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= 0115.0008.p (259 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B3K6S0.1 B3K6S0_9BACI RNA polymerase sigma factor 160 9e-38 B3KD50.1 B3KD50_9BACI RNA polymerase sigma factor 155 3e-36 B1D4T2.1 B1D4T2_9BACL RNA polymerase, sigma-24 subunit, ECF subf... 133 1e-29 C2W961.1 C2W961_BACCE RNA polymerase sigma-70 factor 130 1e-28 C3BLJ8.1 C3BLJ8_9BACI RNA polymerase sigma-70 factor 129 2e-28 >B3K6S0.1 B3K6S0_9BACI RNA polymerase sigma factor Length = 178 Score = 160 bits (405), Expect = 9e-38, Method: Compositional matrix adjust. Identities = 89/188 (47%), Positives = 117/188 (62%), Gaps = 18/188 (9%) Query: 70 ELQDLAHAAAMSEEQLRQIMGFYGNDVWHYIYYLTKSADIADDLAQEVFIKCFYRIGTYR 129 EL+ L M + L +IM YGNDVW+Y Y+LTK +ADD+AQE FIK +Y I T+R Sbjct: 2 ELEYLKQMTVMDSQTLDKIMNEYGNDVWNYAYFLTKQHALADDIAQEAFIKAYYGIHTFR 61 Query: 130 GSSSFKAWLFTIARNTVFSYRKSRFFRSGFWGGVQAIRNNEPVRNSWPDELP--GTARSA 187 G ++ K WL TI R+T F Y+++ FFR D+L ++RSA Sbjct: 62 GQATLKTWLLTITRHTAFRYKQAFFFRKVI----------------LKDKLTASSSSRSA 105 Query: 188 EMEYLGNCRTDEIWSIILQLPDKFREVLVLDLKAELSIQEIAGLTGLSPGTVKSRLHRAR 247 E EYL TDEIW++I+ LP K REVLVLDL E+ + EIA L ++ GTVKSRLHRAR Sbjct: 106 EAEYLDEQYTDEIWAMIMTLPSKLREVLVLDLYYEMPMHEIAKLLHIATGTVKSRLHRAR 165 Query: 248 HKVQEKLR 255 KVQ+ ++ Sbjct: 166 KKVQKLMK 173 >B3KD50.1 B3KD50_9BACI RNA polymerase sigma factor Length = 183 Score = 155 bits (392), Expect = 3e-36, Method: Compositional matrix adjust. Identities = 78/183 (42%), Positives = 108/183 (59%), Gaps = 5/183 (2%) Query: 74 LAHAAAMSEEQLRQIMGFYGNDVWHYIYYLTKSADIADDLAQEVFIKCFYRIGTYRGSSS 133 + H+A + +R +M YG DVW+Y + +T++ ADD+AQ+VFIK + ++RG +S Sbjct: 1 MQHSAELKTSDIRMLMESYGEDVWNYAFAITRNTHTADDVAQDVFIKAYQHFASFRGEAS 60 Query: 134 FKAWLFTIARNTVFSYRKSRFFRSGFWGGVQAIRNNEPVRNSWPDELPGTARSAEMEYLG 193 K WL I RNT SY K F R G Q+ + P + SAE EYL Sbjct: 61 VKTWLLKITRNTALSYLKRAFLRRVVLMGEQSPGTGQKGAMRTP-----ISPSAEAEYLE 115 Query: 194 NCRTDEIWSIILQLPDKFREVLVLDLKAELSIQEIAGLTGLSPGTVKSRLHRARHKVQEK 253 DE+W +L+LP KFR+ LVL L +LSI EI+ +TGLSPGTVKSR++RA+ KV Sbjct: 116 RAEADELWKQVLKLPAKFRDPLVLSLHHQLSIDEISAITGLSPGTVKSRIYRAKQKVAAA 175 Query: 254 LRG 256 +G Sbjct: 176 WKG 178 >B1D4T2.1 B1D4T2_9BACL RNA polymerase, sigma-24 subunit, ECF subfamily Length = 180 Score = 133 bits (335), Expect = 1e-29, Method: Compositional matrix adjust. Identities = 68/172 (39%), Positives = 101/172 (58%), Gaps = 13/172 (7%) Query: 85 LRQIMGFYGNDVWHYIYYLTKSADIADDLAQEVFIKCFYRIGTYRGSSSFKAWLFTIARN 144 LR++M YG D W+ Y +T+ D+ADD+ Q+VF+K + IG++RG+SS + WL ++ RN Sbjct: 17 LRELMDSYGQDAWNLAYVITRRHDLADDVTQDVFLKVYQTIGSFRGASSIRTWLLSMTRN 76 Query: 