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= 0011.0308.p (285 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311600|ref|YP_003775692.1| transcription regulator protein... 587 e-169 gi|300313239|ref|YP_003777331.1| transcription regulator protein... 81 9e-17 gi|300309916|ref|YP_003774008.1| transcription regulator protein... 68 7e-13 gi|300313290|ref|YP_003777382.1| IclR family transcription regul... 61 1e-10 gi|300310378|ref|YP_003774470.1| transcription regulator protein... 59 4e-10 >gi|300311600|ref|YP_003775692.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 292 Score = 587 bits (1513), Expect = e-169, Method: Compositional matrix adjust. Identities = 285/285 (100%), Positives = 285/285 (100%) Query: 1 MRKFSQLLGKCEISFQIFSNIFLICGNDSPKMRNSPYIAAMDSPQTSTIVDRVLHVLAGV 60 MRKFSQLLGKCEISFQIFSNIFLICGNDSPKMRNSPYIAAMDSPQTSTIVDRVLHVLAGV Sbjct: 8 MRKFSQLLGKCEISFQIFSNIFLICGNDSPKMRNSPYIAAMDSPQTSTIVDRVLHVLAGV 67 Query: 61 ARAGKPVSAKQIAAMVQQPVSTVYRHLASLKKWGLLQEHMNSGTFEPGPTGVQLAWGFDQ 120 ARAGKPVSAKQIAAMVQQPVSTVYRHLASLKKWGLLQEHMNSGTFEPGPTGVQLAWGFDQ Sbjct: 68 ARAGKPVSAKQIAAMVQQPVSTVYRHLASLKKWGLLQEHMNSGTFEPGPTGVQLAWGFDQ 127 Query: 121 NSNLVSQSREEISSLVQRSGESVGLLVAINGQMVCIAMEESDQPLRCSFTKGRAHPLLKG 180 NSNLVSQSREEISSLVQRSGESVGLLVAINGQMVCIAMEESDQPLRCSFTKGRAHPLLKG Sbjct: 128 NSNLVSQSREEISSLVQRSGESVGLLVAINGQMVCIAMEESDQPLRCSFTKGRAHPLLKG 187 Query: 181 ASAKSLLAFMPRKLQQKLLTDQLGDKPEELAALETQLEEIRRRGYCISESEVDLGVWGVS 240 ASAKSLLAFMPRKLQQKLLTDQLGDKPEELAALETQLEEIRRRGYCISESEVDLGVWGVS Sbjct: 188 ASAKSLLAFMPRKLQQKLLTDQLGDKPEELAALETQLEEIRRRGYCISESEVDLGVWGVS 247 Query: 241 VPIMTSNGRLEGTITLMAPALRVGNREQELVRMTLESAQRICNRF 285 VPIMTSNGRLEGTITLMAPALRVGNREQELVRMTLESAQRICNRF Sbjct: 248 VPIMTSNGRLEGTITLMAPALRVGNREQELVRMTLESAQRICNRF 292 >gi|300313239|ref|YP_003777331.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 244 Score = 81.3 bits (199), Expect = 9e-17, Method: Compositional matrix adjust. Identities = 69/245 (28%), Positives = 120/245 (48%), Gaps = 17/245 (6%) Query: 50 VDRVLHVLAGVARAGKPVSAKQIAAMVQQPVSTVYRHLASLKKWGLLQEHMNSGTFEPGP 109 + R+L VL + + + I A + ++ YR++ L GLL + M G + GP Sbjct: 4 LSRMLEVLTLFKPSQPVIDIELICAQLGYTPASAYRYVRELGNAGLLVK-MPRG-YAVGP 61 Query: 110 TGVQLAWGFDQNSNLVSQSREEISSLVQRSGESVGLLVAINGQMVCIAMEES-DQPLRCS 168 ++L Q L+S SR+ + LV ++G + L+ + G V ++ES R + Sbjct: 62 KVIELDRHMTQFDPLLSASRDIVGDLVAQTGLEL-LISELYGSTVITILQESGSNDARLN 120 Query: 169 FTKGRAHPLLKGASAKSLLAFM-PRKLQQKLLTDQLGDKPEELAALETQLEE-------I 220 F +G L A+A+ +LA++ PR+L++ G EEL + + + I Sbjct: 121 FGRGTPMDLFHSATARVILAYLLPRQLRKHFD----GASAEELRLVGSNWRDFSKVMLKI 176 Query: 221 RRRGYCISESEVDLGVWGVSVPIMTSNGRLEGTITLMAPALRVGNREQELVR-MTLESAQ 279 R+ GYC+SE E+D G G++ PI R+ G+ITL RV +E + + ++A+ Sbjct: 177 RKDGYCVSEGELDAGKTGIAAPIFDEKQRILGSITLAGNTERVNAFNREFLSGLITDAAR 236 Query: 280 RICNR 284 +I R Sbjct: 237 KITAR 241 >gi|300309916|ref|YP_003774008.