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= 0547.0029.p (175 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... 95 4e-20 BS_sigV [K] COG1595 DNA-directed RNA polymerase specialized sigm... 76 3e-14 CAC3267 [K] COG1595 DNA-directed RNA polymerase specialized sigm... 68 8e-12 DR0180 [K] COG1595 DNA-directed RNA polymerase specialized sigma... 67 1e-11 BH0263 [K] COG1595 DNA-directed RNA polymerase specialized sigma... 66 2e-11 >BH0620 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 177 Score = 95.1 bits (235), Expect = 4e-20, Method: Compositional matrix adjust. Identities = 47/129 (36%), Positives = 75/129 (58%) Query: 24 VSEQKKILYGIAYSYLRNEPDALEVLQEATYRAWSKRKSLKDTGRFAPWMTRILVNCCKD 83 V ++K LY +A++Y+RNE DAL+V+QEA + + +K F+ WMTRI++N D Sbjct: 20 VEKEKDKLYRVAFTYVRNEHDALDVVQEAVVKGYEAYDRIKHLDYFSSWMTRIVINTAID 79 Query: 84 ELKRRKRLTPGHADNGSSSGSMEMTSDRKLDMEQALDGVKQRYRQVLVLKYYRDMTLAEI 143 L++ K + P + +G E +LD+ L +K +LVL+YY D T+ EI Sbjct: 80 LLRKGKDVIPFCPEKSQMNGWTETHIISRLDLFDVLSELKPEETTLLVLRYYHDFTILEI 139 Query: 144 AEVLDRPEG 152 A +++PEG Sbjct: 140 ARFMNKPEG 148 >BS_sigV [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 166 Score = 75.9 bits (185), Expect = 3e-14, Method: Compositional matrix adjust. Identities = 38/130 (29%), Positives = 76/130 (58%), Gaps = 4/130 (3%) Query: 19 LFIRQVSEQKKILYGIAYSYLRNEPDALEVLQEATYRAWSKRKSLKDTGRFAPWMTRILV 78 L + +++ K+ Y +A+SY++N+ DAL+++QE+ +A S +++++ W +ILV Sbjct: 10 LLVTCITDHKQDFYRLAFSYVKNQDDALDIVQESIKKALSSVETVRNPETIKSWFYKILV 69 Query: 79 NCCKDELKRRK--RLTPGHADNGSSSGSMEMTSDRKLDMEQALDGVKQRYRQVLVLKYYR 136 D L+++K R+ S G + D D+ +ALD + RY+ +++L+++ Sbjct: 70 RTAIDFLRKQKKIRVMDDETIEFLSKGKEDHYKDT--DLHEALDELPYRYKTIIILRFFE 127 Query: 137 DMTLAEIAEV 146 D+ L EIAE+ Sbjct: 128 DLKLEEIAEI 137 >CAC3267 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 190 Score = 67.8 bits (164), Expect = 8e-12, Method: Compositional matrix adjust. Identities = 42/139 (30%), Positives = 70/139 (50%), Gaps = 16/139 (11%) Query: 29 KILYGIAYSYLRNEPDALEVLQEATYRAWSKRKSLKDTGRFAPWMTRILVNCCKDELKRR 88 K LY + Y Y +N DA++++QE + + K+ + F PW+ +I VN C + KR Sbjct: 28 KYLYNLCYGYTQNTSDAMDLVQEIYIKVFKNIKNFDENLPFHPWVRKISVNTCLN-FKRD 86 Query: 89 KR-----LTPGHADNG-------SSSGSMEMTSDRKLDMEQALDGVKQ---RYRQVLVLK 133 R L + D+ + +ME +++ E + +K+ YR V++L+ Sbjct: 87 NRGNVMSLNSKYYDSEFEEEDRLAEDYNMEQEVVNRINNEVVKESIKKLTYDYRMVIMLR 146 Query: 134 YYRDMTLAEIAEVLDRPEG 152 YY D++ EIA VLD P G Sbjct: 147 YYEDLSYDEIASVLDMPIG 165 >DR0180 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 229 Score = 67.4 bits (163), Expect = 1e-11, Method: Compositional matrix adjust. Identities = 46/152 (30%), Positives = 74/152 (48%), Gaps = 11/152 (7%) Query: 4 LLEGEWAQAVDGEEQLFIRQVSEQKKILYGIAYSYLRNEPDALEVLQEATYRAWSKRKSL 63 L E AQ + G+E + R +SE + +YG Y N DAL++ QE YRAW ++ Sbjct: 46 LTEDAHAQLLTGDEAAWHRFISEYEGRIYGYLYRLEGNSEDALDLTQEVFYRAWRSIRTF 105 Query: 64 KDTGRFAPWMTRILVNCCKDELKRRKR----LTPGHADNGSSSGSMEMTSDRKLDMEQAL 119 + R PW+ ++ N + +R++ L H D G S + + + EQA Sbjct: 106 RPGERVLPWLYQVARNTQIESHRRKQHARFSLEEAHEDIGFEVTSEARSPVQAAESEQAQ 165 Query: 120 DGVKQ-------RYRQVLVLKYYRDMTLAEIA 144 D V++ YR+ +VL++ D+T EIA Sbjct: 166 DRVQRALMRLAPEYREAVVLRFVEDLTYDEIA 197 >BH0263 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 187 Score = 66.2 bits (160), Expect = 2e-11, Method: Compositional matrix adjust. Identities = 46/151 (30%), Positives = 74/151 (49%), Gaps = 15/151 (9%) Query: 15 GEEQLFIRQVSEQKKILYGIAYSYLRNEPDALEVLQEATYRAWSKRKSLKDTGRFAPWMT 74 G+EQ F V K +Y +AY + N +A +V QEA RA++ + +F+ W+ Sbjct: 15 GDEQAFAELVELYKDKVYQVAYRMVGNVHEAQDVAQEAFLRAYTNIDTYDIQRKFSTWLF 74 Query: 75 RILVNCCKDELKRRK----RLTPGHADNGSSSGSM-----EMTSDRKLDME------QAL 119 RI N D L++RK P +G + S E D+ + ME Q + Sbjct: 75 RIATNVAIDRLRKRKPDFHLEDPVQGADGLTIESQLAADEEPVDDQVIQMETRDWIQQEI 134 Query: 120 DGVKQRYRQVLVLKYYRDMTLAEIAEVLDRP 150 + +YR ++LKY D++L EI+++LD P Sbjct: 135 QALPPKYRMAVLLKYMEDLSLKEISDILDLP 165 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 0.315 0.130 0.371 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: 11,705,743 Number of extensions: 398235 Number of successful extensions: 759 Number of sequences better than 1.0e-05: 12 Number of HSP's gapped: 768 Number of HSP's successfully gapped: 12 Length of query: 175 Length of database: 38,378,431 Length adjustment: 99 Effective length of query: 76 Effective length of database: 26,960,365 Effective search space: 2048987740 Effective search space used: 2048987740 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 (21.6 bits) S2: 112 (47.8 bits)