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= 0029.0003.p (388 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... 276 1e-75 gi|300312761|ref|YP_003776853.1| branched-chain amino acid ABC t... 251 6e-68 gi|300309516|ref|YP_003773608.1| branched-chain amino acid ABC t... 206 2e-54 gi|300313247|ref|YP_003777339.1| branched-chain amino acid ABC t... 167 1e-42 gi|300310991|ref|YP_003775083.1| branched-chain amino acid ABC t... 120 2e-28 >gi|300310948|ref|YP_003775040.1| branched-chain amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 394 Score = 276 bits (707), Expect = 1e-75, Method: Compositional matrix adjust. Identities = 140/347 (40%), Positives = 203/347 (58%) Query: 33 TVLIGLAAPMSGPSGSTGVSLERAAQLAVDDINNSKPVIAGEPVLFKLLPQDDRADPRTG 92 T+ IG A P+SGPSG G S++ QLA+ + N I G+ +L+ QDDRADP T Sbjct: 39 TLAIGFAGPLSGPSGGVGKSMQNGVQLALAEANRRGLRIGGKSWQLRLIAQDDRADPATA 98 Query: 93 ELIADYFVKSKVAAVVGHWNSGVGIPAARIYAAAGIPHVAPAVTAPAYTQQGDASAFRIV 152 E +A V+ +V AVVGHW SG + AA +Y AG+ V P+ + T FR + Sbjct: 99 EFVARSLVQQQVIAVVGHWTSGTSLAAAPVYHRAGVIQVTPSAMSRRLTAMSYPRIFRTI 158 Query: 153 PHDGEGARLTADYVVRELKGVNVAVIDDSTVFGSTYADEFVKSLTTLQGRVTGRYAVSSK 212 P++ RL A Y V +L+ + IDD T FG A++F ++ + +V GRY+VS K Sbjct: 159 PNNESLGRLAAGYAVDKLETRTIVTIDDRTPFGQGLAEQFARTASERGAQVVGRYSVSDK 218 Query: 213 TSDFNSILRSIRDSHPDVVFFAGLDAQAAQLVQDLRRLQIRAPLVGIGGLVGPTFLKLAG 272 TSDFN+ L R PD++FF GLD QA L + +RRL++ A L+ G +G FL AG Sbjct: 219 TSDFNAALLEARKLQPDLIFFGGLDWQAGVLAKSIRRLKLHARLMASPGTLGLPFLMRAG 278 Query: 273 AAGEGVSVVEPGLPSYKGPQWSHFEQAWKARYQDEIYLYAPFAYDAVRVIAAAMREADSV 332 G V+EPG P K P W F Q + + ++ LYA FAY+A + I +R+A S Sbjct: 279 PDANGALVLEPGPPQDKMPGWKSFRQRYSENFDSDMDLYAVFAYEAAQAIIQGIRQAGSA 338 Query: 333 EPAKVTASLHRIRYKGISGTIAFDAQGNLRDPVFTLYRVSGGRWRVV 379 +P ++ ++HR+R++G+SG +AF+ +G+L P FT+Y V RW+ V Sbjct: 339 DPERIAEAMHRLRFEGVSGPVAFNEEGDLLQPSFTMYEVKDQRWQPV 385 >gi|300312761|ref|YP_003776853.1| branched-chain amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 380 Score = 251 bits (641), Expect = 6e-68, Method: Compositional matrix adjust. Identities = 142/377 (37%), Positives = 210/377 (55%), Gaps = 16/377 (4%) Query: 9 LLLALALAGAGCFFASGSAVAQARTVLIGLAAPMSGPSGSTGVSLERAAQLAVDDINNSK 68 L A+ LA AG ++ V I P+SGP+ G E A++AVD++N Sbjct: 10 LTAAIGLAFAGAAYSQ-------EVVKIAHVGPLSGPNAHMGKDNENGARMAVDELNAKG 62 Query: 69 PVIAGEPVLFKLLPQDDRADPRTGELIADYFVKSKVAAVVGHWNSGVGIPAARIYAAAGI 128 I G+ V F+L+ +DD +DP+ +A V KVAAV+GH NSG IPA++IY+ AGI Sbjct: 63 FTIGGKKVKFELVGEDDASDPKQATAVATKLVDQKVAAVIGHLNSGTTIPASKIYSDAGI 122 Query: 129 PHVAPAVTAPAYTQQGDASAFRIVPHDGEGARLTADYVVRELKGVNVAVIDDSTVFGSTY 188 P V+P+ T P YTQQG +AFR+V +D + Y V++L +AVIDD T +G Sbjct: 123 PQVSPSATNPKYTQQGFKTAFRVVANDAQLGAALGKYAVQKLGTKQIAVIDDRTAYGQGV 