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= 0002.0589.p (159 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,... 145 2e-36 gi|300311748|ref|YP_003775840.1| RNA polymerase sigma-70 factor,... 139 1e-34 gi|300309381|ref|YP_003773473.1| RNA polymerase sigma-70 factor ... 130 4e-32 gi|300312828|ref|YP_003776920.1| RNA polymerase sigma-70 factor,... 97 7e-22 gi|300313796|ref|YP_003777888.1| RNA polymerase sigma-70 factor,... 94 7e-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 = 145 bits (365), Expect = 2e-36, Method: Compositional matrix adjust. Identities = 81/152 (53%), Positives = 98/152 (64%) Query: 1 MAGLYTGHHHWLLGWLRRRTGNPELAADLAQDTFLRIMVSRRDFYLDEARALLATIARGL 60 + GLY HH WL+ WL RR L ADLAQDTF+R++ R L E RA L TIA+GL Sbjct: 14 IGGLYREHHGWLVAWLSRRLACRHLGADLAQDTFVRLLGHRPPPDLREPRAYLTTIAKGL 73 Query: 61 VIDHFRRCALEAAFLEMLAQLPPEHVPSPEARLAVLETLNQIDAMLAALPAKVRSAFLLS 120 V H RR LE A+LE LA LP PS E RL VL+TL +ID +L LPA+ R FLL+ Sbjct: 74 VASHLRRRQLETAYLEALAALPEPSQPSAEERLLVLDTLCEIDRILDQLPARARQVFLLA 133 Query: 121 QLDGLSYAEIAVRLEVSLSSVQQYMKRAFMAC 152 QLDGL YA IA L +SLS+V+++M A C Sbjct: 134 QLDGLPYASIAGLLGISLSTVKRHMVLALRHC 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 = 139 bits (350), Expect = 1e-34, Method: Compositional matrix adjust. Identities = 82/153 (53%), Positives = 99/153 (64%), Gaps = 5/153 (3%) Query: 4 LYTGHHHWLLGWLRRRTGNPELAADLAQDTFLRIMVSRRDFYLD---EARALLATIARGL 60 LY+ HH WL WLRRR G+ AADLAQDTFLR++ + LD E RA L+ IA GL Sbjct: 15 LYSEHHGWLQQWLRRRVGSSFDAADLAQDTFLRVL--GKPGALDGVREPRAWLSRIAHGL 72 Query: 61 VIDHFRRCALEAAFLEMLAQLPPEHVPSPEARLAVLETLNQIDAMLAALPAKVRSAFLLS 120 V+D RR +E LE +A LP V SPEARL ++E L IDA+L L + R AFLLS Sbjct: 73 VVDKLRREEVERTCLEAIAHLPEPEVVSPEARLILVEALCMIDALLEGLGERARQAFLLS 132 Query: 121 QLDGLSYAEIAVRLEVSLSSVQQYMKRAFMACY 153 +LD +SY EIA L VSLSSV++YM A CY Sbjct: 133 RLDEMSYPEIARHLGVSLSSVEKYMAAAIRHCY 165 >gi|300309381|ref|YP_003773473.1| RNA polymerase sigma-70 factor protein [Herbaspirillum seropedicae SmR1] Length = 181 Score = 130 bits (328), Expect = 4e-32, Method: Compositional matrix adjust. Identities = 78/154 (50%), Positives = 106/154 (68%), Gaps = 1/154 (0%) Query: 1 MAGLYTGHHHWLLGWLRRRTGNPELAADLAQDTFLRIMVSRR-DFYLDEARALLATIARG 59 + LY HH WL GWL+RR GN E AADLAQDTFLR++ S R + E RA L T+A+ Sbjct: 20 IEALYCDHHSWLKGWLQRRLGNSEQAADLAQDTFLRLLGSERVPSVIHEPRAYLTTVAQR 79 Query: 60 LVIDHFRRCALEAAFLEMLAQLPPEHVPSPEARLAVLETLNQIDAMLAALPAKVRSAFLL 119 LV + +RR LE A+LE LAQ P PSP+ + +LETL ++D +L LP+ VR AFLL