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= 0002.0089.p (351 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310948|ref|YP_003775040.1| branched-chain amino acid ABC t... 255 3e-69 gi|300312761|ref|YP_003776853.1| branched-chain amino acid ABC t... 168 7e-43 gi|300309516|ref|YP_003773608.1| branched-chain amino acid ABC t... 145 3e-36 gi|300313247|ref|YP_003777339.1| branched-chain amino acid ABC t... 132 3e-32 gi|300310991|ref|YP_003775083.1| branched-chain amino acid ABC t... 92 6e-20 >gi|300310948|ref|YP_003775040.1| branched-chain amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 394 Score = 255 bits (652), Expect = 3e-69, Method: Compositional matrix adjust. Identities = 134/352 (38%), Positives = 209/352 (59%), Gaps = 3/352 (0%) Query: 2 VVTIGFAAPLAEFSARQGR---NAAQLAIEEINKGNPSINGRAVVFELLEQDDKADPRIS 58 + IGFA PL+ S G+ N QLA+ E N+ I G++ L+ QDD+ADP + Sbjct: 39 TLAIGFAGPLSGPSGGVGKSMQNGVQLALAEANRRGLRIGGKSWQLRLIAQDDRADPATA 98 Query: 59 EFVARTLANSKAIGVVGHWTSATTGAAAPIYHGAGLAQISPFAWSRSLTQKSYRTIFQII 118 EFVAR+L + I VVGHWTS T+ AAAP+YH AG+ Q++P A SR LT SY IF+ I Sbjct: 99 EFVARSLVQQQVIAVVGHWTSGTSLAAAPVYHRAGVIQVTPSAMSRRLTAMSYPRIFRTI 158 Query: 119 GSDDLGLALAADYLVGEQKLKRVLVLDDGGFLGISMADYFSDHVKAADGEIIQRMSISGN 178 +++ LAA Y V + + + ++ +DD G +A+ F+ +++ R S+S Sbjct: 159 PNNESLGRLAAGYAVDKLETRTIVTIDDRTPFGQGLAEQFARTASERGAQVVGRYSVSDK 218 Query: 179 TSDFNQPLLKARESQAELIFFSGRMIQSDVLARNLQRFHLQAKLLLTGLVVSPAFLKNAG 238 TSDFN LL+AR+ Q +LIFF G Q+ VLA++++R L A+L+ + + FL AG Sbjct: 219 TSDFNAALLEARKLQPDLIFFGGLDWQAGVLAKSIRRLKLHARLMASPGTLGLPFLMRAG 278 Query: 239 DVDSAVLAIVPSTPLDKRPGMSALQKKYAERYGSEMLPFAVYFYDSVQLLAAAAKKANSL 298 + L + P P DK PG + +++Y+E + S+M +AV+ Y++ Q + ++A S Sbjct: 279 PDANGALVLEPGPPQDKMPGWKSFRQRYSENFDSDMDLYAVFAYEAAQAIIQGIRQAGSA 338 Query: 299 ERAKIVNALHEIRYSGISANIAFDANGALLKPGYTLYSYERKGWTPVRVFTG 350 + +I A+H +R+ G+S +AF+ G LL+P +T+Y + + W PV F G Sbjct: 339 DPERIAEAMHRLRFEGVSGPVAFNEEGDLLQPSFTMYEVKDQRWQPVARFNG 390 >gi|300312761|ref|YP_003776853.1| branched-chain amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 380 Score = 168 bits (425), Expect = 7e-43, Method: Compositional matrix adjust. Identities = 107/344 (31%), Positives = 178/344 (51%), Gaps = 8/344 (2%) Query: 2 VVTIGFAAPLAEFSARQGR---NAAQLAIEEINKGNPSINGRAVVFELLEQDDKADPRIS 58 VV I PL+ +A G+ N A++A++E+N +I G+ V FEL+ +DD +DP+ + Sbjct: 27 VVKIAHVGPLSGPNAHMGKDNENGARMAVDELNAKGFTIGGKKVKFELVGEDDASDPKQA 86 Query: 59 EFVARTLANSKAIGVVGHWTSATTGAAAPIYHGAGLAQISPFAWSRSLTQKSYRTIFQII 118 VA L + K V+GH S TT A+ IY AG+ Q+SP A + TQ+ ++T F+++ Sbjct: 87 TAVATKLVDQKVAAVIGHLNSGTTIPASKIYSDAGIPQVSPSATNPKYTQQGFKTAFRVV 146 Query: 119 GSD-DLGLALAADYLVGEQKLKRVLVLDDGGFLGISMADYFSDHVKAADGEIIQRMSISG 177 +D