145 TVFSYRKSRFFRSGFWGGVQAIRNNEPVRNSWPDELPGTARSAEMEYLGNCRTDEIWSII 204 T +Y+++ F R G A + G + SAE E + T E+W+ + Sbjct: 77 TAINYKRTAFMRRVLLIGRSAAHD-------------GESPSAEQEAIRLAFTSELWNAV 123 Query: 205 LQLPDKFREVLVLDLKAELSIQEIAGLTGLSPGTVKSRLHRARHKVQEKLRG 256 L+LP K REVLVL K EL+ +EIA L GTVK+RL RAR ++ +G Sbjct: 124 LELPVKLREVLVLHAKYELTTKEIADALMLPEGTVKTRLSRARKRMNSSWKG 175 >C2W961.1 C2W961_BACCE RNA polymerase sigma-70 factor Length = 174 Score = 130 bits (327), Expect = 1e-28, Method: Compositional matrix adjust. Identities = 72/174 (41%), Positives = 103/174 (59%), Gaps = 14/174 (8%) Query: 81 SEEQLRQIMGFYGNDVWHYIYYLTKSADIADDLAQEVFIKCFYRIGTYRGSSSFKAWLFT 140 + +++ ++ + DVW+Y + +TK ++DD+ QEVFIK F + ++R SS K WL Sbjct: 10 NHDEIDYVIREHWQDVWNYSFIITKDTHLSDDITQEVFIKVFKKWNSFRNESSVKTWLLK 69 Query: 141 IARNTVFSYRKSRFFRSGFWGGVQAIRNNEPVRNSWPDELPGTARSAEMEYLGNCRTDEI 200 I RNT +Y KS +F+ V RN++ E P SAE ++L +E+ Sbjct: 70 ITRNTALNYLKSSYFKRI--SLVSFFRNDK--------EYP----SAEKQFLEKETMNEV 115 Query: 201 WSIILQLPDKFREVLVLDLKAELSIQEIAGLTGLSPGTVKSRLHRARHKVQEKL 254 W +L+LP K REVL+LD K ELS EIA G+S GTVKSRLHRAR +V + L Sbjct: 116 WDSVLKLPQKHREVLILDAKYELSYDEIAETLGVSIGTVKSRLHRARARVSKIL 169 >C3BLJ8.1 C3BLJ8_9BACI RNA polymerase sigma-70 factor Length = 174 Score = 129 bits (325), Expect = 2e-28, Method: Compositional matrix adjust. Identities = 71/174 (40%), Positives = 102/174 (58%), Gaps = 14/174 (8%) Query: 81 SEEQLRQIMGFYGNDVWHYIYYLTKSADIADDLAQEVFIKCFYRIGTYRGSSSFKAWLFT 140 + +++ ++ + DVW+Y + +TK ++DD+ QEVFIK F + ++R SS K WL Sbjct: 10 NHDEIDNVIREHWQDVWNYSFIITKDTHLSDDITQEVFIKVFKKWDSFRNESSVKTWLLK 69 Query: 141 IARNTVFSYRKSRFFRSGFWGGVQAIRNNEPVRNSWPDELPGTARSAEMEYLGNCRTDEI 200 I RNT +Y KS +F+ V R+++ E P SAE ++L +E+ Sbjct: 70 ITRNTALNYLKSSYFKRI--SLVSFFRHDK--------EYP----SAEKQFLQKETMNEV 115 Query: 201 WSIILQLPDKFREVLVLDLKAELSIQEIAGLTGLSPGTVKSRLHRARHKVQEKL 254 W +L LP K REVL+LD K ELS EIA G+S GTVKSRLHRAR +V + L Sbjct: 116 WDTVLNLPQKHREVLILDAKYELSYDEIAETLGVSIGTVKSRLHRARARVSKIL 169 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 0.322 0.137 0.419 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: 1,495,782,783 Number of extensions: 58596014 Number of successful extensions: 131700 Number of sequences better than 1.0e-05: 2220 Number of HSP's gapped: 130752 Number of HSP's successfully gapped: 2220 Length of query: 259 Length of database: 3,060,696,203 Length adjustment: 133 Effective length of query: 126 Effective length of database: 1,807,701,208 Effective search space: 227770352208 Effective search space used: 227770352208 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 (21.9 bits) S2: 130 (54.7 bits)