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= 0034.0015.p (174 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,... 272 9e-75 gi|300313763|ref|YP_003777855.1| RNA polymerase sigma-70 factor,... 153 7e-39 gi|300309381|ref|YP_003773473.1| RNA polymerase sigma-70 factor ... 134 6e-33 gi|300312828|ref|YP_003776920.1| RNA polymerase sigma-70 factor,... 117 5e-28 gi|300312131|ref|YP_003776223.1| RNA polymerase sigma 24 factor ... 108 3e-25 >gi|300311748|ref|YP_003775840.1| RNA polymerase sigma-70 factor, ECF subfamily (sigma-24) transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 174 Score = 272 bits (696), Expect = 9e-75, Method: Compositional matrix adjust. Identities = 132/174 (75%), Positives = 150/174 (86%) Query: 1 MPVPRPADAQHIDSLYREHHGWLQQWLRRKLGSSSDAADLAQDTFLRVLGKPQVLAEVRE 60 MPVP AQ +LY EHHGWLQQWLRR++GSS DAADLAQDTFLRVLGKP L VRE Sbjct: 1 MPVPHTVHAQRFHTLYSEHHGWLQQWLRRRVGSSFDAADLAQDTFLRVLGKPGALDGVRE 60 Query: 61 PRAWLTRIAQGLVVDKVRRDEVERACLEAIAHLPAPEVISPEARMLLVEALATIDAMLEG 120 PRAWL+RIA GLVVDK+RR+EVER CLEAIAHLP PEV+SPEAR++LVEAL IDA+LEG Sbjct: 61 PRAWLSRIAHGLVVDKLRREEVERTCLEAIAHLPEPEVVSPEARLILVEALCMIDALLEG 120 Query: 121 LGAKPREAFLMSRLDDLGYAEIARRMGVSLSSVEKYMAAAIRHCYLMRQAWQAS 174 LG + R+AFL+SRLD++ Y EIAR +GVSLSSVEKYMAAAIRHCYLMRQ+ QA+ Sbjct: 121 LGERARQAFLLSRLDEMSYPEIARHLGVSLSSVEKYMAAAIRHCYLMRQSLQAA 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 = 153 bits (387), Expect = 7e-39, Method: Compositional matrix adjust. Identities = 83/161 (51%), Positives = 114/161 (70%), Gaps = 4/161 (2%) Query: 6 PADA-QHIDSLYREHHGWLQQWLRRKLGSSSDAADLAQDTFLRVLG-KPQVLAEVREPRA 63 PA+A Q I LYREHHGWL WL R+L ADLAQDTF+R+LG +P ++REPRA Sbjct: 7 PAEAHQEIGGLYREHHGWLVAWLSRRLACRHLGADLAQDTFVRLLGHRPP--PDLREPRA 64 Query: 64 WLTRIAQGLVVDKVRRDEVERACLEAIAHLPAPEVISPEARMLLVEALATIDAMLEGLGA 123 +LT IA+GLV +RR ++E A LEA+A LP P S E R+L+++ L ID +L+ L A Sbjct: 65 YLTTIAKGLVASHLRRRQLETAYLEALAALPEPSQPSAEERLLVLDTLCEIDRILDQLPA 124 Query: 124 KPREAFLMSRLDDLGYAEIARRMGVSLSSVEKYMAAAIRHC 164 + R+ FL+++LD L YA IA +G+SLS+V+++M A+RHC Sbjct: 125 RARQVFLLAQLDGLPYASIAGLLGISLSTVKRHMVLALRHC 165 >gi|300309381|ref|YP_003773473.1| RNA polymerase sigma-70 factor protein [Herbaspirillum seropedicae SmR1] Length = 181 Score = 134 bits (336), Expect = 6e-33, Method: Compositional matrix adjust. Identities = 75/166 (45%), Positives = 116/166 (69%), Gaps = 5/166 (3%) Query: 1 MPVPRPADAQHIDSLYREHHGWLQQWLRRKLGSSSDAADLAQDTFLRVLGKPQVLAEVRE 60 MPVP I++LY +HH WL+ WL+R+LG+S AADLAQDTFLR+LG +V + + E Sbjct: 