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= 0001.0708.p (426 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310180|ref|YP_003774272.1| TRAP-type C4-dicarboxylate tran... 773 0.0 gi|300311996|ref|YP_003776088.1| TRAP-type C4-dicarboxylate tran... 217 2e-57 gi|300310440|ref|YP_003774532.1| TrapT dctQ-M fusion permease, d... 172 6e-44 gi|300313111|ref|YP_003777203.1| TRAP-type C4-dicarboxylate tran... 157 2e-39 >gi|300310180|ref|YP_003774272.1| TRAP-type C4-dicarboxylate transport system large permease [Herbaspirillum seropedicae SmR1] Length = 426 Score = 773 bits (1997), Expect = 0.0, Method: Compositional matrix adjust. Identities = 414/426 (97%), Positives = 420/426 (98%) Query: 1 MNALIIFVLLFGLMLTGMPISISLGLTVLTFLFTMTDVPIQSVALKLFTGIEKFEIMAIP 60 MNALIIFVLLF LMLTGMPISISLGLTVLTFLFTMT+VPIQSVALKLFTGIEKFEIMAIP Sbjct: 1 MNALIIFVLLFALMLTGMPISISLGLTVLTFLFTMTEVPIQSVALKLFTGIEKFEIMAIP 60 Query: 61 FFILAGNFLTHGGVARRMINFATSMVGHWYGGLALAGVLACALFAAVSGSSPATVVAIGS 120 FFILAGNFLTHGGVARRMINFATSMVGHW+GGLALAGVLACALFAAVSGSSPATVVAIGS Sbjct: 61 FFILAGNFLTHGGVARRMINFATSMVGHWHGGLALAGVLACALFAAVSGSSPATVVAIGS 120 Query: 121 IILPAMVKQGFPNRFGAGVITTSGALGILIPPSIVMVMYSVSTNTSVGKLFMAGVVPGLL 180 IILPAMVKQGFPNRFGAGVITTSGALGILIPPSIVMVMYSVSTNTSVGKLFMAGVVPGLL Sbjct: 121 IILPAMVKQGFPNRFGAGVITTSGALGILIPPSIVMVMYSVSTNTSVGKLFMAGVVPGLL 180 Query: 181 LAFLLGLTTWYLARKNNYPRLRKATWAERFAAFRKSGWGLFLIVIVMGGIYTGVFTPTEA 240 LAFLLG+TTW+LARKNNYPRL+KATWAER AAFRKSGWGLFLIVIVMGGIYTGVFTPTEA Sbjct: 181 LAFLLGVTTWFLARKNNYPRLKKATWAERAAAFRKSGWGLFLIVIVMGGIYTGVFTPTEA 240 Query: 241 AAMAAVYAFFISVFVYKDLRLSQVPKVLLDSASMSAMLLYIITNAVLFSFLVTSENIPQA 300 AAMAAVYAFFI+VFVYKDL L QVPKVLLDSASMSAMLLYIITNAVLFSFLVTSENIPQA Sbjct: 241 AAMAAVYAFFIAVFVYKDLTLKQVPKVLLDSASMSAMLLYIITNAVLFSFLVTSENIPQA 300 Query: 301 MAAWITDSGLGPITFLLVVNILLLLAGNVMEPSSIVLILAPILFPVAMKLGIDPVHFGIL 360 MAAWITDSGLGPITFLLVVNILLLLAGNVMEPSSIVLILAPILFPVAMKLGIDPVHFGIL Sbjct: 301 MAAWITDSGLGPITFLLVVNILLLLAGNVMEPSSIVLILAPILFPVAMKLGIDPVHFGIL 360 Query: 361 IVVNMEVGMCHPPVGLNLYVASGITKMGITELTIAVMPWLLTMLGFLMLVTYWPTLSLWL 420 IVVNMEVGMCHPPVGLNLYVASGITKMGITELTIAVMPWLLTMLGFL LVTYWP LSLWL Sbjct: 361 IVVNMEVGMCHPPVGLNLYVASGITKMGITELTIAVMPWLLTMLGFLALVTYWPALSLWL 420 Query: 421 PNLIYN 426 PNLIYN Sbjct: 421 PNLIYN 426 >gi|300311996|ref|YP_003776088.1| TRAP-type C4-dicarboxylate transport system large permease [Herbaspirillum seropedicae SmR1] Length = 449 Score = 217 bits (552), Expect = 2e-57, Method: Compositional matrix adjust. Identities = 146/431 (33%), Positives = 240/431 (55%), Gaps = 21/431 (4%) Query: 13 LMLTGMPISISLGLTVLTFL-FTMTDVPIQSVALKLFTGIEKFEIMAIPFFILAGNFLTH 71 +M +GMPI+ +LG+ F+ F M + + ++ ++ I +++IP FIL G + Sbjct: 17 VMCSGMPIAFALGVVATGFMYFFMPESSLDTITQNVYEEIASITLLSIPLFILKGAAIGK 76 Query: 72 GGVARRMINFATSMVGHWYGGLALAGVLACALFAAVSGSSPATVVAIGSIILPAMVKQGF 131 + + + + + GGL +A V ACALFAA++GSSPAT AIGS +P M ++G+ Sbjct: 77 SPAGKDLYSAIHAWLNKVPGGLGIANVFACALFAAMAGSSPATCSAIGSAGIPEMRRRGY 136 Query: 132 PNRFGAGVITTSGALGILIPPSIVMVMYSVSTNTSVGKLFMAGVVPGLLLAFLLGLTTWY 191 F AG+I G LGIL+PPSI M++Y+V+ S+G+LF+AG+ PG+LL L Y Sbjct: 137 SPGFAAGIIAAGGTLGILLPPSITMILYAVAAEQSLGRLFLAGIGPGVLLVLLFAGYAVY 196 Query: 192 LARKNNYPRLRKATWA-----------ERFAAFRKSGW------GLFLIVIVMGGIYTGV 234 ARK RL A ++ E F +K L L++ VM +Y G+ Sbjct: 197 RARKEY--RLAHAVYSAGGAKSAYLDDEHFTLAQKVEMLPRVLPFLILLIGVMVALYGGL 254 Query: 235 FTPTEAAAMAAVYAFFISVFVYKDLRLSQVPKVLLDSASMSAMLLYIITNAVLFSFLVTS 294 TP+E A + A+ A + VY+ + ++ L + S MLL II ++L+S++++ Sbjct: 255 ATPSETAGLGALLALVLIAVVYRIYKPREIAPFLSSTIKESGMLLLIIGMSLLYSYVMSY 314 Query: 295 ENIPQAMAAWITDSGLGPITFLLVVNILLLLAGNVMEPSSIVLILAPILFPVAMKLGIDP 354 +I Q+ A W+ D L L V+ ++++ G + P SI+L+ API+ P G D Sbjct: 315 LHISQSAAQWVVDLHLSKWLLLAVILGMVIVLGFFLPPVSIILMTAPIILPPLKAAGFDL 374 Query: 355 VHFGILIVVNMEVGMCHPPVGLNLYVASGIT-KMGITELTIAVMPWLLTMLGFLMLVTYW 413 + FGI++ V ME+G+ HPPVGLNL+V I + + ++ +P+L M ++L+ + Sbjct: 375 IWFGIVMTVVMEMGLIHPPVGLNLFVIKNIAPDIALGDVIKGTIPFLALMFLAVLLLCMF 434 Query: 414 PTLSLWLPNLI 424 P ++ LP+L+ Sbjct: 435 PGIATLLPDLL 445 >gi|300310440|ref|YP_003774532.1| TrapT dctQ-M fusion permease, dicarboxylate transport protein [Herbaspirillum seropedicae SmR1] Length = 618 Score = 172 bits (435), Expect = 6e-44, Method: Compositional matrix adjust. Identities = 123/420 (29%), Positives = 218/420 (51%), Gaps = 12/420 (2%) Query: 7 FVLLFGLMLT-----GMPISISLGLTVLTFLFTMTDVPIQSVALKLFTGIEKFEIMAIPF 61 V+ FGL+L G+PI+ GL + F+ T+T P+ VA + G+ ++A+P Sbjct: 200 LVVFFGLVLAVSVLLGIPIAFCFGLATVAFMLTVTTSPLAVVAGRFDEGMSSLILLAVPL 259 Query: 62 FILAGNFLTHGGVARRMINFATSMVGHWYGGLALAGVLACALFAAVSGSSPATVVAIGSI 121 FIL G+ + G+A+ M++F S++GH GGL + A L + +SG+ A + A+ + Sbjct: 260 FILLGHLVEMTGMAKAMVDFLASLLGHVRGGLNYVLLGAMLLVSGISGAKTADMAAVAPV 319 Query: 122 ILPAMVKQGFPNRFGAGVITTSGALGILIPPSIVMVMYSVSTNTSVGKLFMAGVVPGLLL 181 +LP M ++G ++ SGA+ IPPS+V++ S+ LF G++PG++L Sbjct: 320 LLPEMKRRGNHEGELISLLAASGAMAETIPPSLVLITIGSVAGVSIAALFTGGIMPGIVL 379 Query: 182 AFLLGLTTWYLARKNNYPRLRKATWAERFAAFRKSGWGLFLIVIVMG---GIYTGVFTPT 238 A LL + LAR + + A R L +++ + + GV T T Sbjct: 380 AVLLAI----LARWRSAEIMEGIQRAPGRVVLRTLIIALPALLLPILIRTAVVEGVATAT 435 Query: 239 EAAAMAAVYAFFISVFVYKDLRLSQVPKVLLDSASMSAMLLYIITNAVLFSFLVTSENIP 298 E + + Y+ + VY+ ++ +L+D+A++S +L+II A S+ +T Sbjct: 436 EVSTIGIAYSVVAGLLVYRKFDWKRLYPMLVDTAALSGAILFIIGTATGMSWALTQSGFS 