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= 0566.0012.p (243 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B3KGX8.1 B3KGX8_9BACI RNA polymerase sigma factor, sigma-70 family 169 2e-40 Q9K889.1 Q9K889_BACHD RNA polymerase ECF-type sigma factor 157 5e-37 B1DM41.1 B1DM41_9BACL RNA polymerase, sigma-24 subunit, ECF subf... 148 4e-34 A9GPT7.1 A9GPT7_SORC5 RNA polymerase sigma factor 107 6e-22 B4UKZ6.1 B4UKZ6_ANASK RNA polymerase sigma factor 97 1e-18 >B3KGX8.1 B3KGX8_9BACI RNA polymerase sigma factor, sigma-70 family Length = 244 Score = 169 bits (427), Expect = 2e-40, Method: Compositional matrix adjust. Identities = 95/208 (45%), Positives = 130/208 (62%), Gaps = 13/208 (6%) Query: 3 EQSYPPLREALFRYCLSLTRSRVEAEDLAQDTWTKTLAYKKFADSPNPEALLLRIAKNTW 62 EQ L L RYCLSLT S +++DL QDTW K L + + NPEALLLRIAKNTW Sbjct: 13 EQGLAELNAVLHRYCLSLTNSSWDSDDLVQDTWIKALEHLQQRSHANPEALLLRIAKNTW 72 Query: 63 IDAMRRKTSLGRV----LEHTQAVAALAQGQMSGQAPESGRSEIEMAFQALIRHLSPLQR 118 ID +RR + R+ LEH L + + S E + IE AFQ L+ HLSPLQR Sbjct: 73 IDRVRRDQTYRRILNEKLEHV-----LTKEEASN---EDSKLNIEFAFQWLMEHLSPLQR 124 Query: 119 TVFVMRDVLDYPAGETAEMLGTTEGAVKAALHRARQALGAVRKELAEDDGPAQPQDLDFR 178 TV ++R+V +Y ETA ML TT+GAVKAALHRA++ L ++ E E+ G A P++ + Sbjct: 125 TVLLLREVYEYSISETANMLQTTDGAVKAALHRAQKVLQSLNPE-EEELGLAMPEEAEMT 183 Query: 179 ILLQALAESYEKGQLPVMLELLRRETAA 206 + LQALAE+Y+ G + ++ L++ ++ Sbjct: 184 LNLQALAEAYQSGDVEAVVRLIQWNSSG 211 >Q9K889.1 Q9K889_BACHD RNA polymerase ECF-type sigma factor Length = 230 Score = 157 bits (398), Expect = 5e-37, Method: Compositional matrix adjust. Identities = 90/212 (42%), Positives = 127/212 (59%), Gaps = 11/212 (5%) Query: 2 DEQSYPPLREALFRYCLSLTRSRVEAEDLAQDTWTKTLAYKKFADSPNPEALLLRIAKNT 61 D + L + + RYCL +T+S +AEDLAQ+TW K + K NPEA LLR+AKN Sbjct: 3 DRKHLKQLHDTVSRYCLFVTKSTWDAEDLAQETWLKAIETLKKQGHQNPEAFLLRVAKNQ 62 Query: 62 WIDAMRRKTSLGRVLEHTQAVAALAQGQMSGQAPESGRSEIEMAFQALIRHLSPLQRTVF 121 WID R+K R+L+ Q + PE G E+E AF AL+ HLSPLQ +VF Sbjct: 63 WIDQSRKKAVFARILK---------QEKPEVTPPEQGLFEMERAFFALVNHLSPLQLSVF 113 Query: 122 VMRDVLDYPAGETAEMLGTTEGAVKAALHRARQALGAVRKELAEDDGPAQPQDLDFRILL 181 ++RDV Y E A+M+ TEGAVKAAL RAR++L VR +L ++ P P + + L Sbjct: 114 LLRDVFGYSTSEAAKMVEKTEGAVKAALRRARKSLALVRDDLETENSPL-PNGEEAKAWL 172 Query: 182 QALAESYEKGQLPVMLELLRRETAAEMTMAVS 213 +A+A +YE G++ +++L+ + A TM VS Sbjct: 173 RAIAVAYEAGEIDTVIDLIDQGVYAR-TMVVS 203 >B1DM41.1 B1DM41_9BACL RNA polymerase, sigma-24 subunit, ECF subfamily Length = 239 Score = 148 bits (373), Expect = 4e-34, Method: Compositional matrix adjust. Identities = 93/191 (48%), Positives = 122/191 (63%), Gaps = 7/191 (3%) Query: 9 LREALFRYCLSLTRSRVEAEDLAQDTWTKTLAYKKFADSPNPEALLLRIAKNTWIDAMRR 68 L++ L RYCL+LT+SRVEAEDL QDTW K + + + NPEA LLRIA+N WID +RR Sbjct: 16 LQQVLGRYCLTLTKSRVEAEDLTQDTWIKVMDSAQLTEHANPEAYLLRIARNNWIDRVRR 75 Query: 69 KTSLGRVLEHTQAVAALAQGQMSGQAPESGRSEIEMAFQALIRHLSPLQRTVFVMRDVLD 