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= 0004.0032.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... 831 0.0 gi|300311996|ref|YP_003776088.1| TRAP-type C4-dicarboxylate tran... 216 2e-57 gi|300310440|ref|YP_003774532.1| TrapT dctQ-M fusion permease, d... 174 1e-44 gi|300313111|ref|YP_003777203.1| TRAP-type C4-dicarboxylate tran... 161 1e-40 >gi|300310180|ref|YP_003774272.1| TRAP-type C4-dicarboxylate transport system large permease [Herbaspirillum seropedicae SmR1] Length = 426 Score = 831 bits (2146), Expect = 0.0, Method: Compositional matrix adjust. Identities = 426/426 (100%), Positives = 426/426 (100%) Query: 1 MNALIIFVLLFALMLTGMPISISLGLTVLTFLFTMTEVPIQSVALKLFTGIEKFEIMAIP 60 MNALIIFVLLFALMLTGMPISISLGLTVLTFLFTMTEVPIQSVALKLFTGIEKFEIMAIP Sbjct: 1 MNALIIFVLLFALMLTGMPISISLGLTVLTFLFTMTEVPIQSVALKLFTGIEKFEIMAIP 60 Query: 61 FFILAGNFLTHGGVARRMINFATSMVGHWHGGLALAGVLACALFAAVSGSSPATVVAIGS 120 FFILAGNFLTHGGVARRMINFATSMVGHWHGGLALAGVLACALFAAVSGSSPATVVAIGS Sbjct: 61 FFILAGNFLTHGGVARRMINFATSMVGHWHGGLALAGVLACALFAAVSGSSPATVVAIGS 120 Query: 121 IILPAMVKQGFPNRFGAGVITTSGALGILIPPSIVMVMYSVSTNTSVGKLFMAGVVPGLL 180 IILPAMVKQGFPNRFGAGVITTSGALGILIPPSIVMVMYSVSTNTSVGKLFMAGVVPGLL Sbjct: 121 IILPAMVKQGFPNRFGAGVITTSGALGILIPPSIVMVMYSVSTNTSVGKLFMAGVVPGLL 180 Query: 181 LAFLLGVTTWFLARKNNYPRLKKATWAERAAAFRKSGWGLFLIVIVMGGIYTGVFTPTEA 240 LAFLLGVTTWFLARKNNYPRLKKATWAERAAAFRKSGWGLFLIVIVMGGIYTGVFTPTEA Sbjct: 181 LAFLLGVTTWFLARKNNYPRLKKATWAERAAAFRKSGWGLFLIVIVMGGIYTGVFTPTEA 240 Query: 241 AAMAAVYAFFIAVFVYKDLTLKQVPKVLLDSASMSAMLLYIITNAVLFSFLVTSENIPQA 300 AAMAAVYAFFIAVFVYKDLTLKQVPKVLLDSASMSAMLLYIITNAVLFSFLVTSENIPQA Sbjct: 241 AAMAAVYAFFIAVFVYKDLTLKQVPKVLLDSASMSAMLLYIITNAVLFSFLVTSENIPQA 300 Query: 301 MAAWITDSGLGPITFLLVVNILLLLAGNVMEPSSIVLILAPILFPVAMKLGIDPVHFGIL 360 MAAWITDSGLGPITFLLVVNILLLLAGNVMEPSSIVLILAPILFPVAMKLGIDPVHFGIL Sbjct: 301 MAAWITDSGLGPITFLLVVNILLLLAGNVMEPSSIVLILAPILFPVAMKLGIDPVHFGIL 360 Query: 361 IVVNMEVGMCHPPVGLNLYVASGITKMGITELTIAVMPWLLTMLGFLALVTYWPALSLWL 420 IVVNMEVGMCHPPVGLNLYVASGITKMGITELTIAVMPWLLTMLGFLALVTYWPALSLWL 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 = 216 bits (551), Expect = 2e-57, Method: Compositional matrix adjust. Identities = 147/436 (33%), Positives = 243/436 (55%), Gaps = 21/436 (4%) Query: 8 VLLFALMLTGMPISISLGLTVLTFL-FTMTEVPIQSVALKLFTGIEKFEIMAIPFFILAG 66 V+ +M +GMPI+ +LG+ F+ F M E + ++ ++ I +++IP FIL G Sbjct: 12 VVTIVVMCSGMPIAFALGVVATGFMYFFMPESSLDTITQNVYEEIASITLLSIPLFILKG 71 Query: 67 NFLTHGGVARRMINFATSMVGHWHGGLALAGVLACALFAAVSGSSPATVVAIGSIILPAM 126 + + + + + + GGL +A V