495 Query: 299 QAMAAWITDSGLGPITFLLVVNILLLLAGNVMEPSSIVLILAPILFPVAMKLGIDPVHFG 358 A+A +T G FLLV ++ G+V+E +++ AP+LFPVA +G+ VH+ Sbjct: 496 HALAEAMTSVPGGKYGFLLVSIAAFIVLGSVLEGIPAMVLFAPLLFPVAKAIGVHEVHYA 555 Query: 359 ILIVVNMEVGMCHPPVGLNLYVASGITKMGITELTIAVMPWLLTMLGFLMLVTYWPTLSL 418 ++I+++M VG+ PP GL Y A I ++ + P+L ++ L++V + P S+ Sbjct: 556 MVIILSMGVGLFAPPFGLGYYAACTIGRVHPDVAVKRIWPYLGALVVGLLIVAFVPWFSI 615 >gi|300313111|ref|YP_003777203.1| TRAP-type C4-dicarboxylate transport system dctQ-M fusion permease large permease [Herbaspirillum seropedicae SmR1] Length = 627 Score = 157 bits (396), Expect = 2e-39, Method: Compositional matrix adjust. Identities = 105/389 (26%), Positives = 205/389 (52%), Gaps = 4/389 (1%) Query: 2 NALIIFVLLFGLMLTG-MPISISLGLTVLTFLFTMTDVPIQSVALKLFTGIEKFEIMAIP 60 N ++ FVLL G+ + G +PI+ + G + +L T P+ V ++ G+ ++++P Sbjct: 204 NLIVFFVLLIGVCVAGGIPIAFAFGTATMAYLALATTAPLMIVVSRMDEGMSSLILLSVP 263 Query: 61 FFILAGNFLTHGGVARRMINFATSMVGHWYGGLALAGVLACALFAAVSGSSPATVVAIGS 120 F+L G+ L G+A+ +I+F +++GH GGL + A L + +SGS A + AI Sbjct: 264 LFVLLGSLLEMSGLAKTLIDFMAALLGHVRGGLQYVLLGAMFLVSGISGSKAADMAAIAP 323 Query: 121 IILPAMVKQGFPNRFGAGVITTSGALGILIPPSIVMVMYSVSTNTSVGKLFMAGVVPGLL 180 + P M K+G ++++SGA+ IPPS+V++ + S+ LF+ G++P + Sbjct: 324 ALFPEMKKRGSKPEELVALLSSSGAMTETIPPSLVLITIGAVCSVSITALFIGGLMPAAI 383 Query: 181 LAFLLGLTTWYLARKNNYPRLRKATWAERFAAFRKSGWGLFLIVIVMGGIYTGVFTPTEA 240 + + W AR+ P +++A + A + L L +++ + GV T TE Sbjct: 384 ATIAIAVVCWMRARREPMPDVKRAPLSLIVKALIAAIPALALPMLIRVAVIEGVATATEV 443 Query: 241 AAMAAVYAFFISVFVY---KDLRLSQVPKVLLDSASMSAMLLYIITNAVLFSFLVTSENI 297 A + Y + + ++ + L ++ +L++SA++S +L II A ++ +T Sbjct: 444 ATIGVAYTVVVGLIMHLFMRHLSFKRLYPMLIESAALSGAILLIIGMATAMAWALTQSGF 503 Query: 298 PQAMAAWITDSGLGPITFLLVVNILLLLAGNVMEPSSIVLILAPILFPVAMKLGIDPVHF 357 + A + G + FLL+ ++ ++ G+++E +++ P+LFPVA LG+ VH+ Sbjct: 504 SAKLVALMQGVPGGGVGFLLITIVIFIVLGSLLEGIPAIVLFGPLLFPVARSLGVHDVHY 563 Query: 358 GILIVVNMEVGMCHPPVGLNLYVASGITK 386 +++++ M +G+ PP G+ Y A I K Sbjct: 564 AMVVILAMGIGLFAPPFGVGFYAACAIGK 592 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 0.142 0.431 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: 1,090,676 Number of extensions: 38901 Number of successful extensions: 200 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 191 Number of HSP's successfully gapped: 4 Length of query: 426 Length of database: 1,619,870 Length adjustment: 88 Effective length of query: 338 Effective length of database: 1,203,190 Effective search space: 406678220 Effective search space used: 406678220 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: 132 (55.5 bits)