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= 0322.0001.p (178 letters) Database: COG 115,334 sequences; 38,378,431 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value BH0620 [K] COG1595 DNA-directed RNA polymerase specialized sigma... 100 1e-21 BS_sigV [K] COG1595 DNA-directed RNA polymerase specialized sigm... 84 1e-16 BH0263 [K] COG1595 DNA-directed RNA polymerase specialized sigma... 84 2e-16 BS_sigW [K] COG1595 DNA-directed RNA polymerase specialized sigm... 77 1e-14 CAC3267 [K] COG1595 DNA-directed RNA polymerase specialized sigm... 66 2e-11 >BH0620 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 177 Score = 100 bits (248), Expect = 1e-21, Method: Compositional matrix adjust. Identities = 56/159 (35%), Positives = 91/159 (57%), Gaps = 2/159 (1%) Query: 22 FYDAVMEHSDQLYHIAYSYLRNRSDALEAVQEATCRAWIKRATLKDPQAFKPWIIRILIY 81 F + V + D+LY +A++Y+RN DAL+ VQEA + + +K F W+ RI+I Sbjct: 16 FEELVEKEKDKLYRVAFTYVRNEHDALDVVQEAVVKGYEAYDRIKHLDYFSSWMTRIVIN 75 Query: 82 VCIDEQRRRKRSVP-TPEAA-MREPVMQDSSSKLEMLWAVEQVKPKYRHVLLLKYYNDMT 139 ID R+ K +P PE + M S+L++ + ++KP+ +L+L+YY+D T Sbjct: 76 TAIDLLRKGKDVIPFCPEKSQMNGWTETHIISRLDLFDVLSELKPEETTLLVLRYYHDFT 135 Query: 140 LTEIADLLGKPEGTIKTWQHKGLKQLRTIMKNRGEWNDQ 178 + EIA + KPEGTIK H+ L ++R M+ G+ +Q Sbjct: 136 ILEIARFMNKPEGTIKAQLHRTLAKVRKRMEKGGDTYEQ 174 >BS_sigV [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 166 Score = 83.6 bits (205), Expect = 1e-16, Method: Compositional matrix adjust. Identities = 40/144 (27%), Positives = 82/144 (56%), Gaps = 2/144 (1%) Query: 25 AVMEHSDQLYHIAYSYLRNRSDALEAVQEATCRAWIKRATLKDPQAFKPWIIRILIYVCI 84 + +H Y +A+SY++N+ DAL+ VQE+ +A T+++P+ K W +IL+ I Sbjct: 14 CITDHKQDFYRLAFSYVKNQDDALDIVQESIKKALSSVETVRNPETIKSWFYKILVRTAI 73 Query: 85 DEQRRRK--RSVPTPEAAMREPVMQDSSSKLEMLWAVEQVKPKYRHVLLLKYYNDMTLTE 142 D R++K R + +D ++ A++++ +Y+ +++L+++ D+ L E Sbjct: 74 DFLRKQKKIRVMDDETIEFLSKGKEDHYKDTDLHEALDELPYRYKTIIILRFFEDLKLEE 133 Query: 143 IADLLGKPEGTIKTWQHKGLKQLR 166 IA++ G+ T+KT ++ LK +R Sbjct: 134 IAEITGENTNTVKTRLYRALKLMR 157 >BH0263 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 187 Score = 83.6 bits (205), Expect = 2e-16, Method: Compositional matrix adjust. Identities = 56/172 (32%), Positives = 89/172 (51%), Gaps = 19/172 (11%) Query: 18 EDNAFYDAVMEHSDQLYHIAYSYLRNRSDALEAVQEATCRAWIKRATLKDPQAFKPWIIR 77 ++ AF + V + D++Y +AY + N +A + QEA RA+ T + F W+ R Sbjct: 16 DEQAFAELVELYKDKVYQVAYRMVGNVHEAQDVAQEAFLRAYTNIDTYDIQRKFSTWLFR 75 Query: 78 ILIYVCIDEQRRRK--------------RSVPTPEAAMREPVMQDSSSKLEML-WAVEQV 