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= 0001.2247.p (173 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312131|ref|YP_003776223.1| RNA polymerase sigma 24 factor ... 320 5e-89 gi|300312828|ref|YP_003776920.1| RNA polymerase sigma-70 factor,... 129 1e-31 gi|300311748|ref|YP_003775840.1| RNA polymerase sigma-70 factor,... 126 1e-30 gi|300309381|ref|YP_003773473.1| RNA polymerase sigma-70 factor ... 115 1e-27 gi|300313763|ref|YP_003777855.1| RNA polymerase sigma-70 factor,... 113 7e-27 >gi|300312131|ref|YP_003776223.1| RNA polymerase sigma 24 factor protein [Herbaspirillum seropedicae SmR1] Length = 173 Score = 320 bits (819), Expect = 5e-89, Method: Compositional matrix adjust. Identities = 166/171 (97%), Positives = 168/171 (98%) Query: 3 GPLHSYTDQPFRHDFLVTEFTNSYSWLKQYLRRQVKSLADAEDVASAAFLEMAGIPDVSI 62 GPLHSY DQPFRHDFLVTEFTNSYSWLKQYLRRQVKSLADAEDVASAAF+EMA +PDVSI Sbjct: 3 GPLHSYADQPFRHDFLVTEFTNSYSWLKQYLRRQVKSLADAEDVASAAFVEMASLPDVSI 62 Query: 63 IREPRALLTTISQRLVFDLWRRRDLEAAYLAALATTEEANTPSPEVVLEVVQTLVNIDRL 122 IREPRALLTTISQRLVFDLWRRRDLEAAYLAALATTEEA TPSPEVVLEVVQTLVNIDRL Sbjct: 63 IREPRALLTTISQRLVFDLWRRRDLEAAYLAALATTEEATTPSPEVVLEVVQTLVNIDRL 122 Query: 123 LYGLSKNARQAFLYSQLDGLTYREIAELLGVSVSMVRKYIAQALAKCYESN 173 LYGLSKNARQAFLYSQLDGLTYREIAELLGVSVSMVRKYIAQALAKCYESN Sbjct: 123 LYGLSKNARQAFLYSQLDGLTYREIAELLGVSVSMVRKYIAQALAKCYESN 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 = 129 bits (325), Expect = 1e-31, Method: Compositional matrix adjust. Identities = 71/165 (43%), Positives = 101/165 (61%), Gaps = 1/165 (0%) Query: 9 TDQPFRHDFLVTEFTNSYSWLKQYLRRQVKSLADAEDVASAAFLEMAGIPDVSIIREPRA 68 +D P + F + WL+ LRR V AEDVA+ F ++ P +REPRA Sbjct: 7 SDHPPAMSRIEAIFIEHHGWLRTRLRRSVGDAFTAEDVAAETFTQLLHSPPPQEVREPRA 66 Query: 69 LLTTISQRLVFDLWRRRDLEAAYLAALA-TTEEANTPSPEVVLEVVQTLVNIDRLLYGLS 127 LLTTIS+R+V++LWRRRDLE A L ALA + + SPE L+++Q L +D+ L GLS Sbjct: 67 LLTTISRRIVYELWRRRDLEEACLQALAHVSGDVQAISPEDQLQLLQALRAMDQALAGLS 126 Query: 128 KNARQAFLYSQLDGLTYREIAELLGVSVSMVRKYIAQALAKCYES 172 AFL +LDGLTY+ I L ++ S+ R+Y+A+ L +CY++ Sbjct: 127 AKECAAFLLYKLDGLTYQAIGAQLRITPSVARRYVAKGLLQCYKA 171 >gi|300311748|ref|YP_003775840.1| RNA polymerase sigma-70 factor, ECF subfamily (sigma-24) transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 174 Score = 126 bits (317), Expect = 1e-30, Method: Compositional matrix adjust. Identities = 71/152 (46%), Positives = 95/152 (62%), Gaps = 1/152 (0%) Query: 20 TEFTNSYSWLKQYLRRQVKSLADAEDVASAAFLEMAGIPD-VSIIREPRALLTTISQRLV 78 T ++ + WL+Q+LRR+V S DA D+A FL + G P + +REPRA L+ I+ LV Sbjct: 14 