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= 0564.0010.p (180 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value C0ZI65.1 C0ZI65_BREBN RNA polymerase ECF-type sigma factor 143 5e-33 Q2BDP2.1 Q2BDP2_9BACI RNA polymerase ECF-type sigma factor 134 3e-30 Q8XMH3.1 Q8XMH3_CLOPE RNA polymerase ECF-type sigma factor 133 5e-30 B1BP62.1 B1BP62_CLOPE RNA polymerase sigma-70 factor, ECF subfamily 133 5e-30 B1BL23.1 B1BL23_CLOPE RNA polymerase sigma-70 factor, ECF subfamily 133 5e-30 >C0ZI65.1 C0ZI65_BREBN RNA polymerase ECF-type sigma factor Length = 177 Score = 143 bits (361), Expect = 5e-33, Method: Compositional matrix adjust. Identities = 72/164 (43%), Positives = 104/164 (63%), Gaps = 4/164 (2%) Query: 11 AQKGDHEAFIRLFRQLETQLYRLAKTILTQDEDCADALQETTLKVYKGLASLKQPKFFKT 70 A++GD EAFI + +Q+E+ LY A++IL ++ED ADALQET LK +K L SL++P+FFKT Sbjct: 10 AKQGDREAFIAVVKQVESSLYHTARSILKKEEDIADALQETILKAFKSLHSLREPQFFKT 69 Query: 71 WVIRILINECNQLLRMRERTVAVAEIPEETAASYAHFEDSRNVDLQSCINRLDESLRLAI 130 W+ RILINECN+++ R R V + E P + + S +DL+ + RLDE RL I Sbjct: 70 WMFRILINECNKIVANRSRNVLMDEFPIQLSLS----PKDELIDLRDAVERLDEQQRLVI 125 Query: 131 VLFYYEDLSIKQIAGVLGISEGXXXXXXXXXXXXXSEQIQPVRE 174 VL Y+ED+ ++Q+A +L ISE E++ RE Sbjct: 126 VLHYFEDMPLRQVAEILEISESAAKMRLSRARNNLMEKLHTFRE 169 >Q2BDP2.1 Q2BDP2_9BACI RNA polymerase ECF-type sigma factor Length = 182 Score = 134 bits (337), Expect = 3e-30, Method: Compositional matrix adjust. Identities = 69/149 (46%), Positives = 96/149 (64%), Gaps = 3/149 (2%) Query: 4 NELDIKKAQKGDHEAFIRLFRQLETQLYRLAKTILTQDEDCADALQETTLKVYKGLASLK 63 +E DI A+KG+ E+F+RL E LYR+A+ +L+ D DCADA+QET LK ++ + LK Sbjct: 11 SEKDIILAKKGNEESFVRLIESCELSLYRVARGLLSNDNDCADAIQETILKSFRSIRKLK 70 Query: 64 QPKFFKTWVIRILINECNQLLRMRERTVAVAEIPEETAASYAHFEDSRNVDLQSCINRLD 123 QPK+FKTW+ RILINEC+ +LR ++ V V +I E S D + I LD Sbjct: 71 QPKYFKTWITRILINECHNILRKKQTVVPVEDI--EYYLSDRFLGDPAQ-SISEAIGELD 127 Query: 124 ESLRLAIVLFYYEDLSIKQIAGVLGISEG 152 E R ++L+YYED S+K+IA +L IS G Sbjct: 128 EKHRAPVILYYYEDFSVKEIAELLEISTG 156 >Q8XMH3.1 Q8XMH3_CLOPE RNA polymerase ECF-type sigma factor Length = 172 Score = 133 bits (335), Expect = 5e-30, Method: Compositional matrix adjust. Identities = 63/145 (43%), Positives = 99/145 (68%), Gaps = 4/145 (2%) Query: 8 IKKAQKGDHEAFIRLFRQLETQLYRLAKTILTQDEDCADALQETTLKVYKGLASLKQPKF 67 + +A+KGD +AF+ L + +YR+A+ IL ED DALQ T +K Y+ + +LK+ +F Sbjct: 15 VSQAKKGDKDAFLSLIDENRLSIYRVARGILNNKEDIEDALQNTIIKSYEKIGTLKKDEF 