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= 0290.0041.p (182 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B3KFZ6.1 B3KFZ6_9BACI RNA polymerase sigma factor, sigma-70 family 333 4e-90 B1DFE9.1 B1DFE9_9BACL RNA polymerase, sigma-24 subunit, ECF subf... 322 1e-86 C0ZB18.1 C0ZB18_BREBN RNA polymerase ECF-type sigma factor 253 7e-66 B1D5J7.1 B1D5J7_9BACL RNA polymerase sigma factor 128 2e-28 C3J776.1 C3J776_9BACI RNA polymerase, sigma-24 subunit, ECF subf... 127 5e-28 >B3KFZ6.1 B3KFZ6_9BACI RNA polymerase sigma factor, sigma-70 family Length = 182 Score = 333 bits (854), Expect = 4e-90, Method: Compositional matrix adjust. Identities = 160/182 (87%), Positives = 174/182 (95%) Query: 1 VVEQGLIRAAQSGDRDALITLLREIEGHVYKTAFYILHNEQDALDASQEALIRVYTKIGS 60 +VEQGLIRAAQSGDRDALITLLREIE HVY+TA+YIL+NEQDA+DA+QEALIRVYTKI S Sbjct: 1 MVEQGLIRAAQSGDRDALITLLREIEQHVYRTAYYILNNEQDAMDAAQEALIRVYTKINS 60 Query: 61 YEEKAQFKTWVQRIVTNICIDKFRRTKPTVSIDEHEMVFPDKHDVEREVLSGYLAEDIRE 120 YEEKAQFKTWVQRIVTNICIDKFRRTKPTVSIDEH+MVF D DVEREV+SGYLA+DI+E Sbjct: 61 YEEKAQFKTWVQRIVTNICIDKFRRTKPTVSIDEHDMVFRDHLDVEREVMSGYLAQDIQE 120 Query: 121 AIDQLPEHHRTVIVLRYLQDFSYNEIADSLDLPLNTVKSYLFRARQQLQNRLQEYQKGGV 180 AI+QLP+HHRTVIVLRYLQD SYNEIAD L+LPLNTVKSYLFRARQQLQN LQE+QKGGV Sbjct: 121 AINQLPDHHRTVIVLRYLQDLSYNEIADCLNLPLNTVKSYLFRARQQLQNMLQEHQKGGV 180 Query: 181 SG 182 SG Sbjct: 181 SG 182 >B1DFE9.1 B1DFE9_9BACL RNA polymerase, sigma-24 subunit, ECF subfamily Length = 182 Score = 322 bits (825), Expect = 1e-86, Method: Compositional matrix adjust. Identities = 152/182 (83%), Positives = 169/182 (92%) Query: 1 VVEQGLIRAAQSGDRDALITLLREIEGHVYKTAFYILHNEQDALDASQEALIRVYTKIGS 60 +VE GLIRAAQSGDRDALITLLREIE HVY+TA+YIL+NEQDA+DA+QEALIR+YTKIGS Sbjct: 1 MVEPGLIRAAQSGDRDALITLLREIETHVYRTAYYILNNEQDAMDAAQEALIRIYTKIGS 60 Query: 61 YEEKAQFKTWVQRIVTNICIDKFRRTKPTVSIDEHEMVFPDKHDVEREVLSGYLAEDIRE 120 YEEKAQFKTW+QRIVTNICIDKFRR+KPTVSIDEHEMVF +K +VE EV+S Y +DIR+ Sbjct: 61 YEEKAQFKTWIQRIVTNICIDKFRRSKPTVSIDEHEMVFREKQNVEDEVMSAYAVQDIRK 120 Query: 121 AIDQLPEHHRTVIVLRYLQDFSYNEIADSLDLPLNTVKSYLFRARQQLQNRLQEYQKGGV 180 AID+LPEHHR V+VLRYLQDFSYNEIADSLDLPLNTVKSYLFRARQQLQ L +YQKGGV Sbjct: 121 AIDKLPEHHRAVVVLRYLQDFSYNEIADSLDLPLNTVKSYLFRARQQLQTLLHDYQKGGV 180 Query: 181 SG 182 G Sbjct: 181 RG 182 >C0ZB18.1 C0ZB18_BREBN RNA polymerase ECF-type sigma factor Length = 181 Score = 253 bits (645), Expect = 7e-66, Method: Compositional matrix adjust. Identities = 119/179 (66%), Positives = 148/179 (82%) Query: 3 EQGLIRAAQSGDRDALITLLREIEGHVYKTAFYILHNEQDALDASQEALIRVYTKIGSYE 62 E LIR AQSGD DAL+ LLR IE VY++A+YIL NEQDALDASQE LIR+Y K+ +Y+ Sbjct: 3 EAELIRMAQSGDHDALVELLRSIETSVYRSAYYILGNEQDALDASQEVLIRIYRKLDTYQ 62 Query: 63 