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= 0030.0172.p (172 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,... 346 6e-97 gi|300313763|ref|YP_003777855.1| RNA polymerase sigma-70 factor,... 151 3e-38 gi|300309381|ref|YP_003773473.1| RNA polymerase sigma-70 factor ... 123 9e-30 gi|300312828|ref|YP_003776920.1| RNA polymerase sigma-70 factor,... 114 6e-27 gi|300312131|ref|YP_003776223.1| RNA polymerase sigma 24 factor ... 113 9e-27 >gi|300311748|ref|YP_003775840.1| RNA polymerase sigma-70 factor, ECF subfamily (sigma-24) transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 174 Score = 346 bits (888), Expect = 6e-97, Method: Compositional matrix adjust. Identities = 172/172 (100%), Positives = 172/172 (100%) Query: 1 VPHTVHAQRFHTLYSEHHGWLQQWLRRRVGSSFDAADLAQDTFLRVLGKPGALDGVREPR 60 VPHTVHAQRFHTLYSEHHGWLQQWLRRRVGSSFDAADLAQDTFLRVLGKPGALDGVREPR Sbjct: 3 VPHTVHAQRFHTLYSEHHGWLQQWLRRRVGSSFDAADLAQDTFLRVLGKPGALDGVREPR 62 Query: 61 AWLSRIAHGLVVDKLRREEVERTCLEAIAHLPEPEVVSPEARLILVEALCMIDALLEGLG 120 AWLSRIAHGLVVDKLRREEVERTCLEAIAHLPEPEVVSPEARLILVEALCMIDALLEGLG Sbjct: 63 AWLSRIAHGLVVDKLRREEVERTCLEAIAHLPEPEVVSPEARLILVEALCMIDALLEGLG 122 Query: 121 ERARQAFLLSRLDEMSYPEIARHLGVSLSSVEKYMAAAIRHCYLMRQSLQAA 172 ERARQAFLLSRLDEMSYPEIARHLGVSLSSVEKYMAAAIRHCYLMRQSLQAA Sbjct: 123 ERARQAFLLSRLDEMSYPEIARHLGVSLSSVEKYMAAAIRHCYLMRQSLQAA 174 >gi|300313763|ref|YP_003777855.1| RNA polymerase sigma-70 factor, ECF subfamily (sigma-24) transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 169 Score = 151 bits (382), Expect = 3e-38, Method: Compositional matrix adjust. Identities = 81/155 (52%), Positives = 105/155 (67%), Gaps = 1/155 (0%) Query: 8 QRFHTLYSEHHGWLQQWLRRRVGSSFDAADLAQDTFLRVLGKPGALDGVREPRAWLSRIA 67 Q LY EHHGWL WL RR+ ADLAQDTF+R+LG D +REPRA+L+ IA Sbjct: 12 QEIGGLYREHHGWLVAWLSRRLACRHLGADLAQDTFVRLLGHRPPPD-LREPRAYLTTIA 70 Query: 68 HGLVVDKLRREEVERTCLEAIAHLPEPEVVSPEARLILVEALCMIDALLEGLGERARQAF 127 GLV LRR ++E LEA+A LPEP S E RL++++ LC ID +L+ L RARQ F Sbjct: 71 KGLVASHLRRRQLETAYLEALAALPEPSQPSAEERLLVLDTLCEIDRILDQLPARARQVF 130 Query: 128 LLSRLDEMSYPEIARHLGVSLSSVEKYMAAAIRHC 162 LL++LD + Y IA LG+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 = 123 bits (308), Expect = 9e-30, Method: Compositional matrix adjust. Identities = 74/171 (43%), Positives = 111/171 (64%), Gaps = 5/171 (2%) Query: 1 VPHTVHAQRFHTLYSEHHGWLQQWLRRRVGSSFDAADLAQDTFLRVLGKPGALDGVREPR 60 VP ++ A LY +HH WL+ WL+RR+G+S AADLAQDTFLR+LG + EPR Sbjct: 16 