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= 0545.0026.p (219 letters) Database: COG 115,334 sequences; 38,378,431 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value CC0648 [K] COG1595 DNA-directed RNA polymerase specialized sigma... 79 6e-15 all2193 [K] COG1595 DNA-directed RNA polymerase specialized sigm... 72 8e-13 sll0687 [K] COG1595 DNA-directed RNA polymerase specialized sigm... 71 1e-12 AGc838 [K] COG1595 DNA-directed RNA polymerase specialized sigma... 69 4e-12 RSc2361 [K] COG1595 DNA-directed RNA polymerase specialized sigm... 69 5e-12 >CC0648 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 205 Score = 78.6 bits (192), Expect = 6e-15, Method: Compositional matrix adjust. Identities = 49/164 (29%), Positives = 87/164 (53%), Gaps = 5/164 (3%) Query: 37 AAFDEFYGWGGXXXVMQIAYRQTQDWMEAEDICHDIFLEVLRKGRAYDASRGTVKAWLAV 96 AAF E + V + R AE++ ++ L V RK +D R + AW+ Sbjct: 40 AAFAELFAHYAPR-VKTLLVRSGSTPSAAEELAQEVMLAVWRKAHYFDPKRASAAAWIFT 98 Query: 97 MTRSRCIDRLRRKARTEPLANPETQLRNQDGPQEDAAVRKLQ-CEALGDALQSLPANQKK 155 + R+ ID LRR + L + L ++ PQ DA + +Q + + A+Q+L +Q + Sbjct: 99 IARNLRIDSLRRG--SSALYAVDLNLGAEEPPQPDAILSGMQDAQIVRSAMQTLNPDQSQ 156 Query: 156 AILGSYYAAHTHQELADSWSVPLGTVKSWIKYGVANMRRQFIKQ 199 AI +++ TH +++++ VPLGTVK+ I++G+ + R FI++ Sbjct: 157 AIEMAFFQEQTHSQISEALGVPLGTVKARIRFGMMKL-RAFIER 199 >all2193 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 201 Score = 71.6 bits (174), Expect = 8e-13, Method: Compositional matrix adjust. Identities = 54/184 (29%), Positives = 88/184 (47%), Gaps = 9/184 (4%) Query: 18 DPHNEAMAAALAKMCEGSTAAFDEFYGWGGXXXVMQIAYRQTQDWMEAEDICHDIFLEVL 77 D +EA+ L G +AA + G V +A + D EAED+ +IFL + Sbjct: 15 DVTDEALFVGLKN---GDSAALSVLFNRHGRL-VYGLALKILADSQEAEDLTQEIFLTLW 70 Query: 78 RKGRAYDASRGTVKAWLAVMTRSRCIDRLRRKARTEPLANPETQ-LRNQDGPQEDAAVRK 136 RK + R V+ +L +TRSR ID++R + R L Q + N+ P+ + Sbjct: 71 RKASSNPDCRFFVR-YLVTITRSRAIDKIRARTRQLKLVEKWGQTMTNEAAPEPTPVEQA 129 Query: 137 LQCEALG---DALQSLPANQKKAILGSYYAAHTHQELADSWSVPLGTVKSWIKYGVANMR 193 E G +AL LP Q++ I +Y+ + E+A +PLGTVK+ + G+ ++ Sbjct: 130 SFAERSGRIHNALAQLPEKQRQVIELAYHQGLSQSEIAKQIDIPLGTVKTSTRQGLLKLK 189 Query: 194 RQFI 197 R + Sbjct: 190 RILL 193 >sll0687 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 185 Score = 71.2 bits (173), Expect = 1e-12, Method: Compositional matrix adjust. Identities = 52/169 (30%), Positives = 92/169 (54%), Gaps = 6/169 (3%) Query: 28 LAKMCEGSTAAFDEFYGWGGXXXVMQIAYRQTQDWMEAEDICHDIFLEVLRKGRAYDASR 87 +A + G + A Y G V ++A R Q +AED+ +IFL L Y++ R Sbjct: 12 MAAVQRGDSFALGVLYNRYGAV-VYRLALRILQRSQDAEDLTQEIFLS-LETTTPYNSQR 69 Query: 88 GTVKAWLAVMTRSRCIDRLRR-KARTEPL-ANPETQLRN-QDGPQEDAAVRKLQCEALGD 