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= 0022.0170.p (165 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313763|ref|YP_003777855.1| RNA polymerase sigma-70 factor,... 325 2e-90 gi|300311748|ref|YP_003775840.1| RNA polymerase sigma-70 factor,... 151 3e-38 gi|300309381|ref|YP_003773473.1| RNA polymerase sigma-70 factor ... 136 8e-34 gi|300312828|ref|YP_003776920.1| RNA polymerase sigma-70 factor,... 99 1e-22 gi|300312131|ref|YP_003776223.1| RNA polymerase sigma 24 factor ... 96 1e-21 >gi|300313763|ref|YP_003777855.1| RNA polymerase sigma-70 factor, ECF subfamily (sigma-24) transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 169 Score = 325 bits (832), Expect = 2e-90, Method: Compositional matrix adjust. Identities = 165/165 (100%), Positives = 165/165 (100%) Query: 1 MSPAEAHQEIGGLYREHHGWLVAWLSRRLACRHLGADLAQDTFVRLLGHRPPPDLREPRA 60 MSPAEAHQEIGGLYREHHGWLVAWLSRRLACRHLGADLAQDTFVRLLGHRPPPDLREPRA Sbjct: 5 MSPAEAHQEIGGLYREHHGWLVAWLSRRLACRHLGADLAQDTFVRLLGHRPPPDLREPRA 64 Query: 61 YLTTIAKGLVASHLRRRQLETAYLEALAALPEPSQPSAEERLLVLDTLCEIDRILDQLPA 120 YLTTIAKGLVASHLRRRQLETAYLEALAALPEPSQPSAEERLLVLDTLCEIDRILDQLPA Sbjct: 65 YLTTIAKGLVASHLRRRQLETAYLEALAALPEPSQPSAEERLLVLDTLCEIDRILDQLPA 124 Query: 121 RARQVFLLAQLDGLPYASIAGLLGISLSTVKRHMVLALRHCLAAL 165 RARQVFLLAQLDGLPYASIAGLLGISLSTVKRHMVLALRHCLAAL Sbjct: 125 RARQVFLLAQLDGLPYASIAGLLGISLSTVKRHMVLALRHCLAAL 169 >gi|300311748|ref|YP_003775840.1| RNA polymerase sigma-70 factor, ECF subfamily (sigma-24) transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 174 Score = 151 bits (381), Expect = 3e-38, Method: Compositional matrix adjust. Identities = 81/155 (52%), Positives = 105/155 (67%), Gaps = 1/155 (0%) Query: 8 QEIGGLYREHHGWLVAWLSRRLACRHLGADLAQDTFVRLLGHRPPPD-LREPRAYLTTIA 66 Q LY EHHGWL WL RR+ ADLAQDTF+R+LG D +REPRA+L+ IA Sbjct: 10 QRFHTLYSEHHGWLQQWLRRRVGSSFDAADLAQDTFLRVLGKPGALDGVREPRAWLSRIA 69 Query: 67 KGLVASHLRRRQLETAYLEALAALPEPSQPSAEERLLVLDTLCEIDRILDQLPARARQVF 126 GLV LRR ++E LEA+A LPEP S E RL++++ LC ID +L+ L RARQ F Sbjct: 70 HGLVVDKLRREEVERTCLEAIAHLPEPEVVSPEARLILVEALCMIDALLEGLGERARQAF 129 Query: 127 LLAQLDGLPYASIAGLLGISLSTVKRHMVLALRHC 161 LL++LD + Y IA LG+SLS+V+++M A+RHC Sbjct: 130 LLSRLDEMSYPEIARHLGVSLSSVEKYMAAAIRHC 164 >gi|300309381|ref|YP_003773473.1| RNA polymerase sigma-70 factor protein [Herbaspirillum seropedicae SmR1] Length = 181 Score = 136 bits (343), Expect = 8e-34, Method: Compositional matrix adjust. Identities = 85/157 (54%), Positives = 111/157 (70%), Gaps = 1/157 (0%) Query: 9 EIGGLYREHHGWLVAWLSRRLACRHLGADLAQDTFVRLLG-HRPPPDLREPRAYLTTIAK 67 I LY +HH WL WL RRL ADLAQDTF+RLLG R P + EPRAYLTT+A+ Sbjct: 19 