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= 0003.0082.p (627 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313111|ref|YP_003777203.1| TRAP-type C4-dicarboxylate tran... 1090 0.0 gi|300310440|ref|YP_003774532.1| TrapT dctQ-M fusion permease, d... 647 0.0 gi|300310180|ref|YP_003774272.1| TRAP-type C4-dicarboxylate tran... 155 9e-39 gi|300311996|ref|YP_003776088.1| TRAP-type C4-dicarboxylate tran... 108 2e-24 >gi|300313111|ref|YP_003777203.1| TRAP-type C4-dicarboxylate transport system dctQ-M fusion permease large permease [Herbaspirillum seropedicae SmR1] Length = 627 Score = 1090 bits (2819), Expect = 0.0, Method: Compositional matrix adjust. Identities = 614/627 (97%), Positives = 621/627 (99%) Query: 1 MMEAAMTYRAPVNMNPAARALVAFNRMVMHVVGAVAAALVVAETVVLLTGVIYRYALHDP 60 MMEAAMTYRAPVNMNP ARALVA NRMVMH+VGAVAAALV+AETVVLLTGVIYRYALHDP Sbjct: 1 MMEAAMTYRAPVNMNPVARALVALNRMVMHLVGAVAAALVLAETVVLLTGVIYRYALHDP 60 Query: 61 LVWSDELASILFIWLSMLGAVLALDRGEHMRLTAIINMCSEKGRVWLETVAALVVCIFVL 120 LVWSDELASILFIWLSMLGAVLALDRGEHMRLTAIIN CSEKGR+WLETVAALVVCIFVL Sbjct: 61 LVWSDELASILFIWLSMLGAVLALDRGEHMRLTAIINKCSEKGRIWLETVAALVVCIFVL 120 Query: 121 MVIHPAVDHAVEQMPITTPALEIPDGLRAAALPVGAILMLLAAVSRMAAMTTMRLLLSAL 180 MVIHPAVDHAVEQMPITTPALEIPDGLRAAALPVGAILMLLAAVSRMAAMTTMRLLLSAL Sbjct: 121 MVIHPAVDHAVEQMPITTPALEIPDGLRAAALPVGAILMLLAAVSRMAAMTTMRLLLSAL 180 Query: 181 AVVAVIAGALWLAKPMLLGMGNYNLIVFFVLLIGVCVAGGIPIAFAFGTATMAYLALATT 240 AVVAVI GALWLAKPMLLGMGNYNLIVFFVLLIGVCVAGGIPIAFAFGTATMAYLALATT Sbjct: 181 AVVAVIGGALWLAKPMLLGMGNYNLIVFFVLLIGVCVAGGIPIAFAFGTATMAYLALATT 240 Query: 241 APLMIVVSRMDEGMSSLILLSVPLFVLLGSLLEMSGLAKTLIDFMAALLGHVRGGLQYVL 300 APLMIVVSRMDEGMSSLILLSVPLFVLLGSLLEMSGLAKTLIDFMAALLGHVRGGLQYVL Sbjct: 241 APLMIVVSRMDEGMSSLILLSVPLFVLLGSLLEMSGLAKTLIDFMAALLGHVRGGLQYVL 300 Query: 301 LGAMFLVSGISGSKAADMAAIAPALFPEMKKRGSKPEELVALLSSSGAMTETIPPSLVLI 360 LGAMFLVSGISGSKAADMAAIAPALFPEMKKRGSKPEELVALLSSSGAMTETIPPSLVLI Sbjct: 301 LGAMFLVSGISGSKAADMAAIAPALFPEMKKRGSKPEELVALLSSSGAMTETIPPSLVLI 360 Query: 361 TIGAVCSVSITALFIGGLMPAAIATIAIAVVCWMRARREPMPDVKRAPVSLIVKTLIAAI 420 TIGAVCSVSITALFIGGLMPAAIATIAIAVVCWMRARREPMPDVKRAP+SLIVK LIAAI Sbjct: 361 TIGAVCSVSITALFIGGLMPAAIATIAIAVVCWMRARREPMPDVKRAPLSLIVKALIAAI 420 Query: 421 PALALPMLIRVAVIEGVATATEVATIGVAYTVVVGLIMHLFLKHLNFKRLYPMLIESAAL 480 