144 G + +L +TRSR ++R+R+ ++R L A L N + P E+AA+ +L + + Sbjct: 70 GNLLNFLLTLTRSRALNRIRQGRSRGRLLKACQHNHLTNVPNLPMENAALSEL-SQRVAS 128 Query: 145 ALQSLPANQKKAILGSYYAAHTHQELADSWSVPLGTVKSWIKYGVANMR 193 AL++LP NQ++ + +YY + E+ ++PLGTVK+ + G+ ++ Sbjct: 129 ALETLPPNQRQVLELAYYEGLSQSEITQKLAIPLGTVKTRSRQGLLKLK 177 >AGc838 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 243 Score = 69.3 bits (168), Expect = 4e-12, Method: Compositional matrix adjust. Identities = 41/144 (28%), Positives = 78/144 (54%), Gaps = 1/144 (0%) Query: 51 VMQIAYRQTQDWMEAEDICHDIFLEVLRKGRAYDASRGTVKAWLAVMTRSRCIDRLRRKA 110 ++ +A R + AE++ + F+ + Y A G+ + W+ + R+R ++ LR + Sbjct: 96 LIAVAERIVKRRELAEEVVQESFVRIWTHAPQYRADHGSARGWIYAIVRNRALNLLRDGS 155 Query: 111 RTEPLANPETQLRNQDGPQEDAAVRKLQCEA-LGDALQSLPANQKKAILGSYYAAHTHQE 169 R + + ET ++ + AA +KL + L + L +L +++ IL +Y A ++H E Sbjct: 156 RELTVQDVETLRDSEQADEVVAAWQKLDRNSRLYECLGALDETKRQGILMAYVAGYSHGE 215 Query: 170 LADSWSVPLGTVKSWIKYGVANMR 193 +A VPLGT KSWI+ G++ +R Sbjct: 216 IAGRLRVPLGTTKSWIRRGLSALR 239 >RSc2361 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 213 Score = 68.9 bits (167), Expect = 5e-12, Method: Compositional matrix adjust. Identities = 58/198 (29%), Positives = 89/198 (44%), Gaps = 15/198 (7%) Query: 7 EDVAKGGETAMDPHNEA--MAAALAKMCEGSTAAFDEFYGWGGXXXV---MQIAYRQTQD 61 +D + A P EA +AA L ++ G A Y ++I R+ D Sbjct: 14 QDAGRPPIAARAPGAEADELAALLQRIGLGEREALRALYARCAAKLFGLALRILVRR--D 71 Query: 62 WMEAEDICHDIFLEVLRKGRAYDASRGTVKAWLAVMTRSRCIDRLRRK-----ARTEPLA 116 W AED+ + F+ + R Y W+A + R+R +D LRR+ A + PL Sbjct: 72 W--AEDVLQESFVNIWRHAADYRPQLAAPMTWMATIVRNRALDCLRRQRAERVAESVPLD 129 Query: 117 NPETQLRNQDGP-QEDAAVRKLQCEALGDALQSLPANQKKAILGSYYAAHTHQELADSWS 175 + P D A+ Q AL + L+ L Q++ + +Y +H ELA S Sbjct: 130 DAHADALADHAPGPADLALAGQQARALAECLKRLDPRQREVVSLAYLRDLSHSELAQVLS 189 Query: 176 VPLGTVKSWIKYGVANMR 193 VPLGTVKSW++ G+ +R Sbjct: 190 VPLGTVKSWMRRGLDRLR 207 Database: COG Posted date: Aug 3, 2010 9:58 AM Number of letters in database: 38,378,431 Number of sequences in database: 115,334 Lambda K H 0.317 0.131 0.403 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 115334 Number of Hits to DB: 16,156,219 Number of extensions: 593293 Number of successful extensions: 2050 Number of sequences better than 1.0e-05: 18 Number of HSP's gapped: 2046 Number of HSP's successfully gapped: 18 Length of query: 219 Length of database: 38,378,431 Length adjustment: 102 Effective length of query: 117 Effective length of database: 26,614,363 Effective search space: 3113880471 Effective search space used: 3113880471 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: 114 (48.5 bits)