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= 0007.0086.p (172 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312828|ref|YP_003776920.1| RNA polymerase sigma-70 factor,... 308 2e-85 gi|300312131|ref|YP_003776223.1| RNA polymerase sigma 24 factor ... 119 2e-28 gi|300311748|ref|YP_003775840.1| RNA polymerase sigma-70 factor,... 114 4e-27 gi|300309381|ref|YP_003773473.1| RNA polymerase sigma-70 factor ... 102 2e-23 gi|300313763|ref|YP_003777855.1| RNA polymerase sigma-70 factor,... 99 1e-22 >gi|300312828|ref|YP_003776920.1| RNA polymerase sigma-70 factor, ECF subfamily (sigma-24) transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 178 Score = 308 bits (788), Expect = 2e-85, Method: Compositional matrix adjust. Identities = 155/172 (90%), Positives = 161/172 (93%), Gaps = 1/172 (0%) Query: 1 MSDPLGAMNQIEAMFIEHHGWLRTRLRRSVGDAFAAEDVAAETFTQLLTSPP-QEVREPR 59 +SD AM++IEA+FIEHHGWLRTRLRRSVGDAF AEDVAAETFTQLL SPP QEVREPR Sbjct: 6 ISDHPPAMSRIEAIFIEHHGWLRTRLRRSVGDAFTAEDVAAETFTQLLHSPPPQEVREPR 65 Query: 60 ALLTTISRRIVYELWRRRDLEAACLQALAHANGEAQVISPEDQLQLLQALRAMDQALAGL 119 ALLTTISRRIVYELWRRRDLE ACLQALAH +G+ Q ISPEDQLQLLQALRAMDQALAGL Sbjct: 66 ALLTTISRRIVYELWRRRDLEEACLQALAHVSGDVQAISPEDQLQLLQALRAMDQALAGL 125 Query: 120 SAKECAAFLLYKLDGLTYQAIGEQLRITPSVARRYVAKGLLQCYKAAGFAPL 171 SAKECAAFLLYKLDGLTYQAIG QLRITPSVARRYVAKGLLQCYKAAGFAPL Sbjct: 126 SAKECAAFLLYKLDGLTYQAIGAQLRITPSVARRYVAKGLLQCYKAAGFAPL 177 >gi|300312131|ref|YP_003776223.1| RNA polymerase sigma 24 factor protein [Herbaspirillum seropedicae SmR1] Length = 173 Score = 119 bits (297), Expect = 2e-28, Method: Compositional matrix adjust. Identities = 71/152 (46%), Positives = 98/152 (64%), Gaps = 2/152 (1%) Query: 15 FIEHHGWLRTRLRRSVGDAFAAEDVAAETFTQLLTSPPQEV-REPRALLTTISRRIVYEL 73 F + WL+ LRR V AEDVA+ F ++ + P + REPRALLTTIS+R+V++L Sbjct: 22 FTNSYSWLKQYLRRQVKSLADAEDVASAAFVEMASLPDVSIIREPRALLTTISQRLVFDL 81 Query: 74 WRRRDLEAACLQALAHANGEAQVISPEDQLQLLQALRAMDQALAGLSAKECAAFLLYKLD 133 WRRRDLEAA L A EA SPE L+++Q L +D+ L GLS AFL +LD Sbjct: 82 WRRRDLEAAYLAA-LATTEEATTPSPEVVLEVVQTLVNIDRLLYGLSKNARQAFLYSQLD 140 Query: 134 GLTYQAIGEQLRITPSVARRYVAKGLLQCYKA 165 GLTY+ I E L ++ S+ R+Y+A+ L +CY++ Sbjct: 141 GLTYREIAELLGVSVSMVRKYIAQALAKCYES 172 >gi|300311748|ref|YP_003775840.1| RNA polymerase sigma-70 factor, ECF subfamily (sigma-24) transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 174 Score = 114 bits (286), Expect = 4e-27, Method: Compositional matrix adjust. Identities = 63/157 (40%), Positives = 95/157 (60%), Gaps = 3/157 (1%) Query: 9 NQIEAMFIEHHGWLRTRLRRSVGDAFAAEDVAAETFTQLLTSPP--QEVREPRALLTTIS 66 + ++ EHHGWL+ LRR VG +F A D+A +TF ++L P VREPRA L+ I+ Sbjct: 10 QRFHTLYSEHHGWLQQWLRRRVGSSFDAADLAQDTFLRVLGKPGALDGVREPRAWLSRIA 69 Query: 67 