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= 0022.0209.p (178 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313796|ref|YP_003777888.1| RNA polymerase sigma-70 factor,... 351 2e-98 gi|300309381|ref|YP_003773473.1| RNA polymerase sigma-70 factor ... 105 1e-24 gi|300311748|ref|YP_003775840.1| RNA polymerase sigma-70 factor,... 105 3e-24 gi|300313763|ref|YP_003777855.1| RNA polymerase sigma-70 factor,... 101 4e-23 gi|300312828|ref|YP_003776920.1| RNA polymerase sigma-70 factor,... 84 8e-18 >gi|300313796|ref|YP_003777888.1| RNA polymerase sigma-70 factor, ECF subfamily (sigma-24) transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 178 Score = 351 bits (901), Expect = 2e-98, Method: Compositional matrix adjust. Identities = 176/178 (98%), Positives = 176/178 (98%) Query: 1 MPAMEELHVDPLETLYRDHHGWLRAWLRRKLGCTEQAADLAHDTFLRLLATRDVLSALKE 60 MPAMEELHVDPLETLYRDHHGWLRAWLRRKLGCTEQAADLAHDTFLRLLATRDVLSALKE Sbjct: 1 MPAMEELHVDPLETLYRDHHGWLRAWLRRKLGCTEQAADLAHDTFLRLLATRDVLSALKE 60 Query: 61 PRAYLVTAARHLLIDRSRRQQIRQAYLDQLERQFGACPELMHAPSAETILQAVQAIEALG 120 PRAYLVTAARHLLIDRSRRQQIRQAYLDQLERQFGACPELMHAPSAETILQAVQAIEALG Sbjct: 61 PRAYLVTAARHLLIDRSRRQQIRQAYLDQLERQFGACPELMHAPSAETILQAVQAIEALG 120 Query: 121 RALQAVRAEAAEAFILHYVQGRRQEELASQFNVSLRTVQGWLAQALIQCHRHLAAPGA 178 RALQA RAEAAEAFILHYVQGRRQEELAS FNVSLRTVQGWLAQALIQCHRHLAAPGA Sbjct: 121 RALQAARAEAAEAFILHYVQGRRQEELASHFNVSLRTVQGWLAQALIQCHRHLAAPGA 178 >gi|300309381|ref|YP_003773473.1| RNA polymerase sigma-70 factor protein [Herbaspirillum seropedicae SmR1] Length = 181 Score = 105 bits (263), Expect = 1e-24, Method: Compositional matrix adjust. Identities = 63/159 (39%), Positives = 97/159 (61%), Gaps = 5/159 (3%) Query: 12 LETLYRDHHGWLRAWLRRKLGCTEQAADLAHDTFLRLLATRDVLSALKEPRAYLVTAARH 71 +E LY DHH WL+ WL+R+LG +EQAADLA DTFLRLL + V S + EPRAYL T A+ Sbjct: 20 IEALYCDHHSWLKGWLQRRLGNSEQAADLAQDTFLRLLGSERVPSVIHEPRAYLTTVAQR 79 Query: 72 LLIDRSRRQQIRQAYLDQLERQFGACPELMHAPSAETILQAVQAIEALGRALQAVRAEAA 131 L+ + RR+++ QAYL+ L + A APS + ++ + L + L + + Sbjct: 80 LVSNLWRREKLEQAYLEALAQAPVAL-----APSPQEQAILLETLLELDQLLDELPSIVR 134 Query: 132 EAFILHYVQGRRQEELASQFNVSLRTVQGWLAQALIQCH 170 AF+L + G ++A+ +S+ TV+ +L +AL +C+ Sbjct: 135 RAFLLSQLDGLTHAQVAAALGISIPTVKRYLVKALQRCY 173 >gi|300311748|ref|YP_003775840.1| RNA polymerase sigma-70 factor, ECF subfamily (sigma-24) transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 174 Score = 105 bits (261), Expect = 3e-24, Method: Compositional matrix adjust. Identities = 61/170 (35%), Positives = 98/170 (57%), Gaps = 5/170 (2%) Query: 1 MPAMEELHVDPLETLYRDHHGWLRAWLRRKLGCTEQAADLAHDTFLRLLATRDVLSALKE 60 MP +H TLY +HHGWL+ WLRR++G + AADLA DTFLR+L L ++E Sbjct: 1 