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= 0560.0020.p (197 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_691149.1| RNA polymerase ECF-type sigma factor [Oceanobac... 82 9e-15 ref|NP_388054.1| RNA polymerase ECF-type sigma factor (sigma-W) ... 80 3e-14 gb|EAI44306.1| unknown [environmental sequence] 79 7e-14 ref|NP_241129.1| RNA polymerase ECF-type sigma factor [Bacillus ... 78 9e-14 ref|ZP_00022293.1| COG1595: DNA-directed RNA polymerase speciali... 77 2e-13 >ref|NP_691149.1| RNA polymerase ECF-type sigma factor [Oceanobacillus iheyensis HTE831] dbj|BAC12184.1| RNA polymerase ECF-type sigma factor (sigma-W) [Oceanobacillus iheyensis HTE831] Length = 187 Score = 81.6 bits (200), Expect = 9e-15, Method: Compositional matrix adjust. Identities = 49/176 (27%), Positives = 95/176 (53%), Gaps = 16/176 (9%) Query: 20 VERVKAGDKQAYGAVISQFERQMYTYCYYILKNHAETEDAVQEIFVRAYENLQHYNRQVS 79 +++VK GD+ A+ V+S ++ +++ +CY +L N E ED QE F+RAY N+ ++ + Sbjct: 9 IKQVKKGDQSAFAEVVSFYQNKIFQHCYRMLGNKHEAEDIAQEAFIRAYINIDSFDEKRK 68 Query: 80 FSAWLYKMAYHHLIN--LKKKQSRWLKL-------VEKYKEQQPVMQIFEHESTVYELLV 130 FS WLY++A + I+ K+K +L ++ Y + ++ E EL Sbjct: 69 FSTWLYRIATNLTIDRIRKRKPDYYLDAEVKGTEGLDMYSQLASTERLPGEEVESRELQR 128 Query: 131 Y-------LTTEERHILLLKAVEQYTFEEIGDIIGLKPATIRKKYERLRHKLVERM 179 Y L + R I++L+ +E+++ +EI +I+ + T++ + R R L +R+ Sbjct: 129 YIHHEISQLPAKYRSIIMLRYLEEFSLQEISEILDIPLGTVKTRIHRGREALRKRL 184 >ref|NP_388054.1| RNA polymerase ECF-type sigma factor (sigma-W) [Bacillus subtilis] sp|Q45585|SIGW_BACSU RNA polymerase sigma factor sigW pir||H69706 RNA polymerase ECF-type sigma factor sigW - Bacillus subtilis dbj|BAA19507.1| YbbL [Bacillus subtilis] emb|CAB11949.1| RNA polymerase ECF(extracytoplasmic function)-type sigma factor (sigma-W) [Bacillus subtilis subsp. subtilis str. 168] Length = 187 Score = 80.1 bits (196), Expect = 3e-14, Method: Compositional matrix adjust. Identities = 46/172 (26%), Positives = 90/172 (52%), Gaps = 16/172 (9%) Query: 20 VERVKAGDKQAYGAVISQFERQMYTYCYYILKNHAETEDAVQEIFVRAYENLQHYNRQVS 79 +++VK GD+ A+ ++ ++ ++Y CY +L N E ED QE F+RAY N+ ++ Sbjct: 9 IKQVKKGDQDAFADIVDIYKDKIYQLCYRMLGNVHEAEDIAQEAFIRAYVNIDSFDINRK 68 Query: 80 FSAWLYKMAYHHLIN--LKKKQSRWL--------------KLVEKYKEQQPVMQIFEHES 123 FS WLY++A + I+ KKK +L ++V + + E + Sbjct: 69 FSTWLYRIATNLTIDRIRKKKPDYYLDAEVAGTEGLTMYSQIVADGVLPEDAVVSLELSN 128 Query: 124 TVYELLVYLTTEERHILLLKAVEQYTFEEIGDIIGLKPATIRKKYERLRHKL 175 T+ + ++ L + R +++LK +++ + EIG+I+ + T++ + R R L Sbjct: 129 TIQQKILKLPDKYRTVIVLKYIDELSLIEIGEILNIPVGTVKTRIHRGREAL 180 >gb|EAI44306.1| unknown [environmental sequence] Length = 179 Score = 78.6 bits (192), Expect = 7e-14, Method: Compositional matrix adjust. Identities = 49/178 (27%), Positives = 92/178 (51%), Gaps = 8/178 (4%) Query: 12 KRNAVEAAVERVKAGDKQAYGAVISQFERQMYTYCYYILKNHAETEDAVQEIFVRAYENL 71 K+N + VE + GD A+ + + F+ +++ + IL+N+ ETED VQ+ F+RA+E + Sbjct: 2 KKNNIPQLVELSQKGDSNAFEILFTTFKTRLHHSIFKILRNYHETEDIVQQAFMRAWEKI 