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= 0001.2727.p (449 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311996|ref|YP_003776088.1| TRAP-type C4-dicarboxylate tran... 865 0.0 gi|300310180|ref|YP_003774272.1| TRAP-type C4-dicarboxylate tran... 214 2e-56 gi|300310440|ref|YP_003774532.1| TrapT dctQ-M fusion permease, d... 132 7e-32 gi|300313111|ref|YP_003777203.1| TRAP-type C4-dicarboxylate tran... 96 5e-21 >gi|300311996|ref|YP_003776088.1| TRAP-type C4-dicarboxylate transport system large permease [Herbaspirillum seropedicae SmR1] Length = 449 Score = 865 bits (2235), Expect = 0.0, Method: Compositional matrix adjust. Identities = 442/449 (98%), Positives = 448/449 (99%) Query: 1 MSPLTLGVLYGVVTILVMCSGMPIAFALGVVATGFMYFFMPESSLDTITQNVYEEIASIT 60 MSPLTLGVLYGVVTI+VMCSGMPIAFALGVVATGFMYFFMPESSLDTITQNVYEEIASIT Sbjct: 1 MSPLTLGVLYGVVTIVVMCSGMPIAFALGVVATGFMYFFMPESSLDTITQNVYEEIASIT 60 Query: 61 LLSIPLFILKGAAIGKSPAGKDLYSAIHAWLNKVPGGLGIANVFACALFAAMAGSSPATC 120 LLSIPLFILKGAAIGKSPAGKDLYSAIHAWLNKVPGGLGIANVFACALFAAMAGSSPATC Sbjct: 61 LLSIPLFILKGAAIGKSPAGKDLYSAIHAWLNKVPGGLGIANVFACALFAAMAGSSPATC 120 Query: 121 SAIGSAGIPEMRRRGYSPGFAAGIIAAGGTLGILLPPSITMILYAVAAEQSLGRLFLAGI 180 SAIGSAGIPEMRRRGYSPGFAAGIIAAGGTLGILLPPSITMILYAVAAEQSLGRLFLAGI Sbjct: 121 SAIGSAGIPEMRRRGYSPGFAAGIIAAGGTLGILLPPSITMILYAVAAEQSLGRLFLAGI 180 Query: 181 GPGVLLVILFAGYAVFRARKEYKLAHAVYTAGGAKSAYLDDEHFTLAQKVEMLPRVLPFL 240 GPGVLLV+LFAGYAV+RARKEY+LAHAVY+AGGAKSAYLDDEHFTLAQKVEMLPRVLPFL Sbjct: 181 GPGVLLVLLFAGYAVYRARKEYRLAHAVYSAGGAKSAYLDDEHFTLAQKVEMLPRVLPFL 240 Query: 241 ILLIGVMVALYGGLATPSETAGLGALLALVLIAVVYRIYKPREIAPFLSSTIKESGMLLL 300 ILLIGVMVALYGGLATPSETAGLGALLALVLIAVVYRIYKPREIAPFLSSTIKESGMLLL Sbjct: 241 ILLIGVMVALYGGLATPSETAGLGALLALVLIAVVYRIYKPREIAPFLSSTIKESGMLLL 300 Query: 301 IIGMSLLYSYVMSYLHISQSAAQWVVDLHLSKWLLLAVILAMVIVLGFFLPPVSIILMTA 360 IIGMSLLYSYVMSYLHISQSAAQWVVDLHLSKWLLLAVIL MVIVLGFFLPPVSIILMTA Sbjct: 301 IIGMSLLYSYVMSYLHISQSAAQWVVDLHLSKWLLLAVILGMVIVLGFFLPPVSIILMTA 360 Query: 361 PIILPPLKAAGFDLIWFGIVMTVVMEMGLIHPPVGLNLFVIKNIAPDIALGDVIKGTIPF 420 PIILPPLKAAGFDLIWFGIVMTVVMEMGLIHPPVGLNLFVIKNIAPDIALGDVIKGTIPF Sbjct: 361 PIILPPLKAAGFDLIWFGIVMTVVMEMGLIHPPVGLNLFVIKNIAPDIALGDVIKGTIPF 420 Query: 421 LALMFLAVLLLCMFPGIATVLPDLLMGAK 449 LALMFLAVLLLCMFPGIAT+LPDLLMGAK Sbjct: 421 LALMFLAVLLLCMFPGIATLLPDLLMGAK 449 >gi|300310180|ref|YP_003774272.1| TRAP-type C4-dicarboxylate transport system large permease [Herbaspirillum seropedicae SmR1] Length = 426 Score = 214 bits (544), Expect = 2e-56, Method: Compositional matrix adjust. Identities = 144/429 (33%), Positives = 238/429 (55%), Gaps = 17/429 (3%) Query: 17 VMCSGMPIAFALGVVATGFMYFFMPESSLDTITQNVYEEIASITLLSIPLFILKGAAIGK 