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= 0006.0056.p (380 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312761|ref|YP_003776853.1| branched-chain amino acid ABC t... 754 0.0 gi|300309516|ref|YP_003773608.1| branched-chain amino acid ABC t... 353 1e-98 gi|300310948|ref|YP_003775040.1| branched-chain amino acid ABC t... 249 4e-67 gi|300310991|ref|YP_003775083.1| branched-chain amino acid ABC t... 190 1e-49 gi|300313247|ref|YP_003777339.1| branched-chain amino acid ABC t... 131 1e-31 >gi|300312761|ref|YP_003776853.1| branched-chain amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 380 Score = 754 bits (1947), Expect = 0.0, Method: Compositional matrix adjust. Identities = 380/380 (100%), Positives = 380/380 (100%) Query: 1 MKLKSAIIPLTAAIGLAFAGAAYSQEVVKIAHVGPLSGPNAHMGKDNENGARMAVDELNA 60 MKLKSAIIPLTAAIGLAFAGAAYSQEVVKIAHVGPLSGPNAHMGKDNENGARMAVDELNA Sbjct: 1 MKLKSAIIPLTAAIGLAFAGAAYSQEVVKIAHVGPLSGPNAHMGKDNENGARMAVDELNA 60 Query: 61 KGFTIGGKKVKFELVGEDDASDPKQATAVATKLVDQKVAAVIGHLNSGTTIPASKIYSDA 120 KGFTIGGKKVKFELVGEDDASDPKQATAVATKLVDQKVAAVIGHLNSGTTIPASKIYSDA Sbjct: 61 KGFTIGGKKVKFELVGEDDASDPKQATAVATKLVDQKVAAVIGHLNSGTTIPASKIYSDA 120 Query: 121 GIPQVSPSATNPKYTQQGFKTAFRVVANDAQLGAALGKYAVQKLGTKQIAVIDDRTAYGQ 180 GIPQVSPSATNPKYTQQGFKTAFRVVANDAQLGAALGKYAVQKLGTKQIAVIDDRTAYGQ Sbjct: 121 GIPQVSPSATNPKYTQQGFKTAFRVVANDAQLGAALGKYAVQKLGTKQIAVIDDRTAYGQ 180 Query: 181 GVADEFAKGAKAAGGTIVGTQYTNDKATDFNAILTSLKGKKPDVVFFGGMDAVGGPMLRQ 240 GVADEFAKGAKAAGGTIVGTQYTNDKATDFNAILTSLKGKKPDVVFFGGMDAVGGPMLRQ Sbjct: 181 GVADEFAKGAKAAGGTIVGTQYTNDKATDFNAILTSLKGKKPDVVFFGGMDAVGGPMLRQ 240 Query: 241 MKQLGISAKFMGGDGICTGSLPGLAGDGLGDDQVICAEAGGVDEAGKKGMDDFRAAYKKK 300 MKQLGISAKFMGGDGICTGSLPGLAGDGLGDDQVICAEAGGVDEAGKKGMDDFRAAYKKK Sbjct: 241 MKQLGISAKFMGGDGICTGSLPGLAGDGLGDDQVICAEAGGVDEAGKKGMDDFRAAYKKK 300 Query: 301 FGIDVVYNAAYAYDATMTVADAMAKAGSADPKKYLPELAKISHKGVTGVIAFDAKGDIKD 360 FGIDVVYNAAYAYDATMTVADAMAKAGSADPKKYLPELAKISHKGVTGVIAFDAKGDIKD Sbjct: 301 FGIDVVYNAAYAYDATMTVADAMAKAGSADPKKYLPELAKISHKGVTGVIAFDAKGDIKD 360 Query: 361 GSLTLYTYKGGQRTLLAVTK 380 GSLTLYTYKGGQRTLLAVTK Sbjct: 361 GSLTLYTYKGGQRTLLAVTK 380 >gi|300309516|ref|YP_003773608.1| branched-chain amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 378 Score = 353 bits (906), Expect = 1e-98, Method: Compositional matrix adjust. Identities = 192/365 (52%), Positives = 245/365 (67%), Gaps = 4/365 (1%) Query: 7 IIPLTAAIGLAFAGAAYSQEVVKIAHVGPLSGPNAHMGKDNENGARMAVDELNAKGFTIG 66 II + A+ AFA A +Q VVKI PL+GP A GKDN+ G MA++ LNA+ T+G Sbjct: 10 IIAASLALIPAFAMAQETQ-VVKIGFSSPLTGPQASAGKDNQGGLMMAIERLNAQPITVG 68 Query: 67 GKKVKFELVGEDDASDPKQATAVATKLVDQKVAAVIGHLNSGTTIPASKIYSDAGIPQVS 126 GKK+KF+++ EDD +DPK AVA KL DQ V A++G NSG TIPAS++Y+DAGI V+ Sbjct: 69 GKKIKFDVIAEDDQADPKSGVAVAQKLADQGVKAIVGPYNSGVTIPASRVYNDAGI-VVA 127 Query: 127 