128 ++S R++E + A + P+ R E+ QAL+ LSPLQR VF++RDV+ Sbjct: 76 QSSHARMMESVRGSA------VYHAMPDESRIGTEVVMQALMTFLSPLQRAVFLLRDVIG 129 Query: 129 YPAGETAEMLGTTEGAVKAALHRARQALGAVRKELAEDDGPAQPQDLDFRILLQALAESY 188 Y A ETA LG T GAVKAALHRAR AL VR+ + P P++ R +L+ALA +Y Sbjct: 130 YSAQETALRLGLTPGAVKAALHRARAALPQVRQAVEAGSLPV-PKEEGLRDVLRALAIAY 188 Query: 189 EKGQLPVMLEL 199 E G + ML L Sbjct: 189 EGGNIEAMLTL 199 >A9GPT7.1 A9GPT7_SORC5 RNA polymerase sigma factor Length = 335 Score = 107 bits (268), Expect = 6e-22, Method: Compositional matrix adjust. Identities = 79/210 (37%), Positives = 101/210 (48%), Gaps = 18/210 (8%) Query: 6 YPPLREALFRYCLSLTRSRVEAEDLAQDTWTKTLAY--KKFADSPNPEALLLRIAKNTWI 63 + PLR L+RYC LTRS +AEDL QDT + F + PNP A L R+A N WI Sbjct: 26 FEPLRPELYRYCRYLTRSPWDAEDLVQDTMARGFVTLGTLFHELPNPRAWLFRVASNLWI 85 Query: 64 DAMRRKTSLGRVLEHTQAVAALAQGQMSGQAPESGRSEIEMAFQALIRHLSPLQRTVFVM 123 D RR+ LE A G AP+ R+ E A L+ HLSP +R V+ Sbjct: 86 DRARRQR-----LERDALGEPAAAPVAPGHAPDE-RASREAA-GTLVAHLSPQERAAVVL 138 Query: 124 RDVLDYPAGETAEMLGTTEGAVKAALHRARQALGAVRKELAEDDGPAQPQDLDFRILLQA 183 +DV D+ E A L T+ GAVKAALHR R L A E D P P +L A Sbjct: 139 KDVFDFSLEEVAASLSTSVGAVKAALHRGRGKLVA-----PEADEPRAPAP----GVLDA 189 Query: 184 LAESYEKGQLPVMLELLRRETAAEMTMAVS 213 ++ LP + LL + E+ V+ Sbjct: 190 FCAAFNARDLPALTSLLLDSSITEIVGVVT 219 >B4UKZ6.1 B4UKZ6_ANASK RNA polymerase sigma factor Length = 327 Score = 97.1 bits (240), Expect = 1e-18, Method: Compositional matrix adjust. Identities = 74/209 (35%), Positives = 95/209 (45%), Gaps = 45/209 (21%) Query: 4 QSYPPLREALFRYCLSLTRSRVEAEDLAQDTWTKTLAYKKFADSP--NPEALLLRIAKNT 61 +Y PLR L+RYC SL RS +A+DL QD + D P NP A L R+A N Sbjct: 24 DTYEPLRPELYRYCRSLARSPWDADDLVQDAMARAFVTLGCMDGPPENPRAWLFRVASNL 83 Query: 62 WIDAMRRKTSLGRVLEHTQAVAALAQGQMSGQAPESG-----RSEIEMAFQALIRHLSPL 116 WID +RR + SG PE R+ E A LI LSP Sbjct: 84 WIDRLRRTR------------------EQSGDVPEGATTPEPRAPREAA-GTLIGRLSPQ 124 Query: 117 QRTVFVMRDVLDYPAGETAEMLGTTEGAVKAALHRARQALGAVRKELAEDD-----GPAQ 171 +R V+++ D E AE L T+ GAVKAALHR R +LAE D P+ Sbjct: 125 ERAAVVLKEAFDLSLEEIAEALSTSVGAVKAALHRG-------RGKLAEPDEAVTASPSA 177 Query: 172 PQDLDFRILLQALAESYEKGQLPVMLELL 200 P +L A E++ G L ++ LL Sbjct: 178 P-------VLDAFCEAFNAGDLDRLVALL 199 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 0.317 0.129 0.360 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: 1,157,051,806 Number of extensions: 42165892 Number of successful extensions: 125714 Number of sequences better than 1.0e-05: 700 Number of HSP's gapped: 126529 Number of HSP's successfully gapped: 700 Length of query: 243 Length of database: 3,060,696,203 Length adjustment: 132 Effective length of query: 111 Effective length of database: 1,817,122,223 Effective search space: 201700566753 Effective search space used: 201700566753 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 (21.7 bits) S2: 129 (54.3 bits)