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= 0264.0033.p (260 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B3KG98.1 B3KG98_9BACI RNA polymerase sigma factor 508 e-142 C0ZG94.1 C0ZG94_BREBN RNA polymerase sigma-G factor 469 e-130 Q9K9U1.1 Q9K9U1_BACHD RNA polymerase sigma factor 446 e-124 Q5WFH5.1 Q5WFH5_BACSK RNA polymerase sigma factor 437 e-121 B0TGC8.1 B0TGC8_HELMI RNA polymerase sigma factor 436 e-121 >B3KG98.1 B3KG98_9BACI RNA polymerase sigma factor Length = 260 Score = 508 bits (1307), Expect = e-142, Method: Compositional matrix adjust. Identities = 246/260 (94%), Positives = 252/260 (96%) Query: 1 MTRNKVEICGVDTAKLPVLTNVEMRELFTSLQQQGERSAREKLVNGNLRLVLSVIQRFNN 60 MTRNKVEICGVDT+KLPVLTNVEMRELF +LQQ ERSAREKLVNGNLRLVLSVIQRFNN Sbjct: 1 MTRNKVEICGVDTSKLPVLTNVEMRELFHNLQQNNERSAREKLVNGNLRLVLSVIQRFNN 60 Query: 61 RGEFVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNPIRVSRSLR 120 RGEFVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNPIRVSRSLR Sbjct: 61 RGEFVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNPIRVSRSLR 120 Query: 121 DIAYKALQVRDSLTNQNSREPTIFEISEALGVPKEDVVFALDAIQDPVSLFEPIYHDGGD 180 DIAYKALQVRD LTN NSREPTIFEISEAL VPKEDVVFALDAIQDPVSLFEPIYHDGGD Sbjct: 121 DIAYKALQVRDQLTNANSREPTIFEISEALNVPKEDVVFALDAIQDPVSLFEPIYHDGGD 180 Query: 181 PIYVMDQISDDKNKDVSWIEEIALREAMQRLGQREKRILSMRFFEGKTQMEVADEIGISQ 240 PIYVMDQISDDKNKDVSWIEEIALREAM +LGQREK ILSMRF+EGKTQMEVADEIGISQ Sbjct: 181 PIYVMDQISDDKNKDVSWIEEIALREAMHKLGQREKMILSMRFYEGKTQMEVADEIGISQ 240 Query: 241 AQVSRLEKSAIQQMQKHVKS 260 AQVSRLEKSAI+QMQKHVK+ Sbjct: 241 AQVSRLEKSAIKQMQKHVKT 260 >C0ZG94.1 C0ZG94_BREBN RNA polymerase sigma-G factor Length = 259 Score = 469 bits (1207), Expect = e-130, Method: Compositional matrix adjust. Identities = 229/260 (88%), Positives = 243/260 (93%), Gaps = 1/260 (0%) Query: 1 MTRNKVEICGVDTAKLPVLTNVEMRELFTSLQQQGERSAREKLVNGNLRLVLSVIQRFNN 60 MTRNKVEICGVDT+KLPVLTN EMR+LF LQ GE +AREKLVNGNLRLVLSVIQRFNN Sbjct: 1 MTRNKVEICGVDTSKLPVLTNKEMRDLFERLQS-GELAAREKLVNGNLRLVLSVIQRFNN 59 Query: 61 RGEFVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNPIRVSRSLR 120 RGEFVDDLFQVGCIGLMKAIDNFDL QNVKFSTYAVPMIIGEIRRYLRDNNPIRVSRSLR Sbjct: 60 RGEFVDDLFQVGCIGLMKAIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNNPIRVSRSLR 119 Query: 121 DIAYKALQVRDSLTNQNSREPTIFEISEALGVPKEDVVFALDAIQDPVSLFEPIYHDGGD 180 DIAYKALQVRD+LTN++SREPTI EIS+ L V KEDVVFALDAIQDPVSLFEPIY DGGD Sbjct: 120 DIAYKALQVRDNLTNKHSREPTIIEISQELNVAKEDVVFALDAIQDPVSLFEPIYQDGGD 179 Query: 181 PIYVMDQISDDKNKDVSWIEEIALREAMQRLGQREKRILSMRFFEGKTQMEVADEIGISQ 240 PIYVMDQISD+KNKDV+W+EEIALRE MQRLG REK ILSMRF+EGKTQMEVA+EIGISQ Sbjct: 180 PIYVMDQISDEKNKDVTWVEEIALREGMQRLGDREKMILSMRFYEGKTQMEVAEEIGISQ 239 Query: 241 AQVSRLEKSAIQQMQKHVKS 260 AQVSRLEK+AI MQKHV+S Sbjct: 240 AQVSRLEKAAIAHMQKHVQS 259 >Q9K9U1.1 Q9K9U1_BACHD RNA polymerase sigma factor Length = 261 Score = 446 bits (1148), Expect = e-124, Method: Compositional matrix adjust. Identities = 219/262 (83%), Positives = 238/262 (90%), Gaps = 3/262 (1%) Query: 1 MTRNKVEICGVDTAKLPVLTNVEMRELFTSLQQQGERSAREKLVNGNLRLVLSVIQRFNN 60 MTRNKVEICGVDT+KLPVL N EMRELF LQ G+ SARE LVNGNLRLVLSVIQRFNN Sbjct: 1 MTRNKVEICGVDTSKLPVLKNQEMRELFARLQS-GDTSARETLVNGNLRLVLSVIQRFNN 59 Query: 61 RGEFVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNPIRVSRSLR 120 RGE+VDDLFQVGCIGLMK+IDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNPIRVSRSLR Sbjct: 60 RGEYVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNPIRVSRSLR 119 Query: 121 