Sbjct: 80 LVSNLWRREKLEQAYLEALAQAPVALAPSPQEQAILLETLLELDQLLDELPSIVRRAFLL 139 Query: 120 SQLDGLSYAEIAVRLEVSLSSVQQYMKRAFMACY 153 SQLDGL++A++A L +S+ +V++Y+ +A CY Sbjct: 140 SQLDGLTHAQVAAALGISIPTVKRYLVKALQRCY 173 >gi|300312828|ref|YP_003776920.1| RNA polymerase sigma-70 factor, ECF subfamily (sigma-24) transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 178 Score = 97.1 bits (240), Expect = 7e-22, Method: Compositional matrix adjust. Identities = 58/155 (37%), Positives = 91/155 (58%), Gaps = 1/155 (0%) Query: 1 MAGLYTGHHHWLLGWLRRRTGNPELAADLAQDTFLRIMVSRRDFYLDEARALLATIARGL 60 + ++ HH WL LRR G+ A D+A +TF +++ S + E RALL TI+R + Sbjct: 16 IEAIFIEHHGWLRTRLRRSVGDAFTAEDVAAETFTQLLHSPPPQEVREPRALLTTISRRI 75 Query: 61 VIDHFRRCALEAAFLEMLAQLPPE-HVPSPEARLAVLETLNQIDAMLAALPAKVRSAFLL 119 V + +RR LE A L+ LA + + SPE +L +L+ L +D LA L AK +AFLL Sbjct: 76 VYELWRRRDLEEACLQALAHVSGDVQAISPEDQLQLLQALRAMDQALAGLSAKECAAFLL 135 Query: 120 SQLDGLSYAEIAVRLEVSLSSVQQYMKRAFMACYR 154 +LDGL+Y I +L ++ S ++Y+ + + CY+ Sbjct: 136 YKLDGLTYQAIGAQLRITPSVARRYVAKGLLQCYK 170 >gi|300313796|ref|YP_003777888.1| RNA polymerase sigma-70 factor, ECF subfamily (sigma-24) transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 178 Score = 93.6 bits (231), Expect = 7e-21, Method: Compositional matrix adjust. Identities = 63/157 (40%), Positives = 86/157 (54%), Gaps = 6/157 (3%) Query: 4 LYTGHHHWLLGWLRRRTGNPELAADLAQDTFLRIMVSRRDFY-LDEARALLATIARGLVI 62 LY HH WL WLRR+ G E AADLA DTFLR++ +R L E RA L T AR L+I Sbjct: 15 LYRDHHGWLRAWLRRKLGCTEQAADLAHDTFLRLLATRDVLSALKEPRAYLVTAARHLLI 74 Query: 63 DHFRRCALEAAFLEMLAQ---LPPE--HVPSPEARLAVLETLNQIDAMLAALPAKVRSAF 117 D RR + A+L+ L + PE H PS E L ++ + + L A A+ AF Sbjct: 75 DRSRRQQIRQAYLDQLERQFGACPELMHAPSAETILQAVQAIEALGRALQAARAEAAEAF 134 Query: 118 LLSQLDGLSYAEIAVRLEVSLSSVQQYMKRAFMACYR 154 +L + G E+A VSL +VQ ++ +A + C+R Sbjct: 135 ILHYVQGRRQEELASHFNVSLRTVQGWLAQALIQCHR 171 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 0.327 0.137 0.407 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: 473,773 Number of extensions: 16959 Number of successful extensions: 122 Number of sequences better than 1.0e-08: 7 Number of HSP's gapped: 116 Number of HSP's successfully gapped: 7 Length of query: 159 Length of database: 1,619,870 Length adjustment: 78 Effective length of query: 81 Effective length of database: 1,250,540 Effective search space: 101293740 Effective search space used: 101293740 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 127 (53.5 bits)