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= 0007.0113.p (205 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312563|ref|YP_003776655.1| transcription regulator protein... 109 2e-25 gi|300310688|ref|YP_003774780.1| transcription regulator protein... 100 7e-23 gi|300309825|ref|YP_003773917.1| TetR family transcription regul... 82 3e-17 >gi|300312563|ref|YP_003776655.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 200 Score = 109 bits (272), Expect = 2e-25, Method: Compositional matrix adjust. Identities = 67/201 (33%), Positives = 107/201 (53%), Gaps = 1/201 (0%) Query: 1 MRVKTVEQRHEFINAAGHLFIQQGYAAVTMEAIAAEAGKSKVTLYNYFSSKEELFEAFVV 60 MR K+ E+R I+ A +F + G+ A +M I+A G SK TLYNYF+SKEE+F ++ Sbjct: 1 MRKKSEERRQAMIDIAAEVFNEIGFEAASMAEISARIGGSKATLYNYFNSKEEIFVEVMI 60 Query: 61 QAGAGAVEELTKVYVEADSARDILQRLGLALLRLVSRPDVIALDRLIIGEARRYPELARI 120 + EEL D + L RL LR+V RP+++A+ RL I A + L + Sbjct: 61 KQVGCQFEELFMALRNEDDVKGGLLRLARHYLRVVFRPEIVAVKRLGIYYAGK-SNLGPL 119 Query: 121 FFENGPKRTVAALAEVIARCMDSGKIDARNAELAALHFKAICAGDLIENLMWGTIAQPTK 180 +E GPKR +AE + M+ GK+ + LAA+ ++ + + +E M + + Sbjct: 120 LYERGPKRGWTRIAEFLQAKMEEGKLHRTDPWLAAMQYRGLMEAEWMEVRMLNVVTDIAE 179 Query: 181 EKLKKISDNAVKVFLDGYRIR 201 ++L + AV+ FL Y+ R Sbjct: 180 DQLDASAQRAVEAFLYLYQPR 200 >gi|300310688|ref|YP_003774780.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 201 Score = 100 bits (250), Expect = 7e-23, Method: Compositional matrix adjust. Identities = 63/202 (31%), Positives = 108/202 (53%), Gaps = 4/202 (1%) Query: 1 MRVKTVEQRHEFINAAGHLFIQQGYAAVTMEAIAAEAGKSKVTLYNYFSSKEELFEAFVV 60 MRVKT E+R + AA +F+++G+ +M I+A G SK TLY+YF SKEELF A V Sbjct: 1 MRVKTAERRDAILAAAAEVFLEEGFEGASMAGISARIGGSKGTLYSYFKSKEELFVA-VT 59 Query: 61 QAGAGAVEELTKVYVEADSA--RDILQRLGLALLRLVSRPDVIALDRLIIGEARRYPELA 118 A E +E D+ + LQ G + + + + R+I+ E+ R ++ Sbjct: 60 HEQAKKQMEPALAALEKDTGDLQKTLQVFGEKAVSFLCQESTLQTHRMIVAESGR-SDIG 118 Query: 119 RIFFENGPKRTVAALAEVIARCMDSGKIDARNAELAALHFKAICAGDLIENLMWGTIAQP 178 R F E+GPK + +A ++R M +G++ + LA L A+ + ++ +M G + Sbjct: 119 RRFHESGPKLGMERIAAFLSRQMQAGRLKQADPMLATLQLCALLDCETVKPMMLGLESAI 178 Query: 179 TKEKLKKISDNAVKVFLDGYRI 200 ++ ++K++ AV+ FL Y + Sbjct: 179 SRPRMKRMVGRAVETFLAAYAV 200 >gi|300309825|ref|YP_003773917.1| TetR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 209 Score = 82.0 bits (201), Expect = 3e-17, Method: Compositional matrix adjust. Identities = 56/175 (32%), Positives = 92/175 (52%), Gaps = 7/175 (4%) Query: 7 EQRHEFINAAGHLFIQQGYAAVTMEAIAAEAGKSKVTLYNYFSSKEELFEAFVVQAGAGA 66 ++ E + AA LF+++GYAA +E +AA+AG SK TLY YF SKE LF++ VV+A Sbjct: 16 DRPQELLAAALQLFVERGYAATRLEDVAAQAGVSKGTLYLYFDSKESLFKS-VVRAHMLP 74 Query: 67 VEELTKVYVEADSAR--DILQRLGLALLRLVSRPDVIALDRLIIGEARRYPELARIFFEN 124 + + + V++ D+L+ L L + SR + + +L++ E+ +PELAR + E Sbjct: 75 LLDEAEARVDSHDGHTADLLRELILGWWQGASRSGLKGIAKLMLAESGNFPELARFYHEE 134 Query: 125 GPKRTVAALAEVIARCMDSGKIDARNAELAALHFKAICAGDLIENLMWGTIAQPT 179 R A L V+ R M G+ +A K + A ++ ++W P Sbjct: 135 ITSRGDATLVRVLERGMARGEFRPLDAHA----LKKVIAAPIMMLMLWDQSLAPC 185 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 0.136 0.380 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: 483,156 Number of extensions: 15096 Number of successful extensions: 60 Number of sequences better than 1.0e-08: 3 Number of HSP's gapped: 58 Number of HSP's successfully gapped: 3 Length of query: 205 Length of database: 1,619,870 Length adjustment: 81 Effective length of query: 124 Effective length of database: 1,236,335 Effective search space: 153305540 Effective search space used: 153305540 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: 41 (22.0 bits) S2: 128 (53.9 bits)