DIAYKALQVRDSLTNQNSRE--PTIFEISEALGVPKEDVVFALDAIQDPVSLFEPIYHDG 178 DIAYKALQVRD L + RE PT+ EI++ LGVPKEDVVFALDAIQDPVSLFEPIY+DG Sbjct: 120 DIAYKALQVRDQLMGEKQREKEPTVQEIAKELGVPKEDVVFALDAIQDPVSLFEPIYNDG 179 Query: 179 GDPIYVMDQISDDKNKDVSWIEEIALREAMQRLGQREKRILSMRFFEGKTQMEVADEIGI 238 GDPIYVMDQISDD+NKDV W++EIAL+EAM RL REK IL+MRF++GKTQMEVA+EIGI Sbjct: 180 GDPIYVMDQISDDRNKDVQWVDEIALKEAMVRLNDREKLILNMRFYQGKTQMEVAEEIGI 239 Query: 239 SQAQVSRLEKSAIQQMQKHVKS 260 SQAQVSRLEK+AIQQM KH +S Sbjct: 240 SQAQVSRLEKAAIQQMSKHAQS 261 >Q5WFH5.1 Q5WFH5_BACSK RNA polymerase sigma factor Length = 261 Score = 437 bits (1124), Expect = e-121, Method: Compositional matrix adjust. Identities = 215/262 (82%), Positives = 234/262 (89%), Gaps = 3/262 (1%) Query: 1 MTRNKVEICGVDTAKLPVLTNVEMRELFTSLQQQGERSAREKLVNGNLRLVLSVIQRFNN 60 MTRNKVEICGVDT+ LPVL N EMRELFT LQ G ARE LVNGNLRLVLSVIQRFNN Sbjct: 1 MTRNKVEICGVDTSTLPVLKNAEMRELFTKLQA-GYEPARETLVNGNLRLVLSVIQRFNN 59 Query: 61 RGEFVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNPIRVSRSLR 120 RGE VDDLFQVGCIGLMK+IDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNPIRVSRSLR Sbjct: 60 RGENVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNPIRVSRSLR 119 Query: 121 DIAYKALQVRDSLTNQNSRE--PTIFEISEALGVPKEDVVFALDAIQDPVSLFEPIYHDG 178 DIAYKALQVRD + + RE PT+ EI+ L VPKEDVVFALDAIQDPVSLFEPIY+DG Sbjct: 120 DIAYKALQVRDQMMAEKKREKEPTVQEIAAVLEVPKEDVVFALDAIQDPVSLFEPIYNDG 179 Query: 179 GDPIYVMDQISDDKNKDVSWIEEIALREAMQRLGQREKRILSMRFFEGKTQMEVADEIGI 238 GDPI+VMDQISD++NKD++W+EEIAL+EAM RL REK IL+MRFF+GKTQMEVA+EIGI Sbjct: 180 GDPIFVMDQISDERNKDINWVEEIALKEAMVRLNDREKTILNMRFFQGKTQMEVAEEIGI 239 Query: 239 SQAQVSRLEKSAIQQMQKHVKS 260 SQAQVSRLEK AIQQM KH++S Sbjct: 240 SQAQVSRLEKGAIQQMNKHIES 261 >B0TGC8.1 B0TGC8_HELMI RNA polymerase sigma factor Length = 265 Score = 436 bits (1122), Expect = e-121, Method: Compositional matrix adjust. Identities = 208/258 (80%), Positives = 235/258 (91%), Gaps = 1/258 (0%) Query: 1 MTRNKVEICGVDTAKLPVLTNVEMRELFTSLQQQGERSAREKLVNGNLRLVLSVIQRFNN 60 M NKVEICGV+T+KLPVLTN EMR LF ++Q GERSAREKL++GNLRLVLSVIQRF N Sbjct: 9 MMVNKVEICGVNTSKLPVLTNAEMRTLFQAMQS-GERSAREKLISGNLRLVLSVIQRFTN 67 Query: 61 RGEFVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNPIRVSRSLR 120 RGE+VDDLFQVGCIGLMKAIDNFDL QNVKFSTYAVPMIIGEIRRYLRDNNPIRVSRSLR Sbjct: 68 RGEYVDDLFQVGCIGLMKAIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNNPIRVSRSLR 127 Query: 121 DIAYKALQVRDSLTNQNSREPTIFEISEALGVPKEDVVFALDAIQDPVSLFEPIYHDGGD 180 DIAYKALQVRD L N+ SREPT+ EI++ALG P+E+VVFALDAIQ+P+SLFEPIYHDGGD Sbjct: 128 DIAYKALQVRDHLVNELSREPTVTEIADALGFPREEVVFALDAIQEPISLFEPIYHDGGD 187 Query: 181 PIYVMDQISDDKNKDVSWIEEIALREAMQRLGQREKRILSMRFFEGKTQMEVADEIGISQ 240 PI+VMDQI D+KN+D W+E IA+REA++RL REK IL++RFFEGKTQMEVADEIGISQ Sbjct: 188 PIFVMDQIGDEKNQDAQWLEGIAVREALRRLNDREKLILTLRFFEGKTQMEVADEIGISQ 247 Query: 241 AQVSRLEKSAIQQMQKHV 258 AQVSRLEK+A+ M+KHV Sbjct: 248 AQVSRLEKAALTHMRKHV 265 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 0.320 0.136 0.374 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: 1,363,689,523 Number of extensions: 53847361 Number of successful extensions: 170337 Number of sequences better than 1.0e-05: 5694 Number of HSP's gapped: 163852 Number of HSP's successfully gapped: 5838 Length of query: 260 Length of database: 3,060,696,203 Length adjustment: 133 Effective length of query: 127 Effective length of database: 1,807,701,208 Effective search space: 229578053416 Effective search space used: 229578053416 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: 130 (54.7 bits)