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: COG 115,334 sequences; 38,378,431 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value lin0443 [K] COG1595 DNA-directed RNA polymerase specialized sigm... 101 1e-21 BH0263 [K] COG1595 DNA-directed RNA polymerase specialized sigma... 75 8e-14 VC2467 [K] COG1595 DNA-directed RNA polymerase specialized sigma... 74 3e-13 PA0762 [K] COG1595 DNA-directed RNA polymerase specialized sigma... 74 3e-13 DR0180 [K] COG1595 DNA-directed RNA polymerase specialized sigma... 73 4e-13 >lin0443 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 301 Score = 101 bits (252), Expect = 1e-21, Method: Compositional matrix adjust. Identities = 7/190 (3%), Positives = 22/190 (11%), Gaps = 15/190 (7%) Query: 69 TELQDLA---HAAAMSEEQLRQIMGFYGNDVWHYIYYLTKSADIADDLAQEVFIKCFYRI 125 + + ++ ++ + Sbjct: 2 SIDKSYCGFIAIVGRPNVGKSTLLNKLLGQKISITSRKAQTTRHRIVGIHTEGAYQAIYV 61 Query: 126 GTYRGSSSFKAWLFTIARNTVFSYRKSRFFRSGFWGGVQAIRNNEPVRNSWPDELPGTAR 185 T K + + S Sbjct: 62 DTPGLHMEEKRAINRLMNKAASSSIGDVELVI--------FVVEGTRWTP----DDEMVL 109 Query: 186 SAEMEYLGNCRTDEIWSIILQLPDKFREVLVLDLKAELSIQEIAGLTGLSPGTVKSRLHR 245 + E +Q L + + Sbjct: 110 NKLREGKAPVILAVNKVDNVQEKADLLPHLQFLASQMNFLDIVPISAETGLNVDTIAAIV 169 Query: 246 ARHKVQEKLR 255 +H + Sbjct: 170 RKHLPEATHH 179 >BH0263 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 187 Score = 75.5 bits (184), Expect = 8e-14, Method: Compositional matrix adjust. Identities = 50/179 (27%), Positives = 81/179 (45%), Gaps = 5/179 (2%) Query: 79 AMSEEQLRQIMGFYGNDVWHYIYYLTKSADIADDLAQEVFIKCFYRIGTYRGSSSFKAWL 138 A E+ +++ Y + V+ Y + + A D+AQE F++ + I TY F WL Sbjct: 14 AGDEQAFAELVELYKDKVYQVAYRMVGNVHEAQDVAQEAFLRAYTNIDTYDIQRKFSTWL 73 Query: 139 FTIARNTVFSYRKSRFFRSGFWGGVQAIRNNEPVRNSWPDELPGTARSAEMEYLGNCRTD 198 F IA N + R VQ DE P + +ME D Sbjct: 74 FRIATNVAIDRLRKRKPDFHLEDPVQGADGLTIESQLAADEEPVDDQVIQMET-----RD 128 Query: 199 EIWSIILQLPDKFREVLVLDLKAELSIQEIAGLTGLSPGTVKSRLHRARHKVQEKLRGM 257 I I LP K+R ++L +LS++EI+ + L TVK+R+HR R +++++R + Sbjct: 129 WIQQEIQALPPKYRMAVLLKYMEDLSLKEISDILDLPVSTVKTRIHRGREALRKRMRHV 187 >VC2467 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 190 Score = 73.6 bits (179), Expect = 3e-13, Method: Compositional matrix adjust. Identities = 55/178 (30%), Positives = 87/178 (48%), Gaps = 29/178 (16%) Query: 92 YGNDVWHYIY-YLTKSADIADDLAQEVFIKCFYRIGTYRGSSSFKAWLFTIARNTVFSYR 150 Y N V + I Y++ S D+AD +AQE FIK + I T+RG S+F WL+ IA NT ++ Sbjct: 29 YQNKVCNLISRYVSNSGDVAD-VAQEAFIKAYRAIPTFRGESAFYTWLYRIAVNTAKNHI 87 Query: 151 KSRFFR----------SGFWGGVQAIRN-NEPVRNSWPDELPGTARSAEMEYLGNCRTDE 