PALALPMLIRVAVIEGVATATEVATIGVAYTVVVGLIMHLF++HL+FKRLYPMLIESAAL Sbjct: 421 PALALPMLIRVAVIEGVATATEVATIGVAYTVVVGLIMHLFMRHLSFKRLYPMLIESAAL 480 Query: 481 SGAILLIIGMATAMAWALTQSGFSAKLVALMQGVPGGGAGFLLITIVIFIVLGSLLEGIP 540 SGAILLIIGMATAMAWALTQSGFSAKLVALMQGVPGGG GFLLITIVIFIVLGSLLEGIP Sbjct: 481 SGAILLIIGMATAMAWALTQSGFSAKLVALMQGVPGGGVGFLLITIVIFIVLGSLLEGIP 540 Query: 541 AIVLFGPLLFPVARSLGVHDVHYAMVVILAMGIGLFAPPFGVGFYAACAIGKVSPDGVFN 600 AIVLFGPLLFPVARSLGVHDVHYAMVVILAMGIGLFAPPFGVGFYAACAIGKVSPDGVFN Sbjct: 541 AIVLFGPLLFPVARSLGVHDVHYAMVVILAMGIGLFAPPFGVGFYAACAIGKVSPDGVFN 600 Query: 601 RVWGYLAALVVALLVVAFVPWISIGFL 627 RVWGYLAALVVALLVVAFVPWISIGFL Sbjct: 601 RVWGYLAALVVALLVVAFVPWISIGFL 627 >gi|300310440|ref|YP_003774532.1| TrapT dctQ-M fusion permease, dicarboxylate transport protein [Herbaspirillum seropedicae SmR1] Length = 618 Score = 647 bits (1670), Expect = 0.0, Method: Compositional matrix adjust. Identities = 351/592 (59%), Positives = 463/592 (78%), Gaps = 5/592 (0%) Query: 36 AAALVVAETVVLLTGVIYRYALHDPLVWSDELASILFIWLSMLGAVLALDRGEHMRLTAI 95 AAALVV E VLL GVI R+ ++P+ W+DELASILF+WL+ LGA +AL RG HMR T + Sbjct: 32 AAALVVGEVAVLLAGVIMRFIFNNPIPWADELASILFLWLANLGAAVALRRGTHMRTTVL 91 Query: 96 INMCSEKGRVWLETVAALVVCIFVLMVIHPAVDHAVEQMPITTPALEIPDGLRAAALPVG 155 + SE+G+ W E +A + C+ +L+++HP ++A ++M + TPAL P+ +RAAA+ VG Sbjct: 92 VGFMSERGKAWAEALAIIAPCVMLLILMHPMWEYAEDEMFVQTPALGWPNTVRAAAVAVG 151 Query: 156 AILMLLAAVSRMAAMTTMRLLLSALAVVAVIAGALWLAKPMLLGMGNYNLIVFFVLLIGV 215 A LM+ ++ R++ + L+ LA++AV+AGA++L L +GN+NL+VFF L++ V Sbjct: 152 AALMIALSLLRISRQKLVDLV-GVLALLAVVAGAMYLGAAWLQAIGNWNLVVFFGLVLAV 210 Query: 216 CVAGGIPIAFAFGTATMAYLALATTAPLMIVVSRMDEGMSSLILLSVPLFVLLGSLLEMS 275 V GIPIAF FG AT+A++ TT+PL +V R DEGMSSLILL+VPLF+LLG L+EM+ Sbjct: 211 SVLLGIPIAFCFGLATVAFMLTVTTSPLAVVAGRFDEGMSSLILLAVPLFILLGHLVEMT 270 Query: 276 GLAKTLIDFMAALLGHVRGGLQYVLLGAMFLVSGISGSKAADMAAIAPALFPEMKKRGSK 335 G+AK ++DF+A+LLGHVRGGL YVLLGAM LVSGISG+K ADMAA+AP L PEMK+RG+ Sbjct: 271 GMAKAMVDFLASLLGHVRGGLNYVLLGAMLLVSGISGAKTADMAAVAPVLLPEMKRRGNH 330 Query: 336 PEELVALLSSSGAMTETIPPSLVLITIGAVCSVSITALFIGGLMPAAIATIAIAVVCWMR 395 EL++LL++SGAM ETIPPSLVLITIG+V VSI ALF GG+MP + + +A++ R Sbjct: 331 EGELISLLAASGAMAETIPPSLVLITIGSVAGVSIAALFTGGIMPGIVLAVLLAILARWR 390 Query: 396 ARREPMPDVKRAPVSLIVKTLIAAIPALALPMLIRVAVIEGVATATEVATIGVAYTVVVG 455 + E M ++RAP ++++TLI A+PAL LP+LIR