61 Query: 72 QHYNRQVSFSAWLYKMAYHHLINLKKKQSRWLKLVEKYKEQQPVMQIFEHE-------ST 124 + +F WLY++ ++ I K SR ++ E ++ + E + + Sbjct: 62 GTFKGNSNFYTWLYRIGFNLAIT-KINSSRENQINEIFESNLAAPENIEKDLESKELSNL 120 Query: 125 VYELLVYLTTEERHILLLKAVEQYTFEEIGDIIGLKPATIRKKYERLRHKLVERMNQK 182 V LL + E+R +L V+ +EEI +I G+ T+R + R R L+E + ++ Sbjct: 121 VKNLLDQVPEEQRTAYILCEVDSKNYEEIANITGVPVGTVRSRIFRARKYLIESLQEQ 178 >ref|NP_241129.1| RNA polymerase ECF-type sigma factor [Bacillus halodurans] pir||G83682 RNA polymerase ECF-type sigma factor sigW [imported] - Bacillus halodurans (strain C-125) dbj|BAB03982.1| RNA polymerase ECF-type sigma factor [Bacillus halodurans] Length = 187 Score = 78.2 bits (191), Expect = 9e-14, Method: Compositional matrix adjust. Identities = 50/176 (28%), Positives = 94/176 (53%), Gaps = 16/176 (9%) Query: 20 VERVKAGDKQAYGAVISQFERQMYTYCYYILKNHAETEDAVQEIFVRAYENLQHYNRQVS 79 V V+AGD+QA+ ++ ++ ++Y Y ++ N E +D QE F+RAY N+ Y+ Q Sbjct: 9 VREVRAGDEQAFAELVELYKDKVYQVAYRMVGNVHEAQDVAQEAFLRAYTNIDTYDIQRK 68 Query: 80 FSAWLYKMAYHHLINLKKKQSRWLKLVEKYK-------------EQQPV-MQIFEHEST- 124 FS WL+++A + I+ +K+ L + + +++PV Q+ + E+ Sbjct: 69 FSTWLFRIATNVAIDRLRKRKPDFHLEDPVQGADGLTIESQLAADEEPVDDQVIQMETRD 128 Query: 125 -VYELLVYLTTEERHILLLKAVEQYTFEEIGDIIGLKPATIRKKYERLRHKLVERM 179 + + + L + R +LLK +E + +EI DI+ L +T++ + R R L +RM Sbjct: 129 WIQQEIQALPPKYRMAVLLKYMEDLSLKEISDILDLPVSTVKTRIHRGREALRKRM 184 >ref|ZP_00022293.1| COG1595: DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Ralstonia metallidurans] Length = 199 Score = 77.0 bits (188), Expect = 2e-13, Method: Compositional matrix adjust. Identities = 48/186 (25%), Positives = 92/186 (49%), Gaps = 17/186 (9%) Query: 11 AKRNAVEAAVERVKAGDKQAYGAVISQFERQMYTYCYYILKNHAETEDAVQEIFVRAYEN 70 ++R A + VERV+ GDK+A+ +++++ R++ ++++ AE ED Q+ F++AY Sbjct: 2 SEREADQLLVERVQQGDKRAFELLVTKYHRKIIRLISRLVRDPAEVEDVAQDAFIKAYRA 61 Query: 71 LQHYNRQVSFSAWLYKMAYHHLINLKKKQSRWLKL--------VEKYKEQQPVMQIFEHE 122 L + + +F WLY++A + N Q R + E + + + + I E Sbjct: 62 LPQFRGESAFYTWLYRIAVNTAKNYLATQGRRPEASSDIDAEEAETFADGEQLRDINTPE 121 Query: 123 S---------TVYELLVYLTTEERHILLLKAVEQYTFEEIGDIIGLKPATIRKKYERLRH 173 S TV + L E R + L+ +E ++EEI + +G T+R + R R Sbjct: 122 SMLHTRQVADTVNRAMEALPEELRTAITLREIEGLSYEEIAEAMGCPIGTVRSRIFRARE 181 Query: 174 KLVERM 179 + E++ Sbjct: 182 AIAEKL 187 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 0.319 0.133 0.382 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: 276,641,983 Number of extensions: 10278941 Number of successful extensions: 37534 Number of sequences better than 1.0e-05: 280 Number of HSP's gapped: 37536 Number of HSP's successfully gapped: 280 Length of query: 197 Length of database: 757,237,578 Length adjustment: 119 Effective length of query: 78 Effective length of database: 434,140,797 Effective search space: 33862982166 Effective search space used: 33862982166 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 122 (51.6 bits)