MPVPHTVHAQRFHTLYSEHHGWLQQWLRRRVGSSFDAADLAQDTFLRVLGKPGALDGVRE 60 Query: 61 PRAYLVTAARHLLIDRSRRQQIRQAYLDQLERQFGACPELMHAPSAETILQAVQAIEALG 120 PRA+L A L++D+ RR+++ + L+ + PE++ +P A IL V+A+ + Sbjct: 61 PRAWLSRIAHGLVVDKLRREEVERTCLEAIAHL--PEPEVV-SPEARLIL--VEALCMID 115 Query: 121 RALQAVRAEAAEAFILHYVQGRRQEELASQFNVSLRTVQGWLAQALIQCH 170 L+ + A +AF+L + E+A VSL +V+ ++A A+ C+ Sbjct: 116 ALLEGLGERARQAFLLSRLDEMSYPEIARHLGVSLSSVEKYMAAAIRHCY 165 >gi|300313763|ref|YP_003777855.1| RNA polymerase sigma-70 factor, ECF subfamily (sigma-24) transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 169 Score = 101 bits (251), Expect = 4e-23, Method: Compositional matrix adjust. Identities = 65/155 (41%), Positives = 85/155 (54%), Gaps = 6/155 (3%) Query: 15 LYRDHHGWLRAWLRRKLGCTEQAADLAHDTFLRLLATRDVLSALKEPRAYLVTAARHLLI 74 LYR+HHGWL AWL R+L C ADLA DTF+RLL R L+EPRAYL T A+ L+ Sbjct: 17 LYREHHGWLVAWLSRRLACRHLGADLAQDTFVRLLGHRPP-PDLREPRAYLTTIAKGLVA 75 Query: 75 DRSRRQQIRQAYLDQLERQFGACPELMHAPSAETILQAVQAIEALGRALQAVRAEAAEAF 134 RR+Q+ AYL+ L A PE PSAE L + + + R L + A A + F Sbjct: 76 SHLRRRQLETAYLEAL----AALPE-PSQPSAEERLLVLDTLCEIDRILDQLPARARQVF 130 Query: 135 ILHYVQGRRQEELASQFNVSLRTVQGWLAQALIQC 169 +L + G +A +SL TV+ + AL C Sbjct: 131 LLAQLDGLPYASIAGLLGISLSTVKRHMVLALRHC 165 >gi|300312828|ref|YP_003776920.1| RNA polymerase sigma-70 factor, ECF subfamily (sigma-24) transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 178 Score = 83.6 bits (205), Expect = 8e-18, Method: Compositional matrix adjust. Identities = 54/170 (31%), Positives = 94/170 (55%), Gaps = 10/170 (5%) Query: 2 PAMEELHVDPLETLYRDHHGWLRAWLRRKLGCTEQAADLAHDTFLRLLATRDVLSALKEP 61 PAM + E ++ +HHGWLR LRR +G A D+A +TF +LL + ++EP Sbjct: 11 PAMSRI-----EAIFIEHHGWLRTRLRRSVGDAFTAEDVAAETFTQLLHSPPP-QEVREP 64 Query: 62 RAYLVTAARHLLIDRSRRQQIRQAYLDQLERQFGACPELMHAPSAETILQAVQAIEALGR 121 RA L T +R ++ + RR+ + +A L L G + A S E LQ +QA+ A+ + Sbjct: 65 RALLTTISRRIVYELWRRRDLEEACLQALAHVSGD----VQAISPEDQLQLLQALRAMDQ 120 Query: 122 ALQAVRAEAAEAFILHYVQGRRQEELASQFNVSLRTVQGWLAQALIQCHR 171 AL + A+ AF+L+ + G + + +Q ++ + ++A+ L+QC++ Sbjct: 121 ALAGLSAKECAAFLLYKLDGLTYQAIGAQLRITPSVARRYVAKGLLQCYK 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 0.134 0.401 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: 519,336 Number of extensions: 16949 Number of successful extensions: 123 Number of sequences better than 1.0e-08: 7 Number of HSP's gapped: 114 Number of HSP's successfully gapped: 7 Length of query: 178 Length of database: 1,619,870 Length adjustment: 79 Effective length of query: 99 Effective length of database: 1,245,805 Effective search space: 123334695 Effective search space used: 123334695 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)