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= 0547.0029.p (175 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B3K4I8.1 B3K4I8_9BACI RNA polymerase sigma factor, sigma-70 family 158 1e-37 B1DKW3.1 B1DKW3_9BACL RNA polymerase, sigma-24 subunit, ECF subf... 127 3e-28 C0ZBE3.1 C0ZBE3_BREBN RNA polymerase ECF-type sigma factor 122 2e-26 B1D9J1.1 B1D9J1_9BACL RNA polymerase, sigma-24 subunit, ECF subf... 111 2e-23 B1HYF8.1 B1HYF8_LYSSC RNA polymerase sigma factor sigV 108 2e-22 >B3K4I8.1 B3K4I8_9BACI RNA polymerase sigma factor, sigma-70 family Length = 176 Score = 158 bits (400), Expect = 1e-37, Method: Compositional matrix adjust. Identities = 77/143 (53%), Positives = 99/143 (69%), Gaps = 1/143 (0%) Query: 10 AQAVDGEEQLFIRQVSEQKKILYGIAYSYLRNEPDALEVLQEATYRAWSKRKSLKDTGRF 69 A A G+E+ F V+E ++ LYGIAYSYL NE DALE LQE RAW K + LK F Sbjct: 9 AAACRGDEEAFYALVTEHRRRLYGIAYSYLHNESDALEALQETVCRAWMKCRKLKHPEAF 68 Query: 70 APWMTRILVNCCKDELKRRKRLTPGHADNGSSSGSMEMTSDRKLDMEQALDGVKQRYRQV 129 PW+ RIL+NCC DE KR+KR+ P + S + EM SD KLD+E+AL +K +YR V Sbjct: 69 VPWLIRILINCCVDEQKRKKRMLPVE-EVRSRETAAEMVSDSKLDLERALSRMKPKYRHV 127 Query: 130 LVLKYYRDMTLAEIAEVLDRPEG 152 L+LKYY+DMT+++IA +LD PEG Sbjct: 128 LILKYYQDMTISDIAHILDVPEG 150 >B1DKW3.1 B1DKW3_9BACL RNA polymerase, sigma-24 subunit, ECF subfamily Length = 180 Score = 127 bits (320), Expect = 3e-28, Method: Compositional matrix adjust. Identities = 66/145 (45%), Positives = 93/145 (64%), Gaps = 3/145 (2%) Query: 10 AQAVDGEEQLFIRQVSEQKKILYGIAYSYLRNEPDALEVLQEATYRAWSKRKSLKDTGRF 69 A A+ G++ I ++ + LYGIAYSY+RNE DALE +QE T R W+KR+SL+D F Sbjct: 8 AAAIKGDDDALIARIQMDQNRLYGIAYSYMRNETDALEAIQETTVRVWNKRRSLRDPKVF 67 Query: 70 APWMTRILVNCCKDELKRRKRLTPGHAD--NGSSSGSMEMTSDRKLDMEQALDGVKQRYR 127 W+TRIL+ C DE K++ R P + + + E DR +DM L + +YR Sbjct: 68 TTWVTRILIRVCLDERKKQLRERPLRNELLERDAQTANEHGIDR-MDMAVQLKKLPSKYR 126 Query: 128 QVLVLKYYRDMTLAEIAEVLDRPEG 152 V+VLKYYRDMT+ EIAE+L++P+G Sbjct: 127 MVIVLKYYRDMTITEIAELLEKPDG 151 >C0ZBE3.1 C0ZBE3_BREBN RNA polymerase ECF-type sigma factor Length = 181 Score = 122 bits (305), Expect = 2e-26, Method: Compositional matrix adjust. Identities = 66/151 (43%), Positives = 95/151 (62%), Gaps = 3/151 (1%) Query: 5 LEGEWAQAVDGEEQLFIRQVSEQKKILYGIAYSYLRNEPDALEVLQEATYRAWSKRKSLK 64 LE ++A +G++ F + VS K LY IAY++LRNE DALE +QEAT R++ K LK Sbjct: 10 LEQLVSRAKNGDDDAFFQLVSLHKDQLYKIAYAFLRNETDALEAIQEATCRSYLKLARLK 69 Query: 65 