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= 0001.2192.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|300311748|ref|YP_003775840.1| RNA polymerase sigma-70 factor,... 291 2e-80 gi|300313763|ref|YP_003777855.1| RNA polymerase sigma-70 factor,... 148 3e-37 gi|300309381|ref|YP_003773473.1| RNA polymerase sigma-70 factor ... 120 8e-29 gi|300312828|ref|YP_003776920.1| RNA polymerase sigma-70 factor,... 109 1e-25 gi|300312131|ref|YP_003776223.1| RNA polymerase sigma 24 factor ... 102 1e-23 >gi|300311748|ref|YP_003775840.1| RNA polymerase sigma-70 factor, ECF subfamily (sigma-24) transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 174 Score = 291 bits (745), Expect = 2e-80, Method: Compositional matrix adjust. Identities = 141/172 (81%), Positives = 156/172 (90%) Query: 1 MSVPHSADAQRFHTLYRQHHGWLQQWLRARLGSSVDAADLAQDTFVRVLGKPRALDEVRE 60 M VPH+ AQRFHTLY +HHGWLQQWLR R+GSS DAADLAQDTF+RVLGKP ALD VRE Sbjct: 1 MPVPHTVHAQRFHTLYSEHHGWLQQWLRRRVGSSFDAADLAQDTFLRVLGKPGALDGVRE 60 Query: 61 PRAWLSRIAHGLVVDKVRRDEVERACLDAIARLPEPQAISPEARLLLVEALAAIDAMLEG 120 PRAWLSRIAHGLVVDK+RR+EVER CL+AIA LPEP+ +SPEARL+LVEAL IDA+LEG Sbjct: 61 PRAWLSRIAHGLVVDKLRREEVERTCLEAIAHLPEPEVVSPEARLILVEALCMIDALLEG 120 Query: 121 LGARAREAFLMSRLEEMSYPEIARSMGVSLSSVEKYMAAAIRHCYLMRQSWQ 172 LG RAR+AFL+SRL+EMSYPEIAR +GVSLSSVEKYMAAAIRHCYLMRQS Q Sbjct: 121 LGERARQAFLLSRLDEMSYPEIARHLGVSLSSVEKYMAAAIRHCYLMRQSLQ 172 >gi|300313763|ref|YP_003777855.1| RNA polymerase sigma-70 factor, ECF subfamily (sigma-24) transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 169 Score = 148 bits (373), Expect = 3e-37, Method: Compositional matrix adjust. Identities = 78/155 (50%), Positives = 107/155 (69%), Gaps = 1/155 (0%) Query: 10 QRFHTLYRQHHGWLQQWLRARLGSSVDAADLAQDTFVRVLGKPRALDEVREPRAWLSRIA 69 Q LYR+HHGWL WL RL ADLAQDTFVR+LG R ++REPRA+L+ IA Sbjct: 12 QEIGGLYREHHGWLVAWLSRRLACRHLGADLAQDTFVRLLGH-RPPPDLREPRAYLTTIA 70 Query: 70 HGLVVDKVRRDEVERACLDAIARLPEPQAISPEARLLLVEALAAIDAMLEGLGARAREAF 129 GLV +RR ++E A L+A+A LPEP S E RLL+++ L ID +L+ L ARAR+ F Sbjct: 71 KGLVASHLRRRQLETAYLEALAALPEPSQPSAEERLLVLDTLCEIDRILDQLPARARQVF 130 Query: 130 LMSRLEEMSYPEIARSMGVSLSSVEKYMAAAIRHC 164 L+++L+ + Y IA +G+SLS+V+++M A+RHC Sbjct: 131 LLAQLDGLPYASIAGLLGISLSTVKRHMVLALRHC 165 >gi|300309381|ref|YP_003773473.1| RNA polymerase sigma-70 factor protein [Herbaspirillum seropedicae SmR1] Length = 181 Score = 120 bits (300), Expect = 8e-29, Method: Compositional matrix adjust. Identities = 69/166 (41%), Positives = 113/166 (68%), Gaps = 5/166 (3%) Query: 1 MSVPHSADAQRFHTLYRQHHGWLQQWLRARLGSSVDAADLAQDTFVRVLGKPRALDEVRE 