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: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF 2,715,099 sequences; 757,237,578 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value ref|NP_241486.1| RNA polymerase ECF-type sigma factor [Bacillus ... 95 5e-19 ref|NP_561475.1| RNA polymerase ECF-type sigma factor [Clostridi... 92 3e-18 ref|ZP_00061095.1| COG1595: DNA-directed RNA polymerase speciali... 92 4e-18 ref|NP_693234.1| RNA polymerase ECF-type sigma factor [Oceanobac... 88 7e-17 ref|NP_781356.1| RNA polymerase sigma factor sigV [Clostridium t... 82 5e-15 >ref|NP_241486.1| RNA polymerase ECF-type sigma factor [Bacillus halodurans] pir||D83727 RNA polymerase ECF-type sigma factor sigV [imported] - Bacillus halodurans (strain C-125) dbj|BAB04339.1| RNA polymerase ECF-type sigma factor [Bacillus halodurans] Length = 177 Score = 95.1 bits (235), Expect = 5e-19, 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 >ref|NP_561475.1| RNA polymerase ECF-type sigma factor [Clostridium perfringens] dbj|BAB80265.1| RNA polymerase ECF-type sigma factor [Clostridium perfringens str. 13] Length = 191 Score = 92.4 bits (228), Expect = 3e-18, Method: Compositional matrix adjust. Identities = 44/142 (30%), Positives = 82/142 (57%) Query: 11 QAVDGEEQLFIRQVSEQKKILYGIAYSYLRNEPDALEVLQEATYRAWSKRKSLKDTGRFA 70 +++ G ++ F + K+ LY +A+ Y+++E DALEV+ E YRA+ + LK F Sbjct: 26 ESMKGNKESFGILIKNNKEYLYKMAFLYVKDEQDALEVIHETVYRAFLNIEKLKKAKFFN 85 Query: 71 PWMTRILVNCCKDELKRRKRLTPGHADNGSSSGSMEMTSDRKLDMEQALDGVKQRYRQVL 130 W+TRIL+N D LK++ + E++++ KLD+ A+D + Y+ V+ Sbjct: 86 TWITRILINVSIDFLKKKGKNEMLDESTPIRKERCEISTEEKLDLYNAIDLLNDNYKTVI 145 Query: 131 VLKYYRDMTLAEIAEVLDRPEG 152 ++ Y+ DM + +I++V++ PE Sbjct: 146 IMMYFNDMKIKDISKVMEIPEN 167 >ref|ZP_00061095.1| COG1595: DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Clostridium thermocellum ATCC 27405] Length = 167 Score = 92.4 bits (228), Expect = 4e-18, Method: Compositional matrix adjust. Identities = 48/125 (38%), Positives = 80/125 (64%), Gaps = 4/125 (3%) Query: 26 EQKKILYGIAYSYLRNEPDALEVLQEATYRAWSKRKSLKDTGRFAPWMTRILVNCCKDEL 85 + K+ Y +AYSY++N DAL+++QE+ Y+A S SLK+ W RI+VN D L Sbjct: 18 KHKENFYRLAYSYVKNADDALDIVQESVYKAISSMDSLKNPDYLKTWFYRIVVNTSLDFL 77 Query: 86 KRRKR-LTPGHADNGS-SSGSMEMTSDRKLDMEQALDGVKQRYRQVLVLKYYRDMTLAEI 143 +R+KR + G GS G+++ D D+++ALD + ++YR ++VL+Y+ D+ + EI Sbjct: 78 RRQKRNVAVGEEILGSFDFGAVDSYGD--FDLQRALDNLPEKYRTIVVLRYFEDLKIDEI 135 Query: 144 AEVLD 148 AE+L+ Sbjct: 136 AEILN 140 >ref|NP_693234.1| RNA polymerase ECF-type sigma factor [Oceanobacillus iheyensis HTE831] dbj|BAC14269.1| RNA polymerase ECF-type sigma factor [Oceanobacillus iheyensis HTE831] Length = 155 Score = 88.2 bits (217), Expect = 7e-17, Method: Compositional matrix adjust. Identities = 40/124 (32%), Positives = 72/124 (58%) Query: 29 KILYGIAYSYLRNEPDALEVLQEATYRAWSKRKSLKDTGRFAPWMTRILVNCCKDELKRR 88 K LY IA +Y++N D +V+QE YR + K L++ F W+T+I +NC D +++ Sbjct: 9 KNLYRIANTYVKNSNDTYDVIQETAYRTYEKLPELRNPQYFKTWITKITINCALDTIRKN 68 Query: 89 KRLTPGHADNGSSSGSMEMTSDRKLDMEQALDGVKQRYRQVLVLKYYRDMTLAEIAEVLD 148 K++ + S+ ++ K+ +EQ LD + ++ R ++VL++Y ++ EI+E LD Sbjct: 69 KKMIIMEPEKVSTKAYYDLDIPLKITVEQLLDRLNEKERTIIVLRFYYALSFKEISEQLD 128 Query: 149 RPEG 152 P G Sbjct: 129 IPYG 132 >ref|NP_781356.1| RNA polymerase sigma factor sigV [Clostridium tetani E88] gb|AAO35293.1| RNA polymerase sigma factor sigV [Clostridium tetani E88] Length = 177 Score = 82.0 bits (201), Expect = 5e-15, Method: Compositional matrix adjust. Identities = 41/142 (28%), Positives = 80/142 (56%), Gaps = 8/142 (5%) Query: 11 QAVDGEEQLFIRQVSEQKKILYGIAYSYLRNEPDALEVLQEATYRAWSKRKSLKDTGRFA 70 +A+ G + F + + K LY IAY Y +NE DALE + E+ Y+A+ +L + F Sbjct: 9 RAIRGNKDAFTSLIKQCKNELYKIAYIYTKNEDDALEAIDESIYKAYISINTLNNPEFFK 68 Query: 71 PWMTRILVNCCKDELKRRKRLTPGHADNGSSSGSMEMTSDRKL-----DMEQALDGVKQR 125 W+ RIL+N C LK++ ++ +N ++ ++ D D+ +A++ + + Sbjct: 69 TWIIRILINECITLLKKKNKIV---LENNNTKFEIQCNDDYDSKFEFEDLYKAINTLNDK 125 Query: 126 YRQVLVLKYYRDMTLAEIAEVL 147 R ++LKY++D+ ++EI++V+ Sbjct: 126 QRTAIILKYFQDLKISEISDVM 147 Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF Posted date: Mar 24, 2004 1:53 AM Number of letters in database: 757,237,578 Number of sequences in database: 2,715,099 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: 2715099 Number of Hits to DB: 232,862,410 Number of extensions: 8503089 Number of successful extensions: 21012 Number of sequences better than 1.0e-05: 88 Number of HSP's gapped: 21091 Number of HSP's successfully gapped: 88 Length of query: 175 Length of database: 757,237,578 Length adjustment: 117 Effective length of query: 58 Effective length of database: 439,570,995 Effective search space: 25495117710 Effective search space used: 25495117710 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: 121 (51.2 bits)