ACALFAA++GSSPAT AIGS +P M Sbjct: 72 AAIGKSPAGKDLYSAIHAWLNKVPGGLGIANVFACALFAAMAGSSPATCSAIGSAGIPEM 131 Query: 127 VKQGFPNRFGAGVITTSGALGILIPPSIVMVMYSVSTNTSVGKLFMAGVVPGLLLAFLLG 186 ++G+ F AG+I G LGIL+PPSI M++Y+V+ S+G+LF+AG+ PG+LL L Sbjct: 132 RRRGYSPGFAAGIIAAGGTLGILLPPSITMILYAVAAEQSLGRLFLAGIGPGVLLVLLFA 191 Query: 187 VTTWFLARKNNYPRLKKATWA---ERAAAFRKSGWGL------------FLIVI--VMGG 229 + ARK RL A ++ ++A + L FLI++ VM Sbjct: 192 GYAVYRARKEY--RLAHAVYSAGGAKSAYLDDEHFTLAQKVEMLPRVLPFLILLIGVMVA 249 Query: 230 IYTGVFTPTEAAAMAAVYAFFIAVFVYKDLTLKQVPKVLLDSASMSAMLLYIITNAVLFS 289 +Y G+ TP+E A + A+ A + VY+ +++ L + S MLL II ++L+S Sbjct: 250 LYGGLATPSETAGLGALLALVLIAVVYRIYKPREIAPFLSSTIKESGMLLLIIGMSLLYS 309 Query: 290 FLVTSENIPQAMAAWITDSGLGPITFLLVVNILLLLAGNVMEPSSIVLILAPILFPVAMK 349 ++++ +I Q+ A W+ D L L V+ ++++ G + P SI+L+ API+ P Sbjct: 310 YVMSYLHISQSAAQWVVDLHLSKWLLLAVILGMVIVLGFFLPPVSIILMTAPIILPPLKA 369 Query: 350 LGIDPVHFGILIVVNMEVGMCHPPVGLNLYVASGIT-KMGITELTIAVMPWLLTMLGFLA 408 G D + FGI++ V ME+G+ HPPVGLNL+V I + + ++ +P+L M + Sbjct: 370 AGFDLIWFGIVMTVVMEMGLIHPPVGLNLFVIKNIAPDIALGDVIKGTIPFLALMFLAVL 429 Query: 409 LVTYWPALSLWLPNLI 424 L+ +P ++ LP+L+ Sbjct: 430 LLCMFPGIATLLPDLL 445 >gi|300310440|ref|YP_003774532.1| TrapT dctQ-M fusion permease, dicarboxylate transport protein [Herbaspirillum seropedicae SmR1] Length = 618 Score = 174 bits (441), Expect = 1e-44, Method: Compositional matrix adjust. Identities = 124/421 (29%), Positives = 222/421 (52%), Gaps = 8/421 (1%) Query: 2 NALIIFVLLFAL-MLTGMPISISLGLTVLTFLFTMTEVPIQSVALKLFTGIEKFEIMAIP 60 N ++ F L+ A+ +L G+PI+ GL + F+ T+T P+ VA + G+ ++A+P Sbjct: 199 NLVVFFGLVLAVSVLLGIPIAFCFGLATVAFMLTVTTSPLAVVAGRFDEGMSSLILLAVP 258 Query: 61 FFILAGNFLTHGGVARRMINFATSMVGHWHGGLALAGVLACALFAAVSGSSPATVVAIGS 120 FIL G+ + G+A+ M++F S++GH GGL + A L + +SG+ A + A+ Sbjct: 259 LFILLGHLVEMTGMAKAMVDFLASLLGHVRGGLNYVLLGAMLLVSGISGAKTADMAAVAP 318 Query: 121 IILPAMVKQGFPNRFGAGVITTSGALGILIPPSIVMVMYSVSTNTSVGKLFMAGVVPGLL 180 ++LP M ++G ++ SGA+ IPPS+V++ S+ LF G++PG++ Sbjct: 319 VLLPEMKRRGNHEGELISLLAASGAMAETIPPSLVLITIGSVAGVSIAALFTGGIMPGIV 378 Query: 181 LAFLLGVTTWFLARKNNYPRLKKATWAERAAAFRKSGWGLFLIVIVMG---GIYTGVFTP 237 LA LL + LAR + ++ A R L +++ + + GV T Sbjct: 379 LAVLLAI----LARWRSAEIMEGIQRAPGRVVLRTLIIALPALLLPILIRTAVVEGVATA 434 Query: 238 TEAAAMAAVYAFFIAVFVYKDLTLKQVPKVLLDSASMSAMLLYIITNAVLFSFLVTSENI 297 TE + + Y+ + VY+ K++ +L+D+A++S +L+II A S+ +T Sbjct: 435 TEVSTIGIAYSVVAGLLVYRKFDWKRLYPMLVDTAALSGAILFIIGTATGMSWALTQSGF 494 Query: 298 PQAMAAWITDSGLGPITFLLVVNILLLLAGNVMEPSSIVLILAPILFPVAMKLGIDPVHF 357 A+A +T G FLLV ++ G+V+E