76 +M +GMPI+ +LG+ F+ F M E + ++ ++ I +++IP FIL G + Sbjct: 13 LMLTGMPISISLGLTVLTFL-FTMTEVPIQSVALKLFTGIEKFEIMAIPFFILAGNFLTH 71 Query: 77 SPAGKDLYSAIHAWLNKVPGGLGIANVFACALFAAMAGSSPATCSAIGSAGIPEMRRRGY 136 + + + + + GGL +A V ACALFAA++GSSPAT AIGS +P M ++G+ Sbjct: 72 GGVARRMINFATSMVGHWHGGLALAGVLACALFAAVSGSSPATVVAIGSIILPAMVKQGF 131 Query: 137 SPGFAAGIIAAGGTLGILLPPSITMILYAVAAEQSLGRLFLAGIGPGVLLVILFAGYAVF 196 F AG+I G LGIL+PPSI M++Y+V+ S+G+LF+AG+ PG+LL L F Sbjct: 132 PNRFGAGVITTSGALGILIPPSIVMVMYSVSTNTSVGKLFMAGVVPGLLLAFLLGVTTWF 191 Query: 197 RARKEYKLAHAVYTAGGAKSAYLDDEHFTLAQKVEMLPRVLPFLILLIGVMVALYGGLAT 256 AR K+ Y + T A++ + L L++ VM +Y G+ T Sbjct: 192 LAR---------------KNNYPRLKKATWAERAAAFRKSGWGLFLIVIVMGGIYTGVFT 236 Query: 257 PSETAGLGALLALVLIAVVYRIYKPREIAPFLSSTIKESGMLLLIIGMSLLYSYVMSYLH 316 P+E A + A+ A + VY+ +++ L + S MLL II ++L+S++++ + Sbjct: 237 PTEAAAMAAVYAFFIAVFVYKDLTLKQVPKVLLDSASMSAMLLYIITNAVLFSFLVTSEN 296 Query: 317 ISQSAAQWVVDLHLSKWLLLAVILAMVIVLGFFLPPVSIILMTAPIILPPLKAAGFDLIW 376 I Q+ A W+ D L L V+ ++++ G + P SI+L+ API+ P G D + Sbjct: 297 IPQAMAAWITDSGLGPITFLLVVNILLLLAGNVMEPSSIVLILAPILFPVAMKLGIDPVH 356 Query: 377 FGIVMTVVMEMGLIHPPVGLNLFVIKNIAPDIALGDVIKGTIPFLALMFLAVLLLCMFPG 436 FGI++ V ME+G+ HPPVGLNL+V I + + ++ +P+L M + L+ +P Sbjct: 357 FGILIVVNMEVGMCHPPVGLNLYVASGIT-KMGITELTIAVMPWLLTMLGFLALVTYWPA 415 Query: 437 IATVLPDLL 445 ++ LP+L+ Sbjct: 416 LSLWLPNLI 424 >gi|300310440|ref|YP_003774532.1| TrapT dctQ-M fusion permease, dicarboxylate transport protein [Herbaspirillum seropedicae SmR1] Length = 618 Score = 132 bits (331), Expect = 7e-32, Method: Compositional matrix adjust. Identities = 121/434 (27%), Positives = 210/434 (48%), Gaps = 24/434 (5%) Query: 5 TLGVLYGVVTILVMCSGMPIAFALGVVATGFMYFFMPESSLDTITQNVYEEIASITLLSI 64 L V +G+V + + G+PIAF G+ FM + S L + E ++S+ LL++ Sbjct: 199 NLVVFFGLVLAVSVLLGIPIAFCFGLATVAFM-LTVTTSPLAVVAGRFDEGMSSLILLAV 257 Query: 65 PLFILKGAAIGKSPAGKDLYSAIHAWLNKVPGGLGIANVFACALFAAMAGSSPATCSAIG 124 PLFIL G + + K + + + L V GGL + A L + ++G+ A +A+ Sbjct: 258 PLFILLGHLVEMTGMAKAMVDFLASLLGHVRGGLNYVLLGAMLLVSGISGAKTADMAAVA 317 Query: 125 SAGIPEMRRRGYSPGFAAGIIAAGGTLGILLPPSITMILYAVAAEQSLGRLFLAGIGPGV 184 +PEM+RRG G ++AA G + +PPS+ +I A S+ LF GI PG+ Sbjct: 318 PVLLPEMKRRGNHEGELISLLAASGAMAETIPPSLVLITIGSVAGVSIAALFTGGIMPGI 377 Query: 185 LLVILFAGYAVFRARKEYKLAHAVYTAGGAKSAYLDDEHFTLAQKVEMLPRVLPFLILLI 244 +L +L A A +R+ ++ + A G + A + +L R Sbjct: 378 VLAVLLAILARWRSA---EIMEGIQRAPG-RVVLRTLIIALPALLLPILIR--------- 424 Query: 245 GVMVALYGGLATPSETAGLGALLALVLIAVVYRIYKPREIAPFLSSTIKESGMLLLIIGM 304 A+ G+AT +E + +G ++V +VYR + + + P L T SG +L IIG Sbjct: 425 ---TAVVEGVATATEVSTIGIAYSVVAGLLVYRKFDWKRLYPMLVDTAALSGAILFIIGT 481 Query: 305 