SIEALYCDHHSWLKGWLQRRLGNSEQAADLAQDTFLRLLGSERVPSVIHEPRAYLTTVAQ 78 Query: 68 GLVASHLRRRQLETAYLEALAALPEPSQPSAEERLLVLDTLCEIDRILDQLPARARQVFL 127 LV++ RR +LE AYLEALA P PS +E+ ++L+TL E+D++LD+LP+ R+ FL Sbjct: 79 RLVSNLWRREKLEQAYLEALAQAPVALAPSPQEQAILLETLLELDQLLDELPSIVRRAFL 138 Query: 128 LAQLDGLPYASIAGLLGISLSTVKRHMVLALRHCLAA 164 L+QLDGL +A +A LGIS+ TVKR++V AL+ C A Sbjct: 139 LSQLDGLTHAQVAAALGISIPTVKRYLVKALQRCYFA 175 >gi|300312828|ref|YP_003776920.1| RNA polymerase sigma-70 factor, ECF subfamily (sigma-24) transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 178 Score = 99.4 bits (246), Expect = 1e-22, Method: Compositional matrix adjust. Identities = 64/160 (40%), Positives = 89/160 (55%), Gaps = 1/160 (0%) Query: 6 AHQEIGGLYREHHGWLVAWLSRRLACRHLGADLAQDTFVRLLGHRPPPDLREPRAYLTTI 65 A I ++ EHHGWL L R + D+A +TF +LL PP ++REPRA LTTI Sbjct: 12 AMSRIEAIFIEHHGWLRTRLRRSVGDAFTAEDVAAETFTQLLHSPPPQEVREPRALLTTI 71 Query: 66 AKGLVASHLRRRQLETAYLEALAALPEPSQP-SAEERLLVLDTLCEIDRILDQLPARARQ 124 ++ +V RRR LE A L+ALA + Q S E++L +L L +D+ L L A+ Sbjct: 72 SRRIVYELWRRRDLEEACLQALAHVSGDVQAISPEDQLQLLQALRAMDQALAGLSAKECA 131 Query: 125 VFLLAQLDGLPYASIAGLLGISLSTVKRHMVLALRHCLAA 164 FLL +LDGL Y +I L I+ S +R++ L C A Sbjct: 132 AFLLYKLDGLTYQAIGAQLRITPSVARRYVAKGLLQCYKA 171 >gi|300312131|ref|YP_003776223.1| RNA polymerase sigma 24 factor protein [Herbaspirillum seropedicae SmR1] Length = 173 Score = 96.3 bits (238), Expect = 1e-21, Method: Compositional matrix adjust. Identities = 66/155 (42%), Positives = 87/155 (56%) Query: 7 HQEIGGLYREHHGWLVAWLSRRLACRHLGADLAQDTFVRLLGHRPPPDLREPRAYLTTIA 66 H + + + WL +L R++ D+A FV + +REPRA LTTI+ Sbjct: 15 HDFLVTEFTNSYSWLKQYLRRQVKSLADAEDVASAAFVEMASLPDVSIIREPRALLTTIS 74 Query: 67 KGLVASHLRRRQLETAYLEALAALPEPSQPSAEERLLVLDTLCEIDRILDQLPARARQVF 126 + LV RRR LE AYL ALA E + PS E L V+ TL IDR+L L ARQ F Sbjct: 75 QRLVFDLWRRRDLEAAYLAALATTEEATTPSPEVVLEVVQTLVNIDRLLYGLSKNARQAF 134 Query: 127 LLAQLDGLPYASIAGLLGISLSTVKRHMVLALRHC 161 L +QLDGL Y IA LLG+S+S V++++ AL C Sbjct: 135 LYSQLDGLTYREIAELLGVSVSMVRKYIAQALAKC 169 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 0.325 0.138 0.418 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: 499,655 Number of extensions: 17774 Number of successful extensions: 89 Number of sequences better than 1.0e-08: 7 Number of HSP's gapped: 84 Number of HSP's successfully gapped: 7 Length of query: 165 Length of database: 1,619,870 Length adjustment: 78 Effective length of query: 87 Effective length of database: 1,250,540 Effective search space: 108796980 Effective search space used: 108796980 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 127 (53.5 bits)