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= 0082.0007.p (125 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,... 102 6e-24 gi|300311748|ref|YP_003775840.1| RNA polymerase sigma-70 factor,... 99 7e-23 gi|300309381|ref|YP_003773473.1| RNA polymerase sigma-70 factor ... 80 6e-17 gi|300312131|ref|YP_003776223.1| RNA polymerase sigma 24 factor ... 80 7e-17 gi|300312828|ref|YP_003776920.1| RNA polymerase sigma-70 factor,... 71 3e-14 >gi|300313763|ref|YP_003777855.1| RNA polymerase sigma-70 factor, ECF subfamily (sigma-24) transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 169 Score = 102 bits (255), Expect = 6e-24, Method: Compositional matrix adjust. Identities = 58/107 (54%), Positives = 71/107 (66%) Query: 12 LDEARALLATIARGLVIDHFRRCALEAAFLEMLAQLPPEHVPSPEARLAVLETLNQVDAM 71 L E RA L TIA+GLV H RR LE A+LE LA LP PS E RL VL+TL ++D + Sbjct: 59 LREPRAYLTTIAKGLVASHLRRRQLETAYLEALAALPEPSQPSAEERLLVLDTLCEIDRI 118 Query: 72 LAALPAKVRSAFLLSQLDGLGYAEIAVRLDVSLSSVQQYMKRAFTAC 118 L LPA+ R FLL+QLDGL YA IA L +SLS+V+++M A C Sbjct: 119 LDQLPARARQVFLLAQLDGLPYASIAGLLGISLSTVKRHMVLALRHC 165 >gi|300311748|ref|YP_003775840.1| RNA polymerase sigma-70 factor, ECF subfamily (sigma-24) transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 174 Score = 99.4 bits (246), Expect = 7e-23, Method: Compositional matrix adjust. Identities = 55/106 (51%), Positives = 68/106 (64%) Query: 14 EARALLATIARGLVIDHFRRCALEAAFLEMLAQLPPEHVPSPEARLAVLETLNQVDAMLA 73 E RA L+ IA GLV+D RR +E LE +A LP V SPEARL ++E L +DA+L Sbjct: 60 EPRAWLSRIAHGLVVDKLRREEVERTCLEAIAHLPEPEVVSPEARLILVEALCMIDALLE 119 Query: 74 ALPAKVRSAFLLSQLDGLGYAEIAVRLDVSLSSVQQYMKRAFTACY 119 L + R AFLLS+LD + Y EIA L VSLSSV++YM A CY Sbjct: 120 GLGERARQAFLLSRLDEMSYPEIARHLGVSLSSVEKYMAAAIRHCY 165 >gi|300309381|ref|YP_003773473.1| RNA polymerase sigma-70 factor protein [Herbaspirillum seropedicae SmR1] Length = 181 Score = 79.7 bits (195), Expect = 6e-17, Method: Compositional matrix adjust. Identities = 51/108 (47%), Positives = 74/108 (68%) Query: 12 LDEARALLATIARGLVIDHFRRCALEAAFLEMLAQLPPEHVPSPEARLAVLETLNQVDAM 71 + E RA L T+A+ LV + +RR LE A+LE LAQ P PSP+ + +LETL ++D + Sbjct: 66 IHEPRAYLTTVAQRLVSNLWRREKLEQAYLEALAQAPVALAPSPQEQAILLETLLELDQL 125 Query: 72 LAALPAKVRSAFLLSQLDGLGYAEIAVRLDVSLSSVQQYMKRAFTACY 119 L LP+ VR AFLLSQLDGL +A++A L +S+ +V++Y+ +A CY Sbjct: 126 LDELPSIVRRAFLLSQLDGLTHAQVAAALGISIPTVKRYLVKALQRCY 173 >gi|300312131|ref|YP_003776223.1| RNA polymerase sigma 24 factor protein [Herbaspirillum seropedicae SmR1] Length = 173 Score = 79.7 bits (195), Expect = 7e-17, Method: Compositional matrix adjust. Identities = 53/106 (50%), Positives = 66/106 (62%) Query: 14 EARALLATIARGLVIDHFRRCALEAAFLEMLAQLPPEHVPSPEARLAVLETLNQVDAMLA 73 E RALL TI++ LV D +RR LEAA+L LA PSPE L V++TL +D +L Sbjct: 65 EPRALLTTISQRLVFDLWRRRDLEAAYLAALATTEEATTPSPEVVLEVVQTLVNIDRLLY 124 Query: 74 ALPAKVRSAFLLSQLDGLGYAEIAVRLDVSLSSVQQYMKRAFTACY 119 L R AFL SQLDGL Y EIA L VS+S V++Y+ +A CY Sbjct: 125 GLSKNARQAFLYSQLDGLTYREIAELLGVSVSMVRKYIAQALAKCY 170 >gi|300312828|ref|YP_003776920.1| RNA polymerase sigma-70 factor, ECF subfamily (sigma-24) transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 178 Score = 70.9 bits (172), Expect = 3e-14, Method: Compositional matrix adjust. Identities = 44/108 (40%), Positives = 65/108 (60%), Gaps = 1/108 (0%) Query: 14 EARALLATIARGLVIDHFRRCALEAAFLEMLAQLPPE-HVPSPEARLAVLETLNQVDAML 72 E RALL TI+R +V + +RR LE A L+ LA + + SPE +L +L+ L +D L Sbjct: 63 EPRALLTTISRRIVYELWRRRDLEEACLQALAHVSGDVQAISPEDQLQLLQALRAMDQAL 122 Query: 73 AALPAKVRSAFLLSQLDGLGYAEIAVRLDVSLSSVQQYMKRAFTACYR 120 A L AK +AFLL +LDGL Y I +L ++ S ++Y+ + CY+ Sbjct: 123 AGLSAKECAAFLLYKLDGLTYQAIGAQLRITPSVARRYVAKGLLQCYK 170 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 0.135 0.385 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: 348,938 Number of extensions: 11694 Number of successful extensions: 88 Number of sequences better than 1.0e-08: 7 Number of HSP's gapped: 87 Number of HSP's successfully gapped: 7 Length of query: 125 Length of database: 1,619,870 Length adjustment: 75 Effective length of query: 50 Effective length of database: 1,264,745 Effective search space: 63237250 Effective search space used: 63237250 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: 125 (52.8 bits)