SLLYSYVMSYLHISQSAAQWVVDLHLSKWLLLAVILAMVIVLGFFLPPVSIILMTAPIIL 364 + S+ ++ S + A+ + + K+ L V +A IVLG L + +++ AP++ Sbjct: 482 ATGMSWALTQSGFSHALAEAMTSVPGGKYGFLLVSIAAFIVLGSVLEGIPAMVLFAPLLF 541 Query: 365 PPLKAAGFDLIWFGIVMTVVMEMGLIHPPVGLNLF---VIKNIAPDIALGDVIKGTIPFL 421 P KA G + + +V+ + M +GL PP GL + I + PD+A +K P+L Sbjct: 542 PVAKAIGVHEVHYAMVIILSMGVGLFAPPFGLGYYAACTIGRVHPDVA----VKRIWPYL 597 Query: 422 ALMFLAVLLLCMFP 435 + + +L++ P Sbjct: 598 GALVVGLLIVAFVP 611 >gi|300313111|ref|YP_003777203.1| TRAP-type C4-dicarboxylate transport system dctQ-M fusion permease large permease [Herbaspirillum seropedicae SmR1] Length = 627 Score = 96.3 bits (238), Expect = 5e-21, Method: Compositional matrix adjust. Identities = 105/393 (26%), Positives = 185/393 (47%), Gaps = 22/393 (5%) Query: 21 GMPIAFALGVVATGFMYFFMPESSLDTITQNVYEEIASITLLSIPLFILKGAAIGKSPAG 80 G+PIAFA G ++ + L + + E ++S+ LLS+PLF+L G+ + S Sbjct: 220 GIPIAFAFGTATMAYLAL-ATTAPLMIVVSRMDEGMSSLILLSVPLFVLLGSLLEMSGLA 278 Query: 81 KDLYSAIHAWLNKVPGGLGIANVFACALFAAMAGSSPATCSAIGSAGIPEMRRRGYSPGF 140 K L + A L V GGL + A L + ++GS A +AI A PEM++RG P Sbjct: 279 KTLIDFMAALLGHVRGGLQYVLLGAMFLVSGISGSKAADMAAIAPALFPEMKKRGSKPEE 338 Query: 141 AAGIIAAGGTLGILLPPSITMILYAVAAEQSLGRLFLAGIGPGVLLVILFAGYAVFRARK 200 ++++ G + +PPS+ +I S+ LF+ G+ P + I A RAR+ Sbjct: 339 LVALLSSSGAMTETIPPSLVLITIGAVCSVSITALFIGGLMPAAIATIAIAVVCWMRARR 398 Query: 201 EYKLAHAVYTAGGAKSAYLDDEHFTLAQKVEMLPRVLPFLILLIGVMVALYGGLATPSET 260 E D + L+ V+ L +P L L + + VA+ G+AT +E Sbjct: 399 E---------------PMPDVKRAPLSLIVKALIAAIPALALPMLIRVAVIEGVATATEV 443 Query: 261 AGLGALLALVLIAVVY---RIYKPREIAPFLSSTIKESGMLLLIIGMSLLYSYVMSYLHI 317 A +G +V+ +++ R + + P L + SG +LLIIGM+ ++ ++ Sbjct: 444 ATIGVAYTVVVGLIMHLFMRHLSFKRLYPMLIESAALSGAILLIIGMATAMAWALTQSGF 503 Query: 318 SQSAAQWVVDLHLSKWLLLAVILAMVIVLGFFLPPVSIILMTAPIILPPLKAAGFDLIWF 377 S + + L + + + IVLG L + I++ P++ P ++ G + + Sbjct: 504 SAKLVALMQGVPGGGVGFLLITIVIFIVLGSLLEGIPAIVLFGPLLFPVARSLGVHDVHY 563 Query: 378 GIVMTVVMEMGLIHPPVGLNLF---VIKNIAPD 407 +V+ + M +GL PP G+ + I ++PD Sbjct: 564 AMVVILAMGIGLFAPPFGVGFYAACAIGKVSPD 596 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 0.328 0.144 0.426 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: 1,208,746 Number of extensions: 45322 Number of successful extensions: 266 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 258 Number of HSP's successfully gapped: 4 Length of query: 449 Length of database: 1,619,870 Length adjustment: 88 Effective length of query: 361 Effective length of database: 1,203,190 Effective search space: 434351590 Effective search space used: 434351590 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 (21.7 bits) S2: 132 (55.5 bits)