: 19 LRQAITMLQYNVQELSEFLYEQSLENPLIE-LGGFEREKKKSSNNSKSTSKQVENQM--E 75 Query: 61 LKAVRQDTLEEVLLEQLNCLSGLPESVIAAARYLIGNINDRXXXXXXXXXXXXXXXXXXX 120 + +V T+++ LL Q+ + E A ++I N++ Sbjct: 76 IYSVDSTTIQQHLLNQIQYYK-IDEEERKVASFIIMNMDGNGYLQETNEELAELLSAPIH 134 Query: 121 VLREALDVVQGFEPAGVGAATLSECLLLQLRRMVPRQPLAEALAAGYLEVXXXXXXXXXX 180 V+ ++++VQ EPAGVGA + ECL LQL+R+ R LAE + + Sbjct: 135 VVDRSVELVQSLEPAGVGARNIQECLTLQLKRLQRRNGLAEEVVEDHFAYFVKKDWRKLV 194 Query: 181 XXXFVTNEEIACAYRTIQSLNPYPGACYGGGTDSYVIPDLYIRSGLRGYEIFCNESALPA 240 +NEE+ A I SL P PG + Y++PD+ ++ + NE +P Sbjct: 195 QVLKCSNEELQSAVNCITSLQPKPGLAFSSDKPLYIVPDMAVKKDGDRLVLQMNERNMPR 254 Query: 241 VTINRYYDGMMNSMSRTSPELQFLKGYHRSAKWLVKCIEERKKTLLLVGRAMLEHQFDFV 300 + I+ Y ++N+ S ++ ++ +W+++ +++RK+TLL V ++E Q DF Sbjct: 255 IEIHSEYSALLNN--SESEVASYVSEKYQHVQWIMRSLKQRKQTLLQVMTIIMEKQRDFF 312 Query: 301 VKGKASLKPLTLRMVSDCIGLHESTVSRAVNGKYVQTPGGLYELKDLLCSAVNSAGGEVS 360 KG L+PL L+ V++ + +HEST+SRA KYVQTP GL+E+K +AV++ E Sbjct: 313 WKGPEYLRPLALKEVAEELSVHESTISRATRNKYVQTPHGLFEMKSFFSNAVSTTEDEAV 372 Query: 361 SVPYIQSRIRELIREEDPGKPLSDQRLSEQLAEEG-LTVARRTVAKYREELGLSSAALRR 419 S ++ I+ LI ED KPLSDQ++S+ L EE + ++RRTVAKYRE++ + +++LR+ Sbjct: 373 STKRVKQFIQTLIGAEDKKKPLSDQKISKLLEEEHEIVISRRTVAKYREQMHIPASSLRK 432 Query: 420 S 420 + Sbjct: 433 T 433 >ref|NP_981538.1| RNA polymerase sigma-54 factor [Bacillus cereus ATCC 10987] gb|AAS44146.1| RNA polymerase sigma-54 factor [Bacillus cereus ATCC 10987] Length = 435 Score = 219 bits (558), Expect = 9e-56, Method: Compositional matrix adjust. Identities = 130/421 (30%), Positives = 224/421 (53%), Gaps = 7/421 (1%) Query: 1 MRQGLEILQLSITDLSTYLERQCEENPMLERLESLEQPEGLENAFETTSWAAKGNPFSGE 60 +RQ + +LQ ++ +LS +L Q ENP++E L E+ + + ++ N E Sbjct: 19 LRQAITMLQYNVQELSEFLYEQSLENPLIE-LGGFEREKKKSSNNSKSTSKQVENQM--E 75 Query: 61 LKAVRQDTLEEVLLEQLNCLSGLPESVIAAARYLIGNINDRXXXXXXXXXXXXXXXXXXX 120 + +V T+++ LL Q+ + E A ++I N++ Sbjct: 76 IYSVDSTTIQQHLLNQIQYYK-IEEEERKVASFIIMNMDGNGYLQETNEELANLLSAPLH 134 Query: 121 VLREALDVVQGFEPAGVGAATLSECLLLQLRRMVPRQPLAEALAAGYLEVXXXXXXXXXX 180 V+ ++++VQ EPAGVGA + ECL LQL+R+ R LAE + + Sbjct: 135 VVDRSVELVQSLEPAGVGARNIQECLTLQLKRLQRRNGLAEEVVEDHFAYFVKKDWRKLV 194 Query: 181 XXXFVTNEEIACAYRTIQSLNPYPGACYGGGTDSYVIPDLYIRSGLRGYEIFCNESALPA 240 +NEE+ A I SL P PG + Y++PD+ ++ + NE +P Sbjct: 195 QMLKCSNEELQSAVNCITSLQPKPGLAFSSDKPLYIVPDMAVKKDGDRLVLQMNERNMPR 254 Query: 241 VTINRYYDGMMNSMSRTSPELQFLKGYHRSAKWLVKCIEERKKTLLLVGRAMLEHQFDFV 300 + I+ Y ++N+ S ++ ++ +W+++ +++RK+TLL V ++E Q DF Sbjct: 255 IEIHSEYSALLNN--SESEVASYVSEKYQHVQWIMRSLKQRKQTLLQVMTIIMEKQRDFF 312 Query: 301 VKGKASLKPLTLRMVSDCIGLHESTVSRAVNGKYVQTPGGLYELKDLLCSAVNSAGGEVS 360 KG LKPL L+ V++ + +HEST+SRA KYVQTP GL+E+K +AV++ E Sbjct: 313 WKGPEYLKPLALKEVAEELSVHESTISRATRNKYVQTPHGLFEMKSFFSNAVSTTEDEAV 372 Query: 361 SVPYIQSRIRELIREEDPGKPLSDQRLSEQLAEEG-LTVARRTVAKYREELGLSSAALRR 419 S ++ I+ L+ E+ KPLSDQ++S+ L EE + ++RRTVAKYRE++ + +++LR+ Sbjct: 373 STKRVKQFIQTLVEAENKKKPLSDQKISKLLEEEHEIVISRRTVAKYREQMHIPASSLRK 432 Query: 420 S 420 + Sbjct: 433 T 433 Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF Posted date: Mar 24, 2004 1:53 AM Number of letters in database: 757,237,578 Number of sequences in database: 2,715,099 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: 2715099 Number of Hits to DB: 553,215,313 Number of extensions: 20731334 Number of successful extensions: 51321 Number of sequences better than 1.0e-05: 297 Number of HSP's gapped: 50725 Number of HSP's successfully gapped: 297 Length of query: 422 Length of database: 757,237,578 Length adjustment: 128 Effective length of query: 294 Effective length of database: 409,704,906 Effective search space: 120453242364 Effective search space used: 120453242364 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: 127 (53.5 bits)