PSATNPKYTQQGFKTAFRVVANDAQLGAALGKYAVQKLGTKQIAVIDDRTAYGQGVADEF 186 A+NPK TQQGF T FRV A+D+QLG + YA ++L K++AVIDDRTAYGQG+A EF Sbjct: 128 TVASNPKITQQGFATLFRVAASDSQLGGKMALYAAKELKFKRVAVIDDRTAYGQGLAQEF 187 Query: 187 AKGAKAAGGTIVGTQYTNDKATDFNAILTSLKGKKPDVVFFGGMDAVGGPMLRQMKQLGI 246 K AKA G +V T +TNDKATDF AILTS+KGKKPD VF GG GGP+ RQMKQLG+ Sbjct: 188 IKVAKANGIDVVSTDFTNDKATDFTAILTSIKGKKPDAVFLGGYAPQGGPIKRQMKQLGV 247 Query: 247 SAKFMGGDGICTGSLPGLAGDGLGDDQVICAEAGGVDEAGKKGMDDFRAAYKKKFGIDVV 306 MGGDGIC+ + L GD +G+ V C + G + + K+G F Y+KK+ Sbjct: 248 DVPLMGGDGICSPEMGRLGGDAIGES-VYCTQGGTMLDKAKEG-KVFSDEYQKKYNRPAE 305 Query: 307 YNAAYAYDATMTVADAMAKAGSADPKKYLPELAKISHKGVTGVIAFDAKGDIKDGSLTLY 366 A YD M +A AM +A S DPK++ P LAKIS+KGV G FDA D+K +T+Y Sbjct: 306 TYAVSFYDGMMLIAQAMKQANSVDPKQFGPALAKISYKGVAGQYDFDANHDLKQSPVTVY 365 Query: 367 TYKGG 371 +K G Sbjct: 366 RFKDG 370 >gi|300310948|ref|YP_003775040.1| branched-chain amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 394 Score = 249 bits (635), Expect = 4e-67, Method: Compositional matrix adjust. Identities = 128/342 (37%), Positives = 196/342 (57%), Gaps = 3/342 (0%) Query: 28 VKIAHVGPLSGPNAHMGKDNENGARMAVDELNAKGFTIGGKKVKFELVGEDDASDPKQAT 87 + I GPLSGP+ +GK +NG ++A+ E N +G IGGK + L+ +DD +DP A Sbjct: 40 LAIGFAGPLSGPSGGVGKSMQNGVQLALAEANRRGLRIGGKSWQLRLIAQDDRADPATAE 99 Query: 88 AVATKLVDQKVAAVIGHLNSGTTIPASKIYSDAGIPQVSPSATNPKYTQQGFKTAFRVVA 147 VA LV Q+V AV+GH SGT++ A+ +Y AG+ QV+PSA + + T + FR + Sbjct: 100 FVARSLVQQQVIAVVGHWTSGTSLAAAPVYHRAGVIQVTPSAMSRRLTAMSYPRIFRTIP 159 Query: 148 NDAQLGAALGKYAVQKLGTKQIAVIDDRTAYGQGVADEFAKGAKAAGGTIVGTQYTNDKA 207 N+ LG YAV KL T+ I IDDRT +GQG+A++FA+ A G +VG +DK Sbjct: 160 NNESLGRLAAGYAVDKLETRTIVTIDDRTPFGQGLAEQFARTASERGAQVVGRYSVSDKT 219 Query: 208 TDFNAILTSLKGKKPDVVFFGGMDAVGGPMLRQMKQLGISAKFMGGDGICTGSLPGLAGD 267 +DFNA L + +PD++FFGG+D G + + +++L + A+ M G T LP L Sbjct: 220 SDFNAALLEARKLQPDLIFFGGLDWQAGVLAKSIRRLKLHARLMASPG--TLGLPFLMRA 277 Query: 268 GLGDDQVICAEAGGVDEAGKKGMDDFRAAYKKKFGIDVVYNAAYAYDATMTVADAMAKAG 327 G + + E G + G FR Y + F D+ A +AY+A + + +AG Sbjct: 278 GPDANGALVLEPGPPQDK-MPGWKSFRQRYSENFDSDMDLYAVFAYEAAQAIIQGIRQAG 336 Query: 328 SADPKKYLPELAKISHKGVTGVIAFDAKGDIKDGSLTLYTYK 369 SADP++ + ++ +GV+G +AF+ +GD+ S T+Y K Sbjct: 337 SADPERIAEAMHRLRFEGVSGPVAFNEEGDLLQPSFTMYEVK 378 >gi|300310991|ref|YP_003775083.1| branched-chain amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 373 Score = 190 bits (483), Expect = 1e-49, Method: Compositional matrix adjust. Identities = 128/344 (37%), Positives = 185/344 (53%), Gaps = 8/344 (2%) Query: 26 EVVKIAHVGPLSGPNAHMGKDNENGARMAVDELNAKGFTIGGKKVKFELVGEDDASDPKQ 85 E VKIA GP++G A G + GA A++++NA G G KFE V DDA +PKQ Sbjct: 27 ETVKIAIAGPMTGAVAQYGDMVKAGALTAIEQINAAG---GANGNKFEAVMMDDACEPKQ 83 Query: 86 ATAVATKLVDQKVAAVIGHLNSGTTIPASKIYSDAGIPQVSPSATNPKYTQ-QGFKTAFR 144 A AVA K+V Q + VIGH+ SG+TIPAS IY + G+ ++PSAT P+ T+ + K FR Sbjct: 84 AVAVANKIVSQGIKYVIGHVCSGSTIPASDIYENEGVVMITPSATAPQLTEAKPHKFIFR 143 Query: 145 VVANDAQLGAALGKYAVQKLGTKQIAVIDDRTAYGQGVADEFAKGAKAAGGTIVGTQYTN 204 + D Q G A +Y ++KL K++AV+ D+ +YGQGVA AA +V + N Sbjct: 144 TIGRDDQQGPAAARYVIEKLKPKKVAVLHDKQSYGQGVASSVKAALDAAKVPVVVFEGIN 203 Query: 205 DKATDFNAILTSLKGKKPDVVFFGGMDAVGGPMLRQMKQLGISAKFMGGDGICTGSLPGL 264 +D++AI+T LK + D V+FGG G ++RQ ++ GI A FMG +G+ + + Sbjct: 204 AGDSDYSAIVTKLKSQGVDFVYFGGYHPEMGLIMRQAREQGIKAVFMGPEGVGNKDITAI 263 Query: 265 AGDGLGDDQVICAEAGGVDEAGKKGMDDFRAAYKKKFGIDVVYNAAYAYDATMTVADAMA 324 AG V D A + F AA + G + AY +ADA+A Sbjct: 264 AGPASEGMLVTLPADFAADPANAALVKAFAAAKRDPNGPFQM----PAYSGVKIIADAIA 319 Query: 325 KAGSADPKKYLPELAKISHKGVTGVIAFDAKGDIKDGSLTLYTY 368 A S DP+K + S K G + +D KGD+K ++T+ Sbjct: 320 GAKSTDPEKVAAYIHANSFKTPIGNVEYDKKGDLKSFKFVVFTW 363 >gi|300313247|ref|YP_003777339.1| branched-chain amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 385 Score = 131 bits (329), Expect = 1e-31, Method: Compositional matrix adjust. Identities = 102/360 (28%), Positives = 168/360 (46%), Gaps = 19/360 (5%) Query: 16 LAFAGAAYSQE--VVKIAHVGPLSGPNAHMGKDNENGARMAVDELNAKGFTIGGKK---V 70 AF A ++QE + + G LS P + + GA++A+DE NA + K+ + Sbjct: 17 WAFMQAGWAQERKTIALGFTGRLSEP---IAQSALQGAQLAIDEANA----LAAKRRSPL 69 Query: 71 KFELVGEDDASDPKQATAVATKLVDQKVAAVIGHLNSGTTIPASKIYSDAGIPQVSPSAT 130 +FEL+ +DD + A +A V +KVA VIG +S + + IY A IPQ+ +AT Sbjct: 70 RFELLPQDDHGNENFAVNIARYYVKEKVAGVIGPWSSDAALATAAIYESAQIPQIGFTAT 129 Query: 131 NPKYTQQGFKTAFRVVANDAQLGAALGKYAVQKLGTKQIAVIDDRTAYGQGVADEFAKGA 190 + ++T G + FRVV +L A L + A + L ++I VI AY + +AD + Sbjct: 130 SSQWTGMGNRMPFRVVGGTRELAATLAEVATRSLQGRRIFVIQSDAAYSRALADTLVENL 189 Query: 191 KAAGGTIVGTQY-TNDKATDFNAILTSLKGKKPDVVFFGGMDAVGGPMLRQMKQLGISAK 249 + I +Y ++TDF+A L + + + DV+ F G+ + + +A+ Sbjct: 190 GGSAQQIALARYQVGRRSTDFHAALKAAEAHQADVIVFVGLYPQARAFIDGANRTRTTAR 249 Query: 250 FMGGDGICTGSLPGLAGDGLGDDQVICAEAGGVDEAGKKGMDDFRAAYKKKFGIDVVYNA 309 + G SLP L V+ E K + Y+++FG + Sbjct: 250 LLLTGGASNLSLPAPLELRL---HVLEYEIARPHCPQWKVVTQ---TYQRRFGAAPTTYS 303 Query: 310 AYAYDATMTVADAMAKAGSADPKKYLPELAKISHKGVTGVIAFDAKGDIKDGSLTLYTYK 369 YAYDA + A+ +AGS + K L ++ H G+ G ++FDA G TL Y+ Sbjct: 304 FYAYDAASVLTAAIVQAGSDNGDKIATALHRMRHAGLHGTLSFDATGANAHPRYTLLRYQ 363 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 0.314 0.133 0.375 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: 1,093,286 Number of extensions: 44232 Number of successful extensions: 173 Number of sequences better than 1.0e-08: 17 Number of HSP's gapped: 158 Number of HSP's successfully gapped: 17 Length of query: 380 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 293 Effective length of database: 1,207,925 Effective search space: 353922025 Effective search space used: 353922025 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 131 (55.1 bits)