122 I V ID R+RK ++ + AA EPV D ++E W +++ Sbjct: 76 IATNVAIDRLRKRKPDFHLEDPVQGADGLTIESQLAADEEPV-DDQVIQMETRDWIQQEI 134 Query: 123 K---PKYRHVLLLKYYNDMTLTEIADLLGKPEGTIKTWQHKGLKQLRTIMKN 171 + PKYR +LLKY D++L EI+D+L P T+KT H+G + LR M++ Sbjct: 135 QALPPKYRMAVLLKYMEDLSLKEISDILDLPVSTVKTRIHRGREALRKRMRH 186 >BS_sigW [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 187 Score = 77.4 bits (189), Expect = 1e-14, Method: Compositional matrix adjust. Identities = 53/182 (29%), Positives = 92/182 (50%), Gaps = 18/182 (9%) Query: 8 MKKLTGAVPRED-NAFYDAVMEHSDQLYHIAYSYLRNRSDALEAVQEATCRAWIKRATLK 66 +KK V + D +AF D V + D++Y + Y L N +A + QEA RA++ + Sbjct: 5 IKKRIKQVKKGDQDAFADIVDIYKDKIYQLCYRMLGNVHEAEDIAQEAFIRAYVNIDSFD 64 Query: 67 DPQAFKPWIIRILIYVCIDEQRRRK-------RSVPTPEAAMREPVM------QDSSSKL 113 + F W+ RI + ID R++K T M ++ +D+ L Sbjct: 65 INRKFSTWLYRIATNLTIDRIRKKKPDYYLDAEVAGTEGLTMYSQIVADGVLPEDAVVSL 124 Query: 114 EMLWAVEQ----VKPKYRHVLLLKYYNDMTLTEIADLLGKPEGTIKTWQHKGLKQLRTIM 169 E+ ++Q + KYR V++LKY ++++L EI ++L P GT+KT H+G + LR + Sbjct: 125 ELSNTIQQKILKLPDKYRTVIVLKYIDELSLIEIGEILNIPVGTVKTRIHRGREALRKQL 184 Query: 170 KN 171 ++ Sbjct: 185 RD 186 >CAC3267 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 190 Score = 66.2 bits (160), Expect = 2e-11, Method: Compositional matrix adjust. Identities = 39/158 (24%), Positives = 81/158 (51%), Gaps = 16/158 (10%) Query: 33 LYHIAYSYLRNRSDALEAVQEATCRAWIKRATLKDPQAFKPWIIRILIYVCIDEQRRRKR 92 LY++ Y Y +N SDA++ VQE + + + F PW+ +I + C++ +R + Sbjct: 30 LYNLCYGYTQNTSDAMDLVQEIYIKVFKNIKNFDENLPFHPWVRKISVNTCLNFKRDNRG 89 Query: 93 SVPT-------PEAAMREPVMQDSSSKLEML---------WAVEQVKPKYRHVLLLKYYN 136 +V + E + + +D + + E++ +++++ YR V++L+YY Sbjct: 90 NVMSLNSKYYDSEFEEEDRLAEDYNMEQEVVNRINNEVVKESIKKLTYDYRMVIMLRYYE 149 Query: 137 DMTLTEIADLLGKPEGTIKTWQHKGLKQLRTIMKNRGE 174 D++ EIA +L P GT+KT ++ L+ ++ + E Sbjct: 150 DLSYDEIASVLDMPIGTVKTKIYRAKNVLKKSLEKKLE 187 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 0.400 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: 12,564,144 Number of extensions: 451032 Number of successful extensions: 880 Number of sequences better than 1.0e-05: 34 Number of HSP's gapped: 867 Number of HSP's successfully gapped: 34 Length of query: 178 Length of database: 38,378,431 Length adjustment: 99 Effective length of query: 79 Effective length of database: 26,960,365 Effective search space: 2129868835 Effective search space used: 2129868835 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: 112 (47.8 bits)