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 265 Score = 68.2 bits (165), Expect = 7e-13, Method: Compositional matrix adjust. Identities = 63/236 (26%), Positives = 110/236 (46%), Gaps = 6/236 (2%) Query: 56 VLAGVARAGKPVSAKQIAAMVQQPVSTVYRHLASLKKWGLLQEHMNSGTFEPGPTGVQLA 115 VL +A P++ Q+AA+ P TVYR LA+L G++ E+ + +E GP + LA Sbjct: 26 VLQLIADQDAPLNIAQLAALSGYPRPTVYRILAALMAEGMVVENPRNKQYEVGPRLINLA 85 Query: 116 WGFDQNSNLVSQSREEISSLVQRSGESVGLLVAINGQMVCIAMEESDQPLRCSFTKGRAH 175 S++ + + E + L + E+V L V + MV I ES Q +R G Sbjct: 86 SRAWDRSDIRTTAIESLRQLRDLTRETVHLAVPSDHSMVYIEKLESPQAVRMDSRIGTRV 145 Query: 176 PLLKGASAKSLLAFMPRKLQQKLL-TDQL----GDKPEELAALETQLEEIRRRGYCISES 230 L + K+ LA + +++L+ T L + ELAAL +E+ R RGY Sbjct: 146 TLYSSSVGKAYLAGLEEAHRERLMRTLHLQAFTANTHTELAALRADVEDTRARGYAEDRE 205 Query: 231 EVDLGVWGVSVPIMTSNGRLEGTITLMAPAL-RVGNREQELVRMTLESAQRICNRF 285 E + ++ I+ ++G +++ P R+ + +Q V+ L++ I + Sbjct: 206 ENEAQIFCYGAAIVGADGVPVACVSVSIPLYRRLPDAQQAYVQPLLQACATISRKL 261 >gi|300313290|ref|YP_003777382.1| IclR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 260 Score = 60.8 bits (146), Expect = 1e-10, Method: Compositional matrix adjust. Identities = 55/252 (21%), Positives = 121/252 (48%), Gaps = 11/252 (4%) Query: 38 IAAMDSPQTSTIVDRVLHVLAGVARAGKPVSAKQIAAMVQQPVSTVYRHLASLKKWGLLQ 97 I A+ P T + R L V+ + + + ++ QI+ P + V R L +LK+ G Sbjct: 7 IDALTDPSFMTSLARGLAVIRAFSDSRRSLTIAQISQKTGIPRAAVRRCLHTLKQLGYAD 66 Query: 98 EHMNSGTFEPGPTGVQLAWGFDQNSNLVSQSREEISSLVQRSGESVGLLVAINGQMVCIA 157 +N+ F P + L + + ++ L ++ ++++ + GES L V + +++ +A Sbjct: 67 SDVNN--FSLRPKILTLGYSYLSSTPLTVSAQPYLNNISRTLGESCSLAVLDDHEVLYVA 124 Query: 158 MEESDQPLRCSFTKGRAHPLLKGASAKSLLAFMPRKLQQKLLTDQLGDKP--EELAALET 215 + + + + G P + +++LA +P Q K D++ + E+ + Sbjct: 125 RSAASRVMSVALNTGSRLPAYCTSLGRAMLAHLPED-QLKAYFDKVKLRALTEKTVVSQK 183 Query: 216 QLEEI----RRRGYCISESEVDLGVWGVSVPIMTSNGRLEGTITLMAPALR--VGNREQE 269 +L +I R GY + + E+++G+ ++VP+ ++G + + + A A R V E+E Sbjct: 184 RLRDILAGVRANGYAVIDEELEVGLRSIAVPVRGASGNVLAALNVGAQAARVSVAQMEEE 243 Query: 270 LVRMTLESAQRI 281 ++ + L AQ + Sbjct: 244 ILPVLLRGAQEL 255 >gi|300310378|ref|YP_003774470.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 282 Score = 59.3 bits (142), Expect = 4e-10, Method: Compositional matrix adjust. Identities = 54/206 (26%), Positives = 101/206 (49%), Gaps = 9/206 (4%) Query: 50 VDRVLHVLAGVARAGKPVSAKQIAAMVQQPVSTVYRHLASLKKWGLLQEHMNSGTFEPGP 109 +D+ L +L ++R+ + ++ QI+ + + V+ ++R + +L++ G L ++ + Sbjct: 36 LDKGLDILELLSRSEQMLTLNQISRQLGRSVNEIFRMVVTLEQRGYLI--ADNDHYRLSL 93 Query: 110 TGVQLAWGFDQNSNLVSQSREEISSLVQRSGESVGLLVAINGQMVCIAMEESDQPLRCSF 169 +LA +LVS + + L R+ +S L V G+++ +A + D P R +F Sbjct: 94 KLFELAHHHQPIRSLVSTALPHMRELASRAVQSTHLTVYEAGRVIVVA--QVDSPERWAF 151 Query: 170 --TKGRAHPLLKGASAKSLLAFMPRKLQQKLLTDQL---GDKPEELAALETQLEEIRRRG 224 G L AS LLAF + +L + G++ E A L Q+E+ R+RG Sbjct: 152 GLKVGALVSLTDTASGHVLLAFRDEAERAAMLAAHVRMDGEQEIETAQLMRQIEDTRKRG 211 Query: 225 YCISESEVDLGVWGVSVPIMTSNGRL 250 + ES GV +S P+M +N R+ Sbjct: 212 HSRMESRQIRGVVNLSYPVMGANNRM 237 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 0.319 0.132 0.381 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: 744,808 Number of extensions: 26892 Number of successful extensions: 100 Number of sequences better than 1.0e-08: 8 Number of HSP's gapped: 100 Number of HSP's successfully gapped: 8 Length of query: 285 Length of database: 1,619,870 Length adjustment: 84 Effective length of query: 201 Effective length of database: 1,222,130 Effective search space: 245648130 Effective search space used: 245648130 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 (21.8 bits) S2: 130 (54.7 bits)