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= 0370.0041.p (195 letters) Database: COG 115,334 sequences; 38,378,431 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value BS_sigW [K] COG1595 DNA-directed RNA polymerase specialized sigm... 67 2e-11 PA1776 [K] COG1595 DNA-directed RNA polymerase specialized sigma... 65 4e-11 BH0263 [K] COG1595 DNA-directed RNA polymerase specialized sigma... 60 3e-09 RSc1055 [K] COG1595 DNA-directed RNA polymerase specialized sigm... 59 5e-09 mll2270 [K] COG1595 DNA-directed RNA polymerase specialized sigm... 58 8e-09 >BS_sigW [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 187 Score = 67.0 bits (162), Expect = 2e-11, Method: Compositional matrix adjust. Identities = 28/73 (38%), Positives = 50/73 (68%) Query: 6 IEQAVARVQAGEVEPYAQIVEAYQKPIHRYCSRLLGSRSEAEDAVQDILVKAYLNIAAYR 65 I++ + +V+ G+ + +A IV+ Y+ I++ C R+LG+ EAED Q+ ++AY+NI ++ Sbjct: 5 IKKRIKQVKKGDQDAFADIVDIYKDKIYQLCYRMLGNVHEAEDIAQEAFIRAYVNIDSFD 64 Query: 66 SVASFSSWLYKIA 78 FS+WLY+IA Sbjct: 65 INRKFSTWLYRIA 77 >PA1776 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 165 Score = 65.5 bits (158), Expect = 4e-11, Method: Compositional matrix adjust. Identities = 38/156 (24%), Positives = 68/156 (43%) Query: 21 YAQIVEAYQKPIHRYCSRLLGSRSEAEDAVQDILVKAYLNIAAYRSVASFSSWLYKIAYH 80 Y +++ YQ+ + C+R LG+ +A+D Q++++K + + + F +WLY I Y+ Sbjct: 5 YEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGKSKFKTWLYSITYN 64 Query: 81 HCXXXXXXXXXXXXXXXXXXXXXXXXXXXXXMDRNIFSEPLAKALSRLSTEERNLLVLRI 140 C + L + L ++ +R +LVLR Sbjct: 65 ECITQYRKERRKRRLMDALSLDPLEEASEEKSPKVEERGGLDRWLVHVNPIDREILVLRF 124 Query: 141 FEEQSFPEIAGILDKNMEAVKKKYRRTLMKLAKMMS 176 E F EIA I+ + A K +Y+R L +L + S Sbjct: 125 VAELEFQEIADIMHMGLSATKMRYKRALDRLREKFS 160 >BH0263 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 187 Score = 59.7 bits (143), Expect = 3e-09, Method: Compositional matrix adjust. Identities = 27/77 (35%), Positives = 51/77 (66%), Gaps = 1/77 (1%) Query: 3 LDWIEQAVAR-VQAGEVEPYAQIVEAYQKPIHRYCSRLLGSRSEAEDAVQDILVKAYLNI 61 +D I++ + R V+AG+ + +A++VE Y+ +++ R++G+ EA+D Q+ ++AY NI Sbjct: 1 MDSIDKRLVREVRAGDEQAFAELVELYKDKVYQVAYRMVGNVHEAQDVAQEAFLRAYTNI 60 Query: 62 AAYRSVASFSSWLYKIA 78 Y FS+WL++IA Sbjct: 61 DTYDIQRKFSTWLFRIA 77 >RSc1055 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 199 Score = 58.9 bits (141), Expect = 5e-09, Method: Compositional matrix adjust. Identities = 46/185 (24%), Positives = 76/185 (41%), Gaps = 11/185 (5%) Query: 10 VARVQAGEVEPYAQIVEAYQKPIHRYCSRLLGSRSEAEDAVQDILVKAYLNIAAYRSVAS 69 V RVQ G+ + +V Y + I R SRL+ +E ED QD +KAY + +R ++ Sbjct: 11 VERVQQGDKRAFELLVVKYHRKIIRLISRLIRDAAEVEDVAQDAFIKAYRALPQFRGESA 70 Query: 70 FSSWLYKIAYHHCXXXXXXXXXXXXXXXXXXXXXXXXXXXXXMDRNI-----------FS 118 F +WLY+IA + R+I + Sbjct: 71 FYTWLYRIAVNTAKNYLATQGRRPESSTDIDTEEAETFADGEQLRDINTPDSMLHTKQVA 130 Query: 119 EPLAKALSRLSTEERNLLVLRIFEEQSFPEIAGILDKNMEAVKKKYRRTLMKLAKMMSAH 178 E + +A+ L E R + LR E S+ EIA ++ + V+ + R +A+ + Sbjct: 131 ETVNRAMEALPEELRTAITLREIEGLSYEEIAEAMECPIGTVRSRIFRAREAIAEKLRPL 190 Query: 179 KGGSE 183 G +E Sbjct: 191 LGTAE 195 >mll2270 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 301 Score = 58.2 bits (139), Expect = 8e-09, Method: Compositional matrix adjust. Identities = 10/143 (6%), Positives = 23/143 (16%), Gaps = 3/143 (2%) Query: 32 IHRYCSRLLGSRSEAEDAVQDILVKAYLNIAAYRSVASFSSWLYKIAYHHCXXXXXXXXX 91 + SR + + + A K A + Sbjct: 27 KLLGQKISITSRKAQTTRHRIVGIHTEGAYQAIYVDTPGLHMEEKRAINRLMNKAASSSI 86 Query: 92 XXXXXXXXXXXXXXXXXXXXMDRNIFSEPLAKALSR---LSTEERNLLVLRIFEEQSFPE 148 M N E A + + + +L + + Sbjct: 87 GDVELVIFVVEGTRWTPDDEMVLNKLREGKAPVILAVNKVDNVQEKADLLPHLQFLASQM 146 Query: 149 IAGILDKNMEAVKKKYRRTLMKL 171 + + Sbjct: 147 NFLDIVPISAETGLNVDTIAAIV 169 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 0.319 0.132 0.379 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: 11,147,487 Number of extensions: 378217 Number of successful extensions: 853 Number of sequences better than 1.0e-05: 10 Number of HSP's gapped: 855 Number of HSP's successfully gapped: 10 Length of query: 195 Length of database: 38,378,431 Length adjustment: 101 Effective length of query: 94 Effective length of database: 26,729,697 Effective search space: 2512591518 Effective search space used: 2512591518 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: 113 (48.1 bits)