199 ++ R + F+ G A++ + P + EL T Sbjct: 88 VAQSRRPPASDVDAEEAEFYEGGDALKELSNPENITLSKELKKT---------------- 131 Query: 200 IWSIILQLPDKFREVLVLDLKAELSIQEIAGLTGLSPGTVKSRLHRARHKVQEKLRGM 257 ++ I LPD + + L LS +EIA + GTV+SR+ RAR V++K++ + Sbjct: 132 VFDAIDALPDDLKTAMTLRELDGLSYEEIAEVMDCPVGTVRSRIFRAREAVEKKIKPL 189 >PA0762 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 193 Score = 73.6 bits (179), Expect = 3e-13, Method: Compositional matrix adjust. Identities = 53/177 (29%), Positives = 81/177 (45%), Gaps = 27/177 (15%) Query: 92 YGNDVWHYIYYLTKSADIADDLAQEVFIKCFYRIGTYRGSSSFKAWLFTIARNTVFSYRK 151 Y + + I A A D+AQE FIK + +G +RG S+F WL+ IA NT ++ Sbjct: 29 YQHKILGLIVRFVHDAQEAQDVAQEAFIKAYRALGNFRGDSAFYTWLYRIAINTAKNHLV 88 Query: 152 SRFFR----------SGFWGGVQAIRNNE-PVRNSWPDELPGTARSAEMEYLGNCRTDEI 200 +R R + F+ G A+++ E P R DE+ T + Sbjct: 89 ARGRRPPDSDVTAEDAEFFEGDHALKDIESPERAMLRDEIEAT----------------V 132 Query: 201 WSIILQLPDKFREVLVLDLKAELSIQEIAGLTGLSPGTVKSRLHRARHKVQEKLRGM 257 I QLP+ R L L LS ++IA + GTV+SR+ RAR + + L+ + Sbjct: 133 HQTIQQLPEDLRTALTLREFEGLSYEDIATVMQCPVGTVRSRIFRAREAIDKALQPL 189 >DR0180 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 229 Score = 73.2 bits (178), Expect = 4e-13, Method: Compositional matrix adjust. Identities = 54/187 (28%), Positives = 90/187 (48%), Gaps = 13/187 (6%) Query: 71 LQDLAHAAAMS--EEQLRQIMGFYGNDVWHYIYYLTKSADIADDLAQEVFIKCFYRIGTY 128 L + AHA ++ E + + Y ++ Y+Y L +++ A DL QEVF + + I T+ Sbjct: 46 LTEDAHAQLLTGDEAAWHRFISEYEGRIYGYLYRLEGNSEDALDLTQEVFYRAWRSIRTF 105 Query: 129 RGSSSFKAWLFTIARNT-VFSYRKSRFFRSGFWGGVQAIRNNEPVRNSWPDELPGTARSA 187 R WL+ +ARNT + S+R+ + R E E+ ARS Sbjct: 106 RPGERVLPWLYQVARNTQIESHRRKQHARFSL----------EEAHEDIGFEVTSEARSP 155 Query: 188 EMEYLGNCRTDEIWSIILQLPDKFREVLVLDLKAELSIQEIAGLTGLSPGTVKSRLHRAR 247 D + +++L ++RE +VL +L+ EIA L G++ GT KSR+ RA+ Sbjct: 156 VQAAESEQAQDRVQRALMRLAPEYREAVVLRFVEDLTYDEIARLQGVATGTAKSRVFRAK 215 Query: 248 HKVQEKL 254 ++ E L Sbjct: 216 EQLAELL 222 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 0.322 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: 115334 Number of Hits to DB: 18,548,904 Number of extensions: 730858 Number of successful extensions: 1317 Number of sequences better than 1.0e-05: 43 Number of HSP's gapped: 1280 Number of HSP's successfully gapped: 43 Length of query: 259 Length of database: 38,378,431 Length adjustment: 104 Effective length of query: 155 Effective length of database: 26,383,695 Effective search space: 4089472725 Effective search space used: 4089472725 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: 115 (48.9 bits)