60 M VP S +A LY HH WL+ WL+ RLG+S AADLAQDTF+R+LG R + E Sbjct: 14 MPVPMSIEA-----LYCDHHSWLKGWLQRRLGNSEQAADLAQDTFLRLLGSERVPSVIHE 68 Query: 61 PRAWLSRIAHGLVVDKVRRDEVERACLDAIARLPEPQAISPEARLLLVEALAAIDAMLEG 120 PRA+L+ +A LV + RR+++E+A L+A+A+ P A SP+ + +L+E L +D +L+ Sbjct: 69 PRAYLTTVAQRLVSNLWRREKLEQAYLEALAQAPVALAPSPQEQAILLETLLELDQLLDE 128 Query: 121 LGARAREAFLMSRLEEMSYPEIARSMGVSLSSVEKYMAAAIRHCYL 166 L + R AFL+S+L+ +++ ++A ++G+S+ +V++Y+ A++ CY Sbjct: 129 LPSIVRRAFLLSQLDGLTHAQVAAALGISIPTVKRYLVKALQRCYF 174 >gi|300312828|ref|YP_003776920.1| RNA polymerase sigma-70 factor, ECF subfamily (sigma-24) transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 178 Score = 109 bits (272), Expect = 1e-25, Method: Compositional matrix adjust. Identities = 62/162 (38%), Positives = 97/162 (59%), Gaps = 2/162 (1%) Query: 5 HSADAQRFHTLYRQHHGWLQQWLRARLGSSVDAADLAQDTFVRVLGKPRALDEVREPRAW 64 H R ++ +HHGWL+ LR +G + A D+A +TF ++L P EVREPRA Sbjct: 9 HPPAMSRIEAIFIEHHGWLRTRLRRSVGDAFTAEDVAAETFTQLLHSPPP-QEVREPRAL 67 Query: 65 LSRIAHGLVVDKVRRDEVERACLDAIARLP-EPQAISPEARLLLVEALAAIDAMLEGLGA 123 L+ I+ +V + RR ++E ACL A+A + + QAISPE +L L++AL A+D L GL A Sbjct: 68 LTTISRRIVYELWRRRDLEEACLQALAHVSGDVQAISPEDQLQLLQALRAMDQALAGLSA 127 Query: 124 RAREAFLMSRLEEMSYPEIARSMGVSLSSVEKYMAAAIRHCY 165 + AFL+ +L+ ++Y I + ++ S +Y+A + CY Sbjct: 128 KECAAFLLYKLDGLTYQAIGAQLRITPSVARRYVAKGLLQCY 169 >gi|300312131|ref|YP_003776223.1| RNA polymerase sigma 24 factor protein [Herbaspirillum seropedicae SmR1] Length = 173 Score = 102 bits (255), Expect = 1e-23, Method: Compositional matrix adjust. Identities = 65/152 (42%), Positives = 92/152 (60%), Gaps = 1/152 (0%) Query: 14 TLYRQHHGWLQQWLRARLGSSVDAADLAQDTFVRVLGKPRALDEVREPRAWLSRIAHGLV 73 T + + WL+Q+LR ++ S DA D+A FV + P + +REPRA L+ I+ LV Sbjct: 20 TEFTNSYSWLKQYLRRQVKSLADAEDVASAAFVEMASLPD-VSIIREPRALLTTISQRLV 78 Query: 74 VDKVRRDEVERACLDAIARLPEPQAISPEARLLLVEALAAIDAMLEGLGARAREAFLMSR 133 D RR ++E A L A+A E SPE L +V+ L ID +L GL AR+AFL S+ Sbjct: 79 FDLWRRRDLEAAYLAALATTEEATTPSPEVVLEVVQTLVNIDRLLYGLSKNARQAFLYSQ 138 Query: 134 LEEMSYPEIARSMGVSLSSVEKYMAAAIRHCY 165 L+ ++Y EIA +GVS+S V KY+A A+ CY Sbjct: 139 LDGLTYREIAELLGVSVSMVRKYIAQALAKCY 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 0.323 0.133 0.396 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: 484,787 Number of extensions: 15831 Number of successful extensions: 122 Number of sequences better than 1.0e-08: 8 Number of HSP's gapped: 117 Number of HSP's successfully gapped: 8 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 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 127 (53.5 bits)