EKAQFKTWVQRIVTNICIDKFRRTKPTVSIDEHEMVFPDKHDVEREVLSGYLAEDIREAI 122 EKA+F TWVQRIV+N+C+DKFR K TVSIDEHE++ PD+++VE E+L L+ DI+EAI Sbjct: 63 EKAKFSTWVQRIVSNVCMDKFRAKKETVSIDEHELIIPDRNNVEEEILLTGLSNDIQEAI 122 Query: 123 DQLPEHHRTVIVLRYLQDFSYNEIADSLDLPLNTVKSYLFRARQQLQNRLQEYQKGGVS 181 +LP+ +R V+VLRYL+D SY EIA++LDLPLNTVKSYLFRARQQLQ L +YQKGG+ Sbjct: 123 GRLPKQYRMVVVLRYLEDLSYQEIAEALDLPLNTVKSYLFRARQQLQELLYDYQKGGIG 181 >B1D5J7.1 B1D5J7_9BACL RNA polymerase sigma factor Length = 188 Score = 128 bits (322), Expect = 2e-28, Method: Compositional matrix adjust. Identities = 67/183 (36%), Positives = 108/183 (59%), Gaps = 10/183 (5%) Query: 1 VVEQGLIRAAQSGDRDALITLLREIEGHVYKTAFYILHNEQDALDASQEALIRVYTKIGS 60 V+E L R A GD+ A L+ + ++ A+ +L+N Q+A D QE +RVY + Sbjct: 3 VLEARLARLALKGDQRAFAELVGLYQDKLFHMAYRMLYNRQEAEDVVQETFLRVYKNLER 62 Query: 61 YEEKAQFKTWVQRIVTNICIDKFRRTKPTVSID----EHE------MVFPDKHDVEREVL 110 Y+E +F TW+ RI TN+CID+ R+ KP+ S+D +HE M+ D E E+L Sbjct: 63 YDESLKFSTWIYRIATNLCIDRLRKRKPSYSLDAESTDHEGLDGYSMIPSDDRTPESELL 122 Query: 111 SGYLAEDIREAIDQLPEHHRTVIVLRYLQDFSYNEIADSLDLPLNTVKSYLFRARQQLQN 170 I E+I+ LP ++T+++LRY+Q+ S EI D LD+P+ T+K+ + R R+ L+ Sbjct: 123 LSETQRIIHESIESLPPKYKTIMMLRYIQEMSLQEIGDVLDMPVTTIKTRVHRGREFLRK 182 Query: 171 RLQ 173 +L+ Sbjct: 183 KLE 185 >C3J776.1 C3J776_9BACI RNA polymerase, sigma-24 subunit, ECF subfamily Length = 190 Score = 127 bits (318), Expect = 5e-28, Method: Compositional matrix adjust. Identities = 70/176 (39%), Positives = 105/176 (59%), Gaps = 10/176 (5%) Query: 7 IRAAQSGDRDALITLLREIEGHVYKTAFYILHNEQDALDASQEALIRVYTKIGSYEEKAQ 66 I+A Q GD++A L+ + +Y+ + +L N +A DA+QEA IR Y I +Y + + Sbjct: 12 IKAIQKGDQNAYADLVDLYKDKIYRLCYRMLGNRHEAEDAAQEAFIRAYIHIDTYNPEMK 71 Query: 67 FKTWVQRIVTNICIDKFRRTKPTVSIDEH---------EMVFPDKH-DVEREVLSGYLAE 116 F TW+ RI TN+ IDK R+ KP V +DE + P + E V S L E Sbjct: 72 FSTWLYRIATNLTIDKLRKRKPDVYLDEEVGGTDGLTMQAQLPSREASPEEAVESLELQE 131 Query: 117 DIREAIDQLPEHHRTVIVLRYLQDFSYNEIADSLDLPLNTVKSYLFRARQQLQNRL 172 ++ AI+QLPE +R+VIVL+Y++D S EI++ L LP+ TVK+ L R R+ L+ +L Sbjct: 132 TVQRAIEQLPEKYRSVIVLKYMEDLSLQEISEILGLPVGTVKTRLHRGREALRRQL 187 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 0.384 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: 1,012,301,386 Number of extensions: 38335681 Number of successful extensions: 128185 Number of sequences better than 1.0e-05: 4456 Number of HSP's gapped: 126142 Number of HSP's successfully gapped: 4456 Length of query: 182 Length of database: 3,060,696,203 Length adjustment: 127 Effective length of query: 55 Effective length of database: 1,864,227,298 Effective search space: 102532501390 Effective search space used: 102532501390 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: 127 (53.5 bits)