AV+EGVATATEV+TIG+AY+VV G Sbjct: 391 S-AEIMEGIQRAPGRVVLRTLIIALPALLLPILIRTAVVEGVATATEVSTIGIAYSVVAG 449 Query: 456 LIMHLFLKHLNFKRLYPMLIESAALSGAILLIIGMATAMAWALTQSGFSAKLVALMQGVP 515 L+++ + ++KRLYPML+++AALSGAIL IIG AT M+WALTQSGFS L M VP Sbjct: 450 LLVY---RKFDWKRLYPMLVDTAALSGAILFIIGTATGMSWALTQSGFSHALAEAMTSVP 506 Query: 516 GGGAGFLLITIVIFIVLGSLLEGIPAIVLFGPLLFPVARSLGVHDVHYAMVVILAMGIGL 575 GG GFLL++I FIVLGS+LEGIPA+VLF PLLFPVA+++GVH+VHYAMV+IL+MG+GL Sbjct: 507 GGKYGFLLVSIAAFIVLGSVLEGIPAMVLFAPLLFPVAKAIGVHEVHYAMVIILSMGVGL 566 Query: 576 FAPPFGVGFYAACAIGKVSPDGVFNRVWGYLAALVVALLVVAFVPWISIGFL 627 FAPPFG+G+YAAC IG+V PD R+W YL ALVV LL+VAFVPW SIGFL Sbjct: 567 FAPPFGLGYYAACTIGRVHPDVAVKRIWPYLGALVVGLLIVAFVPWFSIGFL 618 >gi|300310180|ref|YP_003774272.1| TRAP-type C4-dicarboxylate transport system large permease [Herbaspirillum seropedicae SmR1] Length = 426 Score = 155 bits (392), Expect = 9e-39, Method: Compositional matrix adjust. Identities = 107/389 (27%), Positives = 203/389 (52%), Gaps = 4/389 (1%) Query: 204 NLIVFFVLLIGVCVAGGIPIAFAFGTATMAYLALATTAPLMIVVSRMDEGMSSLILLSVP 263 N ++ FVLL + + G +PI+ + G + +L T P+ V ++ G+ ++++P Sbjct: 2 NALIIFVLLFALMLTG-MPISISLGLTVLTFLFTMTEVPIQSVALKLFTGIEKFEIMAIP 60 Query: 264 LFVLLGSLLEMSGLAKTLIDFMAALLGHVRGGLQYVLLGAMFLVSGISGSKAADMAAIAP 323 F+L G+ L G+A+ +I+F +++GH GGL + A L + +SGS A + AI Sbjct: 61 FFILAGNFLTHGGVARRMINFATSMVGHWHGGLALAGVLACALFAAVSGSSPATVVAIGS 120 Query: 324 ALFPEMKKRGSKPEELVALLSSSGAMTETIPPSLVLITIGAVCSVSITALFIGGLMPAAI 383 + P M K+G ++++SGA+ IPPS+V++ + S+ LF+ G++P + Sbjct: 121 IILPAMVKQGFPNRFGAGVITTSGALGILIPPSIVMVMYSVSTNTSVGKLFMAGVVPGLL 180 Query: 384 ATIAIAVVCWMRARREPMPDVKRAPVSLIVKTLIAAIPALALPMLIRVAVIEGVATATEV 443 + V W AR+ P +K+A + + L L +++ + GV T TE Sbjct: 181 LAFLLGVTTWFLARKNNYPRLKKATWAERAAAFRKSGWGLFLIVIVMGGIYTGVFTPTEA 240 Query: 444 ATIGVAYTVVVGLIMHLFLKHLNFKRLYPMLIESAALSGAILLIIGMATAMAWALTQSGF 503 A + Y + + ++ K L K++ +L++SA++S +L II A ++ +T Sbjct: 241 AAMAAVYAFFIAVFVY---KDLTLKQVPKVLLDSASMSAMLLYIITNAVLFSFLVTSENI 297 Query: 504 SAKLVALMQGVPGGGAGFLLITIVIFIVLGSLLEGIPAIVLFGPLLFPVARSLGVHDVHY 563 + A + G FLL+ ++ ++ G+++E +++ P+LFPVA LG+ VH+ Sbjct: 298 PQAMAAWITDSGLGPITFLLVVNILLLLAGNVMEPSSIVLILAPILFPVAMKLGIDPVHF 357 Query: 564 AMVVILAMGIGLFAPPFGVGFYAACAIGK 592 +++++ M +G+ PP G+ Y A I K Sbjct: 358 GILIVVNMEVGMCHPPVGLNLYVASGITK 386 >gi|300311996|ref|YP_003776088.1| TRAP-type C4-dicarboxylate transport system large permease [Herbaspirillum seropedicae SmR1] Length = 449 Score = 108 bits (269), Expect = 2e-24, Method: Compositional matrix adjust. Identities = 114/434 (26%), Positives = 208/434 (47%), Gaps = 36/434 (8%) Query: 215 VCVAGGIPIAFAFGTATMAYLAL-ATTAPLMIVVSRMDEGMSSLILLSVPLFVLLGSLLE 273 V + G+PIAFA G ++ + L + + E ++S+ LLS+PLF+L G+ + Sbjct: 16 VVMCSGMPIAFALGVVATGFMYFFMPESSLDTITQNVYEEIASITLLSIPLFILKGAAIG 75 Query: 274 MSGLAKTLIDFMAALLGHVRGGLQYVLLGAMFLVSGISGSKAADMAAIAPALFPEMKKRG 333 S K L + A L V GGL + A L + ++GS A +AI A PEM++RG Sbjct: 76 KSPAGKDLYSAIHAWLNKVPGGLGIANVFACALFAAMAGSSPATCSAIGSAGIPEMRRRG 135 Query: 334 SKPEELVALLSSSGAMTETIPPSLVLITIGAVCSVSITALFIGGLMPAAIATIAIAVVCW 393 P ++++ G + +PPS+ +I S+ LF+ G+ P + + A Sbjct: 136 YSPGFAAGIIAAGGTLGILLPPSITMILYAVAAEQSLGRLFLAGIGPGVLLVLLFAGYAV 195 Query: 394 MRARRE---------------PMPDVKRAPVSLIVKTLIAAIPALALPMLIRVAVIEGVA 438 RAR+E D + ++ V+ L +P L L + + VA+ G+A Sbjct: 196 YRARKEYRLAHAVYSAGGAKSAYLDDEHFTLAQKVEMLPRVLPFLILLIGVMVALYGGLA 255 Query: 439 TATEVATIGVAYTVVVGLIMHLFLKHLNFKRLYPMLIESAALSGAILLIIGMATAMAWAL 498 T +E A +G +V+ +++ K + + P L + SG +LLIIGM+ ++ + Sbjct: 256 TPSETAGLGALLALVLIAVVYRIYKP---REIAPFLSSTIKESGMLLLIIGMSLLYSYVM 312 Query: 499 TQ---SGFSAKLVALMQGVPGGGAGFLLITIVI--FIVLGSLLEGIPAIVLFGPLLFPVA 553 + S +A+ V + + +LL+ +++ IVLG L + I++ P++ P Sbjct: 313 SYLHISQSAAQWVVDLH-----LSKWLLLAVILGMVIVLGFFLPPVSIILMTAPIILPPL 367 Query: 554 RSLGVHDVHYAMVVILAMGIGLFAPPFGVGFYAACAIGKVSPD----GVFNRVWGYLAAL 609 ++ G + + +V+ + M +GL PP G+ + I ++PD V +LA + Sbjct: 368 KAAGFDLIWFGIVMTVVMEMGLIHPPVGLNLF---VIKNIAPDIALGDVIKGTIPFLALM 424 Query: 610 VVALLVVAFVPWIS 623 +A+L++ P I+ Sbjct: 425 FLAVLLLCMFPGIA 438 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 0.329 0.141 0.412 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: 1,601,673 Number of extensions: 58781 Number of successful extensions: 447 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 436 Number of HSP's successfully gapped: 4 Length of query: 627 Length of database: 1,619,870 Length adjustment: 91 Effective length of query: 536 Effective length of database: 1,188,985 Effective search space: 637295960 Effective search space used: 637295960 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 133 (55.8 bits)