LG AL Y V + K++ V+DD G +AD F+ KAA G I+ + Sbjct: 147 ANDAQLGAAL-GKYAVQKLGTKQIAVIDDRTAYGQGVADEFAKGAKAAGGTIVGTQYTND 205 Query: 178 NTSDFNQPLLKARESQAELIFFSGRMIQSDVLARNLQRFHLQAKLLLTGLVVSPAFLKNA 237 +DFN L + + +++FF G + R +++ + AK + + + + A Sbjct: 206 KATDFNAILTSLKGKKPDVVFFGGMDAVGGPMLRQMKQLGISAKFMGGDGICTGSLPGLA 265 Query: 238 GDV---DSAVLAIVPSTPLDKRPGMSALQKKYAERYGSEMLPFAVYFYDSVQLLAAAAKK 294 GD D + A + GM + Y +++G +++ A Y YD+ +A A K Sbjct: 266 GDGLGDDQVICAEAGGVDEAGKKGMDDFRAAYKKKFGIDVVYNAAYAYDATMTVADAMAK 325 Query: 295 ANSLERAKIVNALHEIRYSGISANIAFDANGALLKPGYTLYSYE 338 A S + K + L +I + G++ IAFDA G + TLY+Y+ Sbjct: 326 AGSADPKKYLPELAKISHKGVTGVIAFDAKGDIKDGSLTLYTYK 369 >gi|300309516|ref|YP_003773608.1| branched-chain amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 378 Score = 145 bits (367), Expect = 3e-36, Method: Compositional matrix adjust. Identities = 99/342 (28%), Positives = 171/342 (50%), Gaps = 7/342 (2%) Query: 2 VVTIGFAAPLAEFSARQGRN---AAQLAIEEINKGNPSINGRAVVFELLEQDDKADPRIS 58 VV IGF++PL A G++ +AIE +N ++ G+ + F+++ +DD+ADP+ Sbjct: 29 VVKIGFSSPLTGPQASAGKDNQGGLMMAIERLNAQPITVGGKKIKFDVIAEDDQADPKSG 88 Query: 59 EFVARTLANSKAIGVVGHWTSATTGAAAPIYHGAGLAQISPFAWSRSLTQKSYRTIFQII 118 VA+ LA+ +VG + S T A+ +Y+ AG+ ++ A + +TQ+ + T+F++ Sbjct: 89 VAVAQKLADQGVKAIVGPYNSGVTIPASRVYNDAGIV-VATVASNPKITQQGFATLFRVA 147 Query: 119 GSD-DLGLALAADYLVGEQKLKRVLVLDDGGFLGISMADYFSDHVKAADGEIIQRMSISG 177 SD LG +A Y E K KRV V+DD G +A F KA +++ + Sbjct: 148 ASDSQLGGKMAL-YAAKELKFKRVAVIDDRTAYGQGLAQEFIKVAKANGIDVVSTDFTND 206 Query: 178 NTSDFNQPLLKARESQAELIFFSGRMIQSDVLARNLQRFHLQAKLLLTGLVVSPAFLKNA 237 +DF L + + + +F G Q + R +++ + L+ + SP + Sbjct: 207 KATDFTAILTSIKGKKPDAVFLGGYAPQGGPIKRQMKQLGVDVPLMGGDGICSPEMGRLG 266 Query: 238 GD-VDSAVLAIVPSTPLDKRPGMSALQKKYAERYGSEMLPFAVYFYDSVQLLAAAAKKAN 296 GD + +V T LDK +Y ++Y +AV FYD + L+A A K+AN Sbjct: 267 GDAIGESVYCTQGGTMLDKAKEGKVFSDEYQKKYNRPAETYAVSFYDGMMLIAQAMKQAN 326 Query: 297 SLERAKIVNALHEIRYSGISANIAFDANGALLKPGYTLYSYE 338 S++ + AL +I Y G++ FDAN L + T+Y ++ Sbjct: 327 SVDPKQFGPALAKISYKGVAGQYDFDANHDLKQSPVTVYRFK 368 >gi|300313247|ref|YP_003777339.1| branched-chain amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 385 Score = 132 bits (333), Expect = 3e-32, Method: Compositional matrix adjust. Identities = 105/356 (29%), Positives = 164/356 (46%), Gaps = 22/356 (6%) Query: 2 VVTIGFAAPLAEFSARQGRNAAQLAIEEIN-----KGNPSINGRAVVFELLEQDDKADPR 56 + +GF L+E A+ AQLAI+E N + +P + FELL QDD + Sbjct: 30 TIALGFTGRLSEPIAQSALQGAQLAIDEANALAAKRRSP------LRFELLPQDDHGNEN 83 Query: 57 ISEFVARTLANSKAIGVVGHWTSATTGAAAPIYHGAGLAQISPFAWSRSLTQKSYRTIFQ 116 + +AR K GV+G W+S A A IY A + QI A S T R F+ Sbjct: 84 FAVNIARYYVKEKVAGVIGPWSSDAALATAAIYESAQIPQIGFTATSSQWTGMGNRMPFR 143 Query: 