14 MPVP-----MSIEALYCDHHSWLKGWLQRRLGNSEQAADLAQDTFLRLLGSERVPSVIHE 68 Query: 61 PRAWLTRIAQGLVVDKVRRDEVERACLEAIAHLPAPEVISPEARMLLVEALATIDAMLEG 120 PRA+LT +AQ LV + RR+++E+A LEA+A P SP+ + +L+E L +D +L+ Sbjct: 69 PRAYLTTVAQRLVSNLWRREKLEQAYLEALAQAPVALAPSPQEQAILLETLLELDQLLDE 128 Query: 121 LGAKPREAFLMSRLDDLGYAEIARRMGVSLSSVEKYMAAAIRHCYL 166 L + R AFL+S+LD L +A++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 = 117 bits (293), Expect = 5e-28, Method: Compositional matrix adjust. Identities = 65/161 (40%), Positives = 100/161 (62%), Gaps = 2/161 (1%) Query: 6 PADAQHIDSLYREHHGWLQQWLRRKLGSSSDAADLAQDTFLRVLGKPQVLAEVREPRAWL 65 P I++++ EHHGWL+ LRR +G + A D+A +TF ++L P EVREPRA L Sbjct: 10 PPAMSRIEAIFIEHHGWLRTRLRRSVGDAFTAEDVAAETFTQLLHSPPP-QEVREPRALL 68 Query: 66 TRIAQGLVVDKVRRDEVERACLEAIAHLPAP-EVISPEARMLLVEALATIDAMLEGLGAK 124 T I++ +V + RR ++E ACL+A+AH+ + ISPE ++ L++AL +D L GL AK Sbjct: 69 TTISRRIVYELWRRRDLEEACLQALAHVSGDVQAISPEDQLQLLQALRAMDQALAGLSAK 128 Query: 125 PREAFLMSRLDDLGYAEIARRMGVSLSSVEKYMAAAIRHCY 165 AFL+ +LD L Y I ++ ++ S +Y+A + CY Sbjct: 129 ECAAFLLYKLDGLTYQAIGAQLRITPSVARRYVAKGLLQCY 169 >gi|300312131|ref|YP_003776223.1| RNA polymerase sigma 24 factor protein [Herbaspirillum seropedicae SmR1] Length = 173 Score = 108 bits (270), Expect = 3e-25, Method: Compositional matrix adjust. Identities = 66/150 (44%), Positives = 92/150 (61%), Gaps = 1/150 (0%) Query: 16 YREHHGWLQQWLRRKLGSSSDAADLAQDTFLRVLGKPQVLAEVREPRAWLTRIAQGLVVD 75 + + WL+Q+LRR++ S +DA D+A F+ + P V + +REPRA LT I+Q LV D Sbjct: 22 FTNSYSWLKQYLRRQVKSLADAEDVASAAFVEMASLPDV-SIIREPRALLTTISQRLVFD 80 Query: 76 KVRRDEVERACLEAIAHLPAPEVISPEARMLLVEALATIDAMLEGLGAKPREAFLMSRLD 135 RR ++E A L A+A SPE + +V+ L ID +L GL R+AFL S+LD Sbjct: 81 LWRRRDLEAAYLAALATTEEATTPSPEVVLEVVQTLVNIDRLLYGLSKNARQAFLYSQLD 140 Query: 136 DLGYAEIARRMGVSLSSVEKYMAAAIRHCY 165 L Y EIA +GVS+S V KY+A A+ CY Sbjct: 141 GLTYREIAELLGVSVSMVRKYIAQALAKCY 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 0.322 0.134 0.400 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: 542,187 Number of extensions: 19711 Number of successful extensions: 102 Number of sequences better than 1.0e-08: 8 Number of HSP's gapped: 98 Number of HSP's successfully gapped: 8 Length of query: 174 Length of database: 1,619,870 Length adjustment: 79 Effective length of query: 95 Effective length of database: 1,245,805 Effective search space: 118351475 Effective search space used: 118351475 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 (22.0 bits) S2: 127 (53.5 bits)