TLYSEHHGWLQQWLRRRVGSSFDAADLAQDTFLRVLGKPGALDGVREPRAWLSRIAHGLV 73 Query: 79 FDLWRRRDLEAAYLAALATTEEANTPSPEVVLEVVQTLVNIDRLLYGLSKNARQAFLYSQ 138 D RR ++E L A+A E SPE L +V+ L ID LL GL + ARQAFL S+ Sbjct: 74 VDKLRREEVERTCLEAIAHLPEPEVVSPEARLILVEALCMIDALLEGLGERARQAFLLSR 133 Query: 139 LDGLTYREIAELLGVSVSMVRKYIAQALAKCY 170 LD ++Y EIA LGVS+S V KY+A A+ CY Sbjct: 134 LDEMSYPEIARHLGVSLSSVEKYMAAAIRHCY 165 >gi|300309381|ref|YP_003773473.1| RNA polymerase sigma-70 factor protein [Herbaspirillum seropedicae SmR1] Length = 181 Score = 115 bits (289), Expect = 1e-27, Method: Compositional matrix adjust. Identities = 69/150 (46%), Positives = 101/150 (67%), Gaps = 1/150 (0%) Query: 22 FTNSYSWLKQYLRRQVKSLADAEDVASAAFLEMAGIPDV-SIIREPRALLTTISQRLVFD 80 + + +SWLK +L+R++ + A D+A FL + G V S+I EPRA LTT++QRLV + Sbjct: 24 YCDHHSWLKGWLQRRLGNSEQAADLAQDTFLRLLGSERVPSVIHEPRAYLTTVAQRLVSN 83 Query: 81 LWRRRDLEAAYLAALATTEEANTPSPEVVLEVVQTLVNIDRLLYGLSKNARQAFLYSQLD 140 LWRR LE AYL ALA A PSP+ +++TL+ +D+LL L R+AFL SQLD Sbjct: 84 LWRREKLEQAYLEALAQAPVALAPSPQEQAILLETLLELDQLLDELPSIVRRAFLLSQLD 143 Query: 141 GLTYREIAELLGVSVSMVRKYIAQALAKCY 170 GLT+ ++A LG+S+ V++Y+ +AL +CY Sbjct: 144 GLTHAQVAAALGISIPTVKRYLVKALQRCY 173 >gi|300313763|ref|YP_003777855.1| RNA polymerase sigma-70 factor, ECF subfamily (sigma-24) transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 169 Score = 113 bits (283), Expect = 7e-27, Method: Compositional matrix adjust. Identities = 65/148 (43%), Positives = 86/148 (58%) Query: 22 FTNSYSWLKQYLRRQVKSLADAEDVASAAFLEMAGIPDVSIIREPRALLTTISQRLVFDL 81 + + WL +L R++ D+A F+ + G +REPRA LTTI++ LV Sbjct: 18 YREHHGWLVAWLSRRLACRHLGADLAQDTFVRLLGHRPPPDLREPRAYLTTIAKGLVASH 77 Query: 82 WRRRDLEAAYLAALATTEEANTPSPEVVLEVVQTLVNIDRLLYGLSKNARQAFLYSQLDG 141 RRR LE AYL ALA E + PS E L V+ TL IDR+L L ARQ FL +QLDG Sbjct: 78 LRRRQLETAYLEALAALPEPSQPSAEERLLVLDTLCEIDRILDQLPARARQVFLLAQLDG 137 Query: 142 LTYREIAELLGVSVSMVRKYIAQALAKC 169 L Y IA LLG+S+S V++++ AL C Sbjct: 138 LPYASIAGLLGISLSTVKRHMVLALRHC 165 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 0.321 0.134 0.377 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: 425,708 Number of extensions: 12825 Number of successful extensions: 80 Number of sequences better than 1.0e-08: 7 Number of HSP's gapped: 74 Number of HSP's successfully gapped: 7 Length of query: 173 Length of database: 1,619,870 Length adjustment: 79 Effective length of query: 94 Effective length of database: 1,245,805 Effective search space: 117105670 Effective search space used: 117105670 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 (21.9 bits) S2: 127 (53.5 bits)