117 IIGSDDLGLALAADYLVGEQKLKRVLVLDDGGFLGISMADYFSDHVKAADGEI-IQRMSI 175 ++G A A+ + +R+ V+ ++AD +++ + +I + R + Sbjct: 144 VVGGTRELAATLAEVATRSLQGRRIFVIQSDAAYSRALADTLVENLGGSAQQIALARYQV 203 Query: 176 SGNTSDFNQPLLKARESQAELIFFSGRMIQSDVLARNLQRFHLQAKLLLTGLVVS---PA 232 ++DF+ L A QA++I F G Q+ R A+LLLTG + PA Sbjct: 204 GRRSTDFHAALKAAEAHQADVIVFVGLYPQARAFIDGANRTRTTARLLLTGGASNLSLPA 263 Query: 233 FLKNAGDVDSAVLAIVPSTPLDKRPGMSALQKKYAERYGSEMLPFAVYFYDSVQLLAAAA 292 L ++ VL + P P + + Y R+G+ ++ Y YD+ +L AA Sbjct: 264 PL----ELRLHVLEYEIARP--HCPQWKVVTQTYQRRFGAAPTTYSFYAYDAASVLTAAI 317 Query: 293 KKANSLERAKIVNALHEIRYSGISANIAFDANGALLKPGYTLYSYERKGWTPVRVF 348 +A S KI ALH +R++G+ ++FDA GA P YTL Y+ + W V VF Sbjct: 318 VQAGSDNGDKIATALHRMRHAGLHGTLSFDATGANAHPRYTLLRYQER-WQAVEVF 372 >gi|300310991|ref|YP_003775083.1| branched-chain amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 373 Score = 92.0 bits (227), Expect = 6e-20, Method: Compositional matrix adjust. Identities = 87/341 (25%), Positives = 152/341 (44%), Gaps = 8/341 (2%) Query: 3 VTIGFAAPLAEFSARQG---RNAAQLAIEEINKGNPSINGRAVVFELLEQDDKADPRISE 59 V I A P+ A+ G + A AIE+IN NG FE + DD +P+ + Sbjct: 29 VKIAIAGPMTGAVAQYGDMVKAGALTAIEQINAAG-GANGNK--FEAVMMDDACEPKQAV 85 Query: 60 FVARTLANSKAIGVVGHWTSATTGAAAPIYHGAGLAQISPFAWSRSLTQ-KSYRTIFQII 118 VA + + V+GH S +T A+ IY G+ I+P A + LT+ K ++ IF+ I Sbjct: 86 AVANKIVSQGIKYVIGHVCSGSTIPASDIYENEGVVMITPSATAPQLTEAKPHKFIFRTI 145 Query: 119 GSDDLGLALAADYLVGEQKLKRVLVLDDGGFLGISMADYFSDHVKAADGEIIQRMSISGN 178 G DD AA Y++ + K K+V VL D G +A + AA ++ I+ Sbjct: 146 GRDDQQGPAAARYVIEKLKPKKVAVLHDKQSYGQGVASSVKAALDAAKVPVVVFEGINAG 205 Query: 179 TSDFNQPLLKARESQAELIFFSGRMIQSDVLARNLQRFHLQAKLLLTGLVVSPAFLKNAG 238 SD++ + K + + ++F G + ++ R + ++A + V + AG Sbjct: 206 DSDYSAIVTKLKSQGVDFVYFGGYHPEMGLIMRQAREQGIKAVFMGPEGVGNKDITAIAG 265 Query: 239 DVDSAVLAIVPSTPLDKRPGMSALQKKYAERYGSEMLPFAVYFYDSVQLLAAAAKKANSL 298 +L +P+ P +AL K +A PF + Y V+++A A A S Sbjct: 266 PASEGMLVTLPAD-FAADPANAALVKAFAAAKRDPNGPFQMPAYSGVKIIADAIAGAKST 324 Query: 299 ERAKIVNALHEIRYSGISANIAFDANGALLKPGYTLYSYER 339 + K+ +H + N+ +D G L + ++++ + Sbjct: 325 DPEKVAAYIHANSFKTPIGNVEYDKKGDLKSFKFVVFTWHK 365 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 0.134 0.379 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: 1,006,361 Number of extensions: 37484 Number of successful extensions: 157 Number of sequences better than 1.0e-08: 5 Number of HSP's gapped: 149 Number of HSP's successfully gapped: 5 Length of query: 351 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 265 Effective length of database: 1,212,660 Effective search space: 321354900 Effective search space used: 321354900 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: 131 (55.1 bits)