RRIVYELWRRRDLEAACLQALAHANGEAQVISPEDQLQLLQALRAMDQALAGLSAKECAA 126 +V + RR ++E CL+A+AH E +V+SPE +L L++AL +D L GL + A Sbjct: 70 HGLVVDKLRREEVERTCLEAIAHLP-EPEVVSPEARLILVEALCMIDALLEGLGERARQA 128 Query: 127 FLLYKLDGLTYQAIGEQLRITPSVARRYVAKGLLQCY 163 FLL +LD ++Y I L ++ S +Y+A + CY Sbjct: 129 FLLSRLDEMSYPEIARHLGVSLSSVEKYMAAAIRHCY 165 >gi|300309381|ref|YP_003773473.1| RNA polymerase sigma-70 factor protein [Herbaspirillum seropedicae SmR1] Length = 181 Score = 102 bits (253), Expect = 2e-23, Method: Compositional matrix adjust. Identities = 69/157 (43%), Positives = 98/157 (62%), Gaps = 3/157 (1%) Query: 11 IEAMFIEHHGWLRTRLRRSVGDAFAAEDVAAETFTQLLTSP--PQEVREPRALLTTISRR 68 IEA++ +HH WL+ L+R +G++ A D+A +TF +LL S P + EPRA LTT+++R Sbjct: 20 IEALYCDHHSWLKGWLQRRLGNSEQAADLAQDTFLRLLGSERVPSVIHEPRAYLTTVAQR 79 Query: 69 IVYELWRRRDLEAACLQALAHANGEAQVISPEDQLQLLQALRAMDQALAGLSAKECAAFL 128 +V LWRR LE A L+ALA A A SP++Q LL+ L +DQ L L + AFL Sbjct: 80 LVSNLWRREKLEQAYLEALAQAP-VALAPSPQEQAILLETLLELDQLLDELPSIVRRAFL 138 Query: 129 LYKLDGLTYQAIGEQLRITPSVARRYVAKGLLQCYKA 165 L +LDGLT+ + L I+ +RY+ K L +CY A Sbjct: 139 LSQLDGLTHAQVAAALGISIPTVKRYLVKALQRCYFA 175 >gi|300313763|ref|YP_003777855.1| RNA polymerase sigma-70 factor, ECF subfamily (sigma-24) transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 169 Score = 99.4 bits (246), Expect = 1e-22, Method: Compositional matrix adjust. Identities = 66/166 (39%), Positives = 92/166 (55%), Gaps = 2/166 (1%) Query: 1 MSDPLGAMNQIEAMFIEHHGWLRTRLRRSVGDAFAAEDVAAETFTQLLTS-PPQEVREPR 59 + P A +I ++ EHHGWL L R + D+A +TF +LL PP ++REPR Sbjct: 4 LMSPAEAHQEIGGLYREHHGWLVAWLSRRLACRHLGADLAQDTFVRLLGHRPPPDLREPR 63 Query: 60 ALLTTISRRIVYELWRRRDLEAACLQALAHANGEAQVISPEDQLQLLQALRAMDQALAGL 119 A LTTI++ +V RRR LE A L+ALA A E S E++L +L L +D+ L L Sbjct: 64 AYLTTIAKGLVASHLRRRQLETAYLEALA-ALPEPSQPSAEERLLVLDTLCEIDRILDQL 122 Query: 120 SAKECAAFLLYKLDGLTYQAIGEQLRITPSVARRYVAKGLLQCYKA 165 A+ FLL +LDGL Y +I L I+ S +R++ L C A Sbjct: 123 PARARQVFLLAQLDGLPYASIAGLLGISLSTVKRHMVLALRHCLAA 168 Database: BlastDatabases/689/689 Posted date: Apr 10, 2011 12:15 AM Number of letters in database: 1,619,870 Number of sequences in database: 4735 Lambda K H 0.322 0.134 0.391 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 4735 Number of Hits to DB: 522,711 Number of extensions: 19068 Number of successful extensions: 125 Number of sequences better than 1.0e-08: 7 Number of HSP's gapped: 113 Number of HSP's successfully gapped: 7 Length of query: 172 Length of database: 1,619,870 Length adjustment: 79 Effective length of query: 93 Effective length of database: 1,245,805 Effective search space: 115859865 Effective search space used: 115859865 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 (22.0 bits) S2: 127 (53.5 bits)