DTGRFAPWMTRILVNCCKDELKRRKRLT-PGHADNGSSSGSMEMTSDR--KLDMEQALDG 121 T F W+TRIL++ C DE KRRKR+ D+ S S+ M ++ +E+AL Sbjct: 70 QTAYFRTWLTRILIHICLDEQKRRKRIILSAMEDDIESRASIPMDDQNVERIQIEEALAR 129 Query: 122 VKQRYRQVLVLKYYRDMTLAEIAEVLDRPEG 152 ++ YR +++LKY+ D T+ +IAEVL PEG Sbjct: 130 LRPNYRHIIILKYFEDRTIRDIAEVLGHPEG 160 >B1D9J1.1 B1D9J1_9BACL RNA polymerase, sigma-24 subunit, ECF subfamily Length = 179 Score = 111 bits (278), Expect = 2e-23, Method: Compositional matrix adjust. Identities = 61/149 (40%), Positives = 91/149 (61%), Gaps = 8/149 (5%) Query: 10 AQAVDGEEQLFIRQVSEQKKILYGIAYSYLRNEPDALEVLQEATYRAWSKRKSLKDTGRF 69 A A G++ F +++QK+ +Y IAYSYL+NE DALE +QEAT RA+ + LK+ F Sbjct: 8 AAAKRGDDAAFYSLITQQKEKMYRIAYSYLKNETDALEAVQEATCRAYMQIHKLKEPEFF 67 Query: 70 APWMTRILVNCCKDELKRRKRLTPGHA------DNGSSSGSMEMTSDRKLDMEQALDGVK 123 W+ RIL+N C DE KR+ R T G D ++SG + ++ +E A++ + Sbjct: 68 GSWLIRILMNYCADEAKRKARRTDGQQAAAAALDLHATSGESALLE--RVMLESAVEQLD 125 Query: 124 QRYRQVLVLKYYRDMTLAEIAEVLDRPEG 152 Y++V+ LKYY D+T+ EIA L +PEG Sbjct: 126 ANYQKVIQLKYYHDLTITEIARTLQKPEG 154 >B1HYF8.1 B1HYF8_LYSSC RNA polymerase sigma factor sigV Length = 177 Score = 108 bits (269), Expect = 2e-22, Method: Compositional matrix adjust. Identities = 52/139 (37%), Positives = 90/139 (64%), Gaps = 1/139 (0%) Query: 15 GEEQLFIRQVSEQKKILYGIAYSYLRNEPDALEVLQEATYRAWSKRKSLKDTGRFAPWMT 74 G+ + F + E+K+ +Y +AY Y+RNE DALEV QE+ Y+A + +LK+ G F+ W+ Sbjct: 9 GDSEAFQILIHEEKEKMYRMAYMYMRNEDDALEVFQESLYKALNAINTLKNDGYFSTWLM 68 Query: 75 RILVNCCKDELKRRKRLTPGHADNGSSSGSMEMT-SDRKLDMEQALDGVKQRYRQVLVLK 133 RIL+N LK++++L + + E + ++ LD+ QA+D ++++Y+ VL+L+ Sbjct: 69 RILINTAIATLKKKQKLVSINMEIFDQIEDTEHSGTEEHLDLLQAMDDIEEKYKTVLLLR 128 Query: 134 YYRDMTLAEIAEVLDRPEG 152 +Y+D T+ +IA LD PEG Sbjct: 129 FYQDYTVKQIAAFLDCPEG 147 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 0.315 0.130 0.371 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: 944,386,451 Number of extensions: 34957754 Number of successful extensions: 96555 Number of sequences better than 1.0e-05: 718 Number of HSP's gapped: 97200 Number of HSP's successfully gapped: 718 Length of query: 175 Length of database: 3,060,696,203 Length adjustment: 126 Effective length of query: 49 Effective length of database: 1,873,648,313 Effective search space: 91808767337 Effective search space used: 91808767337 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 (21.6 bits) S2: 126 (53.1 bits)