74 Query: 68 FKTWVIRILINECNQLLRMRERTVAVAEIPEETAASYAHFEDSRNVDLQSCINRLDESLR 127 FKTW+IRILINECN +LR ++T+ + ++ E + S +D N++L S +N L E LR Sbjct: 75 FKTWIIRILINECNLILRRNKKTIFLDKLENEKSYS----DDYGNIELTSVVNSLSEDLR 130 Query: 128 LAIVLFYYEDLSIKQIAGVLGISEG 152 + VL+Y+ED+S K+I+ +L I+EG Sbjct: 131 ITTVLYYFEDMSTKEISEMLNIAEG 155 >B1BP62.1 B1BP62_CLOPE RNA polymerase sigma-70 factor, ECF subfamily Length = 172 Score = 133 bits (335), Expect = 5e-30, Method: Compositional matrix adjust. Identities = 63/145 (43%), Positives = 99/145 (68%), Gaps = 4/145 (2%) Query: 8 IKKAQKGDHEAFIRLFRQLETQLYRLAKTILTQDEDCADALQETTLKVYKGLASLKQPKF 67 + +A+KGD +AF+ L + +YR+A+ IL ED DALQ T +K Y+ + +LK+ +F Sbjct: 15 VSQAKKGDKDAFLSLIDENRLSIYRVARGILNNKEDIEDALQNTIIKSYEKIGTLKKDEF 74 Query: 68 FKTWVIRILINECNQLLRMRERTVAVAEIPEETAASYAHFEDSRNVDLQSCINRLDESLR 127 FKTW+IRILINECN +LR ++T+ + ++ E + S +D N++L S +N L E LR Sbjct: 75 FKTWIIRILINECNLILRRNKKTIFLDKLENEKSYS----DDYGNIELTSVVNSLSEDLR 130 Query: 128 LAIVLFYYEDLSIKQIAGVLGISEG 152 + VL+Y+ED+S K+I+ +L I+EG Sbjct: 131 ITTVLYYFEDMSTKEISEMLNIAEG 155 >B1BL23.1 B1BL23_CLOPE RNA polymerase sigma-70 factor, ECF subfamily Length = 172 Score = 133 bits (335), Expect = 5e-30, Method: Compositional matrix adjust. Identities = 63/145 (43%), Positives = 99/145 (68%), Gaps = 4/145 (2%) Query: 8 IKKAQKGDHEAFIRLFRQLETQLYRLAKTILTQDEDCADALQETTLKVYKGLASLKQPKF 67 + +A+KGD +AF+ L + +YR+A+ IL ED DALQ T +K Y+ + +LK+ +F Sbjct: 15 VSQAKKGDKDAFLSLIDENRLSIYRVARGILNNKEDIEDALQNTIIKSYEKIGTLKKDEF 74 Query: 68 FKTWVIRILINECNQLLRMRERTVAVAEIPEETAASYAHFEDSRNVDLQSCINRLDESLR 127 FKTW+IRILINECN +LR ++T+ + ++ E + S +D N++L S +N L E LR Sbjct: 75 FKTWIIRILINECNLILRRNKKTIFLDKLENEKSYS----DDYGNIELTSVVNSLSEDLR 130 Query: 128 LAIVLFYYEDLSIKQIAGVLGISEG 152 + VL+Y+ED+S K+I+ +L I+EG Sbjct: 131 ITTVLYYFEDMSTKEISEMLNIAEG 155 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 0.135 0.376 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: 851,649,039 Number of extensions: 28180871 Number of successful extensions: 71139 Number of sequences better than 1.0e-05: 1502 Number of HSP's gapped: 71736 Number of HSP's successfully gapped: 1502 Length of query: 180 Length of database: 3,060,696,203 Length adjustment: 127 Effective length of query: 53 Effective length of database: 1,864,227,298 Effective search space: 98804046794 Effective search space used: 98804046794 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: 126 (53.1 bits)