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= 0001.0182.p (325 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300309514|ref|YP_003773606.1| AraC family transcription regul... 425 e-120 gi|300310404|ref|YP_003774496.1| AraC family transcription regul... 111 1e-25 gi|300311726|ref|YP_003775818.1| AraC family transcription regul... 93 3e-20 gi|300311760|ref|YP_003775852.1| transcription regulator protein... 92 8e-20 gi|300313807|ref|YP_003777899.1| AraC family transcription regul... 67 3e-12 >gi|300309514|ref|YP_003773606.1| AraC family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 323 Score = 425 bits (1093), Expect = e-120, Method: Compositional matrix adjust. Identities = 245/318 (77%), Positives = 272/318 (85%), Gaps = 2/318 (0%) Query: 1 MDALSRLLSLHPVRAGLDIRCRFGQPWHLPHPALPEGVAPYHFILEGQAQLQLAQGEPLA 60 MDALS LL LHPVRA LDIRCRFGQPWHL + A P+G APYHFILEGQAQLQ GEPLA Sbjct: 1 MDALSHLLFLHPVRAALDIRCRFGQPWHLQNAAQPQGTAPYHFILEGQAQLQWGAGEPLA 60 Query: 61 LQAGDLVVLTRGAAHGIFTAPAAQAIAPRQGVTAAPVQLHVNDDQGGGAQPLSDFLCGQF 120 LQAGDLVVL RGAAHG+FTAPAAQA A R T APV LHVN G GA LSDFLCGQF Sbjct: 61 LQAGDLVVLVRGAAHGLFTAPAAQAAAVRVASTTAPVALHVNGQAGEGAPALSDFLCGQF 120 Query: 121 HFDAPHSNALVQALPEVLLVRGAELPDGDGLRTLAALLRNECGGADGRG--ELRAGAQAV 178 FDAPHS+AL+QALP++L +RGAELP+G GLRTLA LLR+ECGG++G E R GAQAV Sbjct: 121 TFDAPHSHALMQALPDLLWIRGAELPEGHGLRTLATLLRDECGGSEGIDAIEARPGAQAV 180 Query: 179 VAALAAALFGLAIRAWLAQGGPQPGLLALLAHPVLQEALQAMLEAPHEDWSLPRLAALCH 238 VA+LAAALFGLA+RAWLAQ GP PGLLALLAHP+L +A+QAML+AP EDWSLPRLAALCH Sbjct: 181 VASLAAALFGLAVRAWLAQSGPTPGLLALLAHPLLHKAMQAMLKAPAEDWSLPRLAALCH 240 Query: 239 MSRATFVRRFQEVGGATPGEVVQQLRMSQAARFLSYSKMSTAQIGEAVGYQSEAAFNRVF 298 MSRATF+RRF EVG +TP +V+ QLRM+QAAR LSYSK +TAQIGEAVGYQSEAAFNRVF Sbjct: 241 MSRATFIRRFAEVGASTPAQVLMQLRMAQAARLLSYSKQATAQIGEAVGYQSEAAFNRVF 300 Query: 299 KKFSGMGPGAYRRKMRGA 316 +K+SGMGPGAYRR+ R A Sbjct: 301 RKYSGMGPGAYRRQARAA 318 >gi|300310404|ref|YP_003774496.1| AraC family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 344 Score = 111 bits (277), Expect = 1e-25, Method: Compositional matrix adjust. Identities = 91/300 (30%), Positives = 137/300 (45%), Gaps = 25/300 (8%) Query: 25 QPWHLPHPALPEGVAPYHFILEGQAQLQLAQGEPLALQAGDLVVLTRGAAHGIFTAPAAQ 84 +PW + PA E A +HF+ +G +Q+ Q L L GD V+L RGA H + +AP Sbjct: 54 EPWAVAFPARRE--ATFHFVAQGGCWMQVGQQAWLQLNTGDAVLLPRGAPHALASAPGLP 111 Query: 85 AIAP-RQGVTAAPVQLHVNDDQGGG-----AQPLS-----DFLCGQFHFDAPHSNALVQA 133 + + A L + DD G G A P S G F+ + L+ Sbjct: 112 TVEIGKLARKALADNLFLIDDSGNGLADAPAHPASLPPSHVLFSGTLRFNLDPLHPLLMM 171 Query: 134 LPEVLLVRGAELPDGDG--LRTLAALLRNECGGADGRGELRAGAQAVVAALAAALFGLAI 191 +PE + R +L D L L A+ R R GA ++A LA L I Sbjct: 172 MPEAM--RACDLAQRDPAVLALLDAMEREVALN-------RIGACGILARLADVLAASII 222 Query: 192 RAWL-AQGGPQPGLLALLAHPVLQEALQAMLEAPHEDWSLPRLAALCHMSRATFVRRFQE 250 R W+ G +A + P + L A+ + P DWS+ LAAL SR++F+ +F Sbjct: 223 RGWVECACSDASGWIAAVRCPQVGRVLAAVHQHPERDWSVAELAALMGASRSSFIDKFSA 282 Query: 251 VGGATPGEVVQQLRMSQAARFLSYSKMSTAQIGEAVGYQSEAAFNRVFKKFSGMGPGAYR 310 G TP + V +++M QA +++ + A + +GY SEA+F+R FK+ G P R Sbjct: 283 AVGETPAKYVARVKMFQARHWIAREGLRVAVVANRLGYDSEASFSRAFKRIIGHPPSEAR 342 >gi|300311726|ref|YP_003775818.1| AraC family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 304 Score = 92.8 bits (229), Expect = 3e-20, Method: Compositional matrix adjust. Identities = 82/281 (29%), Positives = 