VPMSIEA-----LYCDHHSWLKGWLQRRLGNSEQAADLAQDTFLRLLGSERVPSVIHEPR 70 Query: 61 AWLSRIAHGLVVDKLRREEVERTCLEAIAHLPEPEVVSPEARLILVEALCMIDALLEGLG 120 A+L+ +A LV + RRE++E+ LEA+A P SP+ + IL+E L +D LL+ L Sbjct: 71 AYLTTVAQRLVSNLWRREKLEQAYLEALAQAPVALAPSPQEQAILLETLLELDQLLDELP 130 Query: 121 ERARQAFLLSRLDEMSYPEIARHLGVSLSSVEKYMAAAIRHCYLMRQSLQA 171 R+AFLLS+LD +++ ++A LG+S+ +V++Y+ A++ CY S A Sbjct: 131 SIVRRAFLLSQLDGLTHAQVAAALGISIPTVKRYLVKALQRCYFADISFSA 181 >gi|300312828|ref|YP_003776920.1| RNA polymerase sigma-70 factor, ECF subfamily (sigma-24) transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 178 Score = 114 bits (284), Expect = 6e-27, Method: Compositional matrix adjust. Identities = 63/162 (38%), Positives = 97/162 (59%), Gaps = 2/162 (1%) Query: 3 HTVHAQRFHTLYSEHHGWLQQWLRRRVGSSFDAADLAQDTFLRVLGKPGALDGVREPRAW 62 H R ++ EHHGWL+ LRR VG +F A D+A +TF ++L P + VREPRA Sbjct: 9 HPPAMSRIEAIFIEHHGWLRTRLRRSVGDAFTAEDVAAETFTQLLHSPPPQE-VREPRAL 67 Query: 63 LSRIAHGLVVDKLRREEVERTCLEAIAHLP-EPEVVSPEARLILVEALCMIDALLEGLGE 121 L+ I+ +V + RR ++E CL+A+AH+ + + +SPE +L L++AL +D L GL Sbjct: 68 LTTISRRIVYELWRRRDLEEACLQALAHVSGDVQAISPEDQLQLLQALRAMDQALAGLSA 127 Query: 122 RARQAFLLSRLDEMSYPEIARHLGVSLSSVEKYMAAAIRHCY 163 + AFLL +LD ++Y I L ++ 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 = 113 bits (282), Expect = 9e-27, Method: Compositional matrix adjust. Identities = 69/152 (45%), Positives = 94/152 (61%), Gaps = 1/152 (0%) Query: 12 TLYSEHHGWLQQWLRRRVGSSFDAADLAQDTFLRVLGKPGALDGVREPRAWLSRIAHGLV 71 T ++ + WL+Q+LRR+V S DA D+A F+ + P + +REPRA L+ I+ LV Sbjct: 20 TEFTNSYSWLKQYLRRQVKSLADAEDVASAAFVEMASLPD-VSIIREPRALLTTISQRLV 78 Query: 72 VDKLRREEVERTCLEAIAHLPEPEVVSPEARLILVEALCMIDALLEGLGERARQAFLLSR 131 D RR ++E L A+A E SPE L +V+ L ID LL GL + ARQAFL S+ Sbjct: 79 FDLWRRRDLEAAYLAALATTEEATTPSPEVVLEVVQTLVNIDRLLYGLSKNARQAFLYSQ 138 Query: 132 LDEMSYPEIARHLGVSLSSVEKYMAAAIRHCY 163 LD ++Y EIA LGVS+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 0.324 0.136 0.411 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: 569,856 Number of extensions: 22805 Number of successful extensions: 129 Number of sequences better than 1.0e-08: 9 Number of HSP's gapped: 122 Number of HSP's successfully gapped: 9 Length of query: 172 Length of database: 1,619,870 Length adjustment: 79 Effective length of query: 93 Effective length of database: 1,245,805 Effective search space: 115859865 Effective search space used: 115859865 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)