182 Query: 189 ADEFVKSLTTLQGRVTGRYAVSSKTSDFNSILRSIRDSHPDVVFFAGLDAQAAQLVQDLR 248 ADEF K G + G + K +DFN+IL S++ PDVVFF G+DA +++ ++ Sbjct: 183 ADEFAKGAKAAGGTIVGTQYTNDKATDFNAILTSLKGKKPDVVFFGGMDAVGGPMLRQMK 242 Query: 249 RLQIRAPLVGIGGLVGPTFLKLAGAAGEG-----VSVVEPGLPSYKGPQ-WSHFEQAWKA 302 +L I A +G G+ + L G AG+G V E G G + F A+K Sbjct: 243 QLGISAKFMGGDGICTGS---LPGLAGDGLGDDQVICAEAGGVDEAGKKGMDDFRAAYKK 299 Query: 303 RYQDEIYLYAPFAYDAVRVIAAAMREADSVEPAKVTASLHRIRYKGISGTIAFDAQGNLR 362 ++ ++ A +AYDA +A AM +A S +P K L +I +KG++G IAFDA+G+++ Sbjct: 300 KFGIDVVYNAAYAYDATMTVADAMAKAGSADPKKYLPELAKISHKGVTGVIAFDAKGDIK 359 Query: 363 DPVFTLYRVSGGRWRVV 379 D TLY GG+ ++ Sbjct: 360 DGSLTLYTYKGGQRTLL 376 >gi|300309516|ref|YP_003773608.1| branched-chain amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 378 Score = 206 bits (525), Expect = 2e-54, Method: Compositional matrix adjust. Identities = 119/346 (34%), Positives = 183/346 (52%), Gaps = 2/346 (0%) Query: 30 QARTVLIGLAAPMSGPSGSTGVSLERAAQLAVDDINNSKPVIAGEPVLFKLLPQDDRADP 89 + + V IG ++P++GP S G + +A++ +N + G+ + F ++ +DD+ADP Sbjct: 26 ETQVVKIGFSSPLTGPQASAGKDNQGGLMMAIERLNAQPITVGGKKIKFDVIAEDDQADP 85 Query: 90 RTGELIADYFVKSKVAAVVGHWNSGVGIPAARIYAAAGIPHVAPAVTAPAYTQQGDASAF 149 ++G +A V A+VG +NSGV IPA+R+Y AGI VA + P TQQG A+ F Sbjct: 86 KSGVAVAQKLADQGVKAIVGPYNSGVTIPASRVYNDAGI-VVATVASNPKITQQGFATLF 144 Query: 150 RIVPHDGEGARLTADYVVRELKGVNVAVIDDSTVFGSTYADEFVKSLTTLQGRVTGRYAV 209 R+ D + A Y +ELK VAVIDD T +G A EF+K V Sbjct: 145 RVAASDSQLGGKMALYAAKELKFKRVAVIDDRTAYGQGLAQEFIKVAKANGIDVVSTDFT 204 Query: 210 SSKTSDFNSILRSIRDSHPDVVFFAGLDAQAAQLVQDLRRLQIRAPLVGIGGLVGPTFLK 269 + K +DF +IL SI+ PD VF G Q + + +++L + PL+G G+ P + Sbjct: 205 NDKATDFTAILTSIKGKKPDAVFLGGYAPQGGPIKRQMKQLGVDVPLMGGDGICSPEMGR 264 Query: 270 LAG-AAGEGVSVVEPGLPSYKGPQWSHFEQAWKARYQDEIYLYAPFAYDAVRVIAAAMRE 328 L G A GE V + G K + F ++ +Y YA YD + +IA AM++ Sbjct: 265 LGGDAIGESVYCTQGGTMLDKAKEGKVFSDEYQKKYNRPAETYAVSFYDGMMLIAQAMKQ 324 Query: 329 ADSVEPAKVTASLHRIRYKGISGTIAFDAQGNLRDPVFTLYRVSGG 374 A+SV+P + +L +I YKG++G FDA +L+ T+YR G Sbjct: 325 ANSVDPKQFGPALAKISYKGVAGQYDFDANHDLKQSPVTVYRFKDG 370 >gi|300313247|ref|YP_003777339.1| branched-chain amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 385 Score = 167 bits (424), Expect = 1e-42, Method: Compositional matrix adjust. Identities = 113/354 (31%), Positives = 174/354 (49%), Gaps = 19/354 (5%) Query: 32 RTVLIGLAAPMSGPSGSTGVSLERAAQLAVDDINNSKPVIAGEPVLFKLLPQDDRADPRT 91 +T+ +G +S P + + + AQLA+D+ N + P+ F+LLPQDD + Sbjct: 29 KTIALGFTGRLSEPIAQSAL---QGAQLAIDEAN-ALAAKRRSPLRFELLPQDDHGNENF 84 Query: 92 GELIADYFVKSKVAAVVGHWNSGVGIPAARIYAAAGIPHVAPAVTAPAYTQQGDASAFRI 151 IA Y+VK KVA V+G W+S + A IY +A IP + T+ +T G+ FR+ Sbjct: 85 AVNIARYYVKEKVAGVIGPWSSDAALATAAIYESAQIPQIGFTATSSQWTGMGNRMPFRV 