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= 0188.0085.p (206 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_240981.1| RNA polymerase sigma-H factor (sigma-30) [Bacil... 334 7e-91 sp|P02964|RPSH_BACLI RNA polymerase sigma-H factor (Sigma-30) >g... 331 5e-90 pir||S26567 transcription initiation factor sigma H - Bacillus m... 328 4e-89 ref|NP_976421.1| RNA polymerase sigma-30 factor [Bacillus cereus... 327 9e-89 ref|NP_829995.1| RNA polymerase sigma-H factor [Bacillus cereus ... 327 1e-88 >ref|NP_240981.1| RNA polymerase sigma-H factor (sigma-30) [Bacillus halodurans] pir||C83664 RNA polymerase sigma-H factor (sigma-30) sigH [imported] - Bacillus halodurans (strain C-125) dbj|BAB03834.1| RNA polymerase sigma-H factor (sigma-30) [Bacillus halodurans] Length = 217 Score = 334 bits (857), Expect = 7e-91, Method: Compositional matrix adjust. Identities = 165/204 (80%), Positives = 183/204 (89%), Gaps = 2/204 (0%) Query: 3 SEYDF--ISDEEIVEIFRGGDSGALEHLINKYRNFVRAKARSYFLIGADREDIVQEGMIG 60 S DF I D +V R GD ALE+LI+KY+NFVRAKARSYFLIGAD EDIVQEGMIG Sbjct: 10 SNLDFNQIEDVGLVNRVRNGDGAALEYLIHKYKNFVRAKARSYFLIGADHEDIVQEGMIG 69 Query: 61 LYKAIRDFKGDKLSSFKAFAELCITRQIITAIKTATRQKHIPLNSYVSLDKPIYDEDSDR 120 LYKAIRDFKGDKLSSFKAFAELCITRQIITAIKTATRQKHIPLNSYVSLDKP+YDE+SDR Sbjct: 70 LYKAIRDFKGDKLSSFKAFAELCITRQIITAIKTATRQKHIPLNSYVSLDKPLYDEESDR 129 Query: 121 TLMDVICGTQVLDPEELIINQEEFIGLEDKMAEILSDLERKVLMLYLDGRSYQEIAEDLK 180 TL+DV+CG++V DPEEL+INQEEF +E KM E+LSDLERKVLMLYLDGRSYQEI+ +L Sbjct: 130 TLLDVVCGSRVTDPEELLINQEEFDDIEVKMGELLSDLERKVLMLYLDGRSYQEISAELN 189 Query: 181 RHVKSIDNALQRVKRKLERYLEVR 204 RHVKSIDNALQRVKRKLERY+E++ Sbjct: 190 RHVKSIDNALQRVKRKLERYMELK 213 >sp|P02964|RPSH_BACLI RNA polymerase sigma-H factor (Sigma-30) pir||SZBSSL transcription initiation factor sigma H - Bacillus licheniformis gb|AAA22755.1| RNA polymerase sigma-30 factor Length = 223 Score = 331 bits (849), Expect = 5e-90, Method: Compositional matrix adjust. Identities = 161/198 (81%), Positives = 183/198 (92%) Query: 8 ISDEEIVEIFRGGDSGALEHLINKYRNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRD 67 + DE+++E+ GDS AL++LI KYRNFVRAKARSYFLIGADREDIVQEGMIGLYK+IRD Sbjct: 23 LEDEQVIEMVHVGDSDALDYLITKYRNFVRAKARSYFLIGADREDIVQEGMIGLYKSIRD 82 Query: 68 FKGDKLSSFKAFAELCITRQIITAIKTATRQKHIPLNSYVSLDKPIYDEDSDRTLMDVIC 127 F+ DKL+SFKAFAELCITRQIITAIKTATRQKHIPLNSYVSLDKPIYDE+SDRTL+DVI Sbjct: 83 FREDKLTSFKAFAELCITRQIITAIKTATRQKHIPLNSYVSLDKPIYDEESDRTLLDVIS 142 Query: 128 GTQVLDPEELIINQEEFIGLEDKMAEILSDLERKVLMLYLDGRSYQEIAEDLKRHVKSID 187 G +V++PEELIINQEEF +E KM E+LSDLERKVL LYLDGRSYQEI+E+L RHVKSID Sbjct: 143 GAKVMNPEELIINQEEFDDIELKMGELLSDLERKVLALYLDGRSYQEISEELNRHVKSID 202 Query: 188 NALQRVKRKLERYLEVRD 205 NALQRVKRKLE+YLE+R+ Sbjct: 203 NALQRVKRKLEKYLELRE 220 >pir||S26567 transcription initiation factor sigma H - Bacillus megaterium emb|CAA41793.1| sigma H factor [Bacillus megaterium] Length = 216 Score = 328 bits (841), Expect = 4e-89, Method: Compositional matrix adjust. Identities = 161/196 (82%), Positives = 183/196 (93%) Query: 10 DEEIVEIFRGGDSGALEHLINKYRNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDFK 69 DE +V++ GD ALE+LI+KY+NFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDF+ Sbjct: 18 DETVVDLVHKGDIDALEYLIHKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDFR 77 Query: 70 GDKLSSFKAFAELCITRQIITAIKTATRQKHIPLNSYVSLDKPIYDEDSDRTLMDVICGT 129 DKL+SFKAFAELCITRQIITAIKTATRQKHIPLNSYVSLDKPIYDE+SDRTLMDVI GT Sbjct: 78 EDKLTSFKAFAELCITRQIITAIKTATRQKHIPLNSYVSLDKPIYDEESDRTLMDVISGT 137 Query: 130 QVLDPEELIINQEEFIGLEDKMAEILSDLERKVLMLYLDGRSYQEIAEDLKRHVKSIDNA 189 +V +PEEL+IN+E+F +E KMAE+LSDLERKVL+LYLDG+SYQEI+E+L RHVKSIDNA Sbjct: 138 KVANPEELLINREKFDDIELKMAELLSDLERKVLVLYLDGQSYQEISEELNRHVKSIDNA 197 Query: 190 LQRVKRKLERYLEVRD 205 LQRVKRKLERYLE+R+ Sbjct: 198 LQRVKRKLERYLEIRE 213 >ref|NP_976421.1| RNA polymerase sigma-30 factor [Bacillus cereus ATCC 10987] gb|AAS39029.1| RNA polymerase sigma-30 factor [Bacillus cereus ATCC 10987] Length = 219 Score = 327 bits (838), Expect = 9e-89, Method: Compositional matrix adjust. Identities = 157/199 (78%), Positives = 183/199 (91%) Query: 8 ISDEEIVEIFRGGDSGALEHLINKYRNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRD 67 + DE IVE+ R G++ ALE+LI+KY+NFVRAK+RSYFL+GADREDIVQEGMIGL+KAIRD Sbjct: 16 LEDEAIVELVRKGNTDALEYLIHKYKNFVRAKSRSYFLVGADREDIVQEGMIGLFKAIRD 75 Query: 68 FKGDKLSSFKAFAELCITRQIITAIKTATRQKHIPLNSYVSLDKPIYDEDSDRTLMDVIC 127 +K DKLSSFKAFAELCITRQIITAIKTATRQKHIPLNSYVSLDKPIYDE+SDRTL+DVI Sbjct: 76 YKEDKLSSFKAFAELCITRQIITAIKTATRQKHIPLNSYVSLDKPIYDEESDRTLLDVIS 135 Query: 128 GTQVLDPEELIINQEEFIGLEDKMAEILSDLERKVLMLYLDGRSYQEIAEDLKRHVKSID 187 +V DPEE+II+QEE+ +E K++E+LSDLERKVL LYLDGRSYQEI+E L RHVKSID Sbjct: 136 EAKVTDPEEMIISQEEYTDIESKISELLSDLERKVLSLYLDGRSYQEISEQLNRHVKSID 195 Query: 188 NALQRVKRKLERYLEVRDN 206 NALQRVKRKLERY+E+R++ Sbjct: 196 NALQRVKRKLERYMEMRES 214 >ref|NP_829995.1| RNA polymerase sigma-H factor [Bacillus cereus ATCC 14579] gb|AAP07196.1| RNA polymerase sigma-H factor [Bacillus cereus ATCC 14579] Length = 219 Score = 327 bits (838), Expect = 1e-88, Method: Compositional matrix adjust. Identities = 157/199 (78%), Positives = 183/199 (91%) Query: 8 ISDEEIVEIFRGGDSGALEHLINKYRNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRD 67 + DE IVE+ R G++ ALE+LI+KY+NFVRAK+RSYFL+GADREDIVQEGMIGL+KAIRD Sbjct: 16 LEDEAIVELVRKGNTDALEYLIHKYKNFVRAKSRSYFLVGADREDIVQEGMIGLFKAIRD 75 Query: 68 FKGDKLSSFKAFAELCITRQIITAIKTATRQKHIPLNSYVSLDKPIYDEDSDRTLMDVIC 127 +K DKLSSFKAFAELCITRQIITAIKTATRQKHIPLNSYVSLDKPIYDE+SDRTL+DVI Sbjct: 76 YKEDKLSSFKAFAELCITRQIITAIKTATRQKHIPLNSYVSLDKPIYDEESDRTLLDVIS 135 Query: 128 GTQVLDPEELIINQEEFIGLEDKMAEILSDLERKVLMLYLDGRSYQEIAEDLKRHVKSID 187 +V DPEE+II+QEE+ +E K++E+LSDLERKVL LYLDGRSYQEI+E L RHVKSID Sbjct: 136 EAKVTDPEEMIISQEEYTDIESKISELLSDLERKVLSLYLDGRSYQEISEQLNRHVKSID 195 Query: 188 NALQRVKRKLERYLEVRDN 206 NALQRVKRKLERY+E+R++ Sbjct: 196 NALQRVKRKLERYMEMRES 214 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 0.321 0.139 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: 287,892,351 Number of extensions: 11634018 Number of successful extensions: 42113 Number of sequences better than 1.0e-05: 96 Number of HSP's gapped: 42160 Number of HSP's successfully gapped: 96 Length of query: 206 Length of database: 757,237,578 Length adjustment: 120 Effective length of query: 86 Effective length of database: 431,425,698 Effective search space: 37102610028 Effective search space used: 37102610028 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: 123 (52.0 bits)