120/281 (42%), Gaps = 31/281 (11%) Query: 37 GVAPYHFILEGQAQLQLAQGEPLALQAGDLVVLTRGAAHGIFTAPAAQAIAPRQGVTAAP 96 G + +LEG +L + + EP L AGD V+L P V A P Sbjct: 36 GKPSFCIMLEGSCRLAVDEQEPTTLSAGDFVLL-----------PTTPGFTISSFVPAPP 84 Query: 97 VQLHVNDDQGG--------GAQPLSDFLCGQFHFDAPHSNALVQALPEVLLVRGAELPDG 148 V L N G QP L G F F + LV LP+V+ V+G+ Sbjct: 85 VHLDPNKVPEGLELRYGEQTGQPDMRSLGGSFEFGCADPSLLVSLLPKVVHVQGS----- 139 Query: 149 DGLRTLAALLRNECGGADGRGELRAGAQAVVAALAAALFGLAIRAWLAQGGPQPGLLALL 208 L L ++ E G + G++ +++ LA L A+R+ + P PGLL L Sbjct: 140 TRLSQLVQMVGEEASGG------KPGSEFMLSRLAEMLLVEAMRSSTSTSAP-PGLLRGL 192 Query: 209 AHPVLQEALQAMLEAPHEDWSLPRLAALCHMSRATFVRRFQEVGGATPGEVVQQLRMSQA 268 L AL+ M + WS+ +LA + +SR++F RF G P + RM A Sbjct: 193 GDERLAVALKHMHARIEQRWSVAQLARIAALSRSSFFERFTRTLGVAPMAYLLAWRMEIA 252 Query: 269 ARFLSYSKMSTAQIGEAVGYQSEAAFNRVFKKFSGMGPGAY 309 L ++S ++I E GY S +AF+ F + G PG Y Sbjct: 253 RELLRRGELSVSEIAERTGYGSTSAFSVAFTRQVGQPPGLY 293 >gi|300311760|ref|YP_003775852.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 319 Score = 91.7 bits (226), Expect = 8e-20, Method: Compositional matrix adjust. Identities = 86/292 (29%), Positives = 127/292 (43%), Gaps = 56/292 (19%) Query: 41 YHFILEGQAQLQLAQGEPLALQAGDLVVLTRGAAHGIFTAPAAQAIAPRQGVTAAPVQLH 100 Y +L+G +L+ A G + L+AGD V+ A HG A LH Sbjct: 43 YCAVLDGSCRLEPAAGPAILLEAGDFVLAP--ALHGF-----------------ALTSLH 83 Query: 101 VND----DQGGGAQPLSD---------------FLCGQFHFDAPHSNALVQALPEVLLVR 141 ND D+ L D + G F++P S LV LP++++VR Sbjct: 84 TNDATLLDESNPPPLLPDGRYHLGTPEGPAEVQLVAGHCVFESPDSVLLVSLLPDLVVVR 143 Query: 142 GAELPDGDGLRTLAALLRNECGGADGRGELRAGAQAVVAALAAALFGLAIRAWLAQGGP- 200 L TL L+ +E RA A LA L L I A + P Sbjct: 144 A-----HTRLATLVQLVGDES---------RAQRPAREVVLARLLEVLLIEALRSSNDPT 189 Query: 201 ---QPGLLALLAHPVLQEALQAMLEAPHEDWSLPRLAALCHMSRATFVRRFQEVGGATPG 257 PGLL LA L +A++A+ P +DW++PRLA + +SR++F RF+ G TP Sbjct: 190 VAASPGLLRGLADVRLAQAIRALHAQPAQDWNVPRLARVAALSRSSFFERFRREVGLTPM 249 Query: 258 EVVQQLRMSQAARFLSYSKMSTAQIGEAVGYQSEAAFNRVFKKFSGMGPGAY 309 + + RM+ A R L + S A++ VGY S + F+ F + G+ P + Sbjct: 250 DYLLAWRMALAKRLLLRADGSIAEVALQVGYSSASTFSVAFSRHVGLPPSQF 301 >gi|300313807|ref|YP_003777899.1| AraC family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 299 Score = 66.6 bits (161), Expect = 3e-12, Method: Compositional matrix adjust. Identities = 38/118 (32%), Positives = 66/118 (55%), Gaps = 1/118 (0%) Query: 198 GGPQPGL-LALLAHPVLQEALQAMLEAPHEDWSLPRLAALCHMSRATFVRRFQEVGGATP 256 G P P L A L+ + A +LE + S+P +A C+MS + F+R F+ G TP Sbjct: 182 GAPAPTLRTAPLSRLHEERAKMMLLEKVKGNVSIPEIARECNMSASYFLRAFKASTGHTP 241 Query: 257 GEVVQQLRMSQAARFLSYSKMSTAQIGEAVGYQSEAAFNRVFKKFSGMGPGAYRRKMR 314 + + R+ A ++L ++++ A+I A + ++ F+RVF + G PGA+RR++R Sbjct: 242 HQWLMVQRVEMAQQYLRSTQLTLAEIALACDFYDQSHFSRVFSQVVGSTPGAWRRRLR 299 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 0.136 0.410 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: 923,951 Number of extensions: 34813 Number of successful extensions: 184 Number of sequences better than 1.0e-08: 7 Number of HSP's gapped: 182 Number of HSP's successfully gapped: 7 Length of query: 325 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 240 Effective length of database: 1,217,395 Effective search space: 292174800 Effective search space used: 292174800 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 (21.9 bits) S2: 131 (55.1 bits)