144 Query: 152 VPHDGEGARLTADYVVRELKGVNVAVIDDSTVFGSTYADEFVKSL-TTLQGRVTGRYAVS 210 V E A A+ R L+G + VI + AD V++L + Q RY V Sbjct: 145 VGGTRELAATLAEVATRSLQGRRIFVIQSDAAYSRALADTLVENLGGSAQQIALARYQVG 204 Query: 211 SKTSDFNSILRSIRDSHPDVVFFAGLDAQAAQLVQDLRRLQIRAPLVGIGG-----LVGP 265 +++DF++ L++ DV+ F GL QA + R + A L+ GG L P Sbjct: 205 RRSTDFHAALKAAEAHQADVIVFVGLYPQARAFIDGANRTRTTARLLLTGGASNLSLPAP 264 Query: 266 TFLKLAGAAGEGVSVVEPGLPSYKGPQWSHFEQAWKARYQDEIYLYAPFAYDAVRVIAAA 325 L+L V+E + PQW Q ++ R+ Y+ +AYDA V+ AA Sbjct: 265 LELRL--------HVLEYEIARPHCPQWKVVTQTYQRRFGAAPTTYSFYAYDAASVLTAA 316 Query: 326 MREADSVEPAKVTASLHRIRYKGISGTIAFDAQGNLRDPVFTLYRVSGGRWRVV 379 + +A S K+ +LHR+R+ G+ GT++FDA G P +TL R RW+ V Sbjct: 317 IVQAGSDNGDKIATALHRMRHAGLHGTLSFDATGANAHPRYTLLRYQ-ERWQAV 369 >gi|300310991|ref|YP_003775083.1| branched-chain amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 373 Score = 120 bits (301), Expect = 2e-28, Method: Compositional matrix adjust. Identities = 93/341 (27%), Positives = 160/341 (46%), Gaps = 5/341 (1%) Query: 30 QARTVLIGLAAPMSGPSGSTGVSLERAAQLAVDDINNSKPVIAGEPVLFKLLPQDDRADP 89 A TV I +A PM+G G ++ A A++ IN + + F+ + DD +P Sbjct: 25 HAETVKIAIAGPMTGAVAQYGDMVKAGALTAIEQINAAGGANGNK---FEAVMMDDACEP 81 Query: 90 RTGELIADYFVKSKVAAVVGHWNSGVGIPAARIYAAAGIPHVAPAVTAPAYTQ-QGDASA 148 + +A+ V + V+GH SG IPA+ IY G+ + P+ TAP T+ + Sbjct: 82 KQAVAVANKIVSQGIKYVIGHVCSGSTIPASDIYENEGVVMITPSATAPQLTEAKPHKFI 141 Query: 149 FRIVPHDGEGARLTADYVVRELKGVNVAVIDDSTVFGSTYADEFVKSLTTLQGRVTGRYA 208 FR + D + A YV+ +LK VAV+ D +G A +L + V Sbjct: 142 FRTIGRDDQQGPAAARYVIEKLKPKKVAVLHDKQSYGQGVASSVKAALDAAKVPVVVFEG 201 Query: 209 VSSKTSDFNSILRSIRDSHPDVVFFAGLDAQAAQLVQDLRRLQIRAPLVGIGGLVGPTFL 268 +++ SD+++I+ ++ D V+F G + +++ R I+A +G G+ Sbjct: 202 INAGDSDYSAIVTKLKSQGVDFVYFGGYHPEMGLIMRQAREQGIKAVFMGPEGVGNKDIT 261 Query: 269 KLAGAAGEGVSVVEPGLPSYKGPQWSHFEQAWKARYQDEIYLYAPFAYDAVRVIAAAMRE 328 +AG A EG+ V P P + +A+ A +D + AY V++IA A+ Sbjct: 262 AIAGPASEGMLVTLPA-DFAADPANAALVKAFAAAKRDPNGPFQMPAYSGVKIIADAIAG 320 Query: 329 ADSVEPAKVTASLHRIRYKGISGTIAFDAQGNLRDPVFTLY 369 A S +P KV A +H +K G + +D +G+L+ F ++ Sbjct: 321 AKSTDPEKVAAYIHANSFKTPIGNVEYDKKGDLKSFKFVVF 361 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 0.135 0.393 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: 1,165,099 Number of extensions: 52446 Number of successful extensions: 262 Number of sequences better than 1.0e-08: 8 Number of HSP's gapped: 248 Number of HSP's successfully gapped: 8 Length of query: 388 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 301 Effective length of database: 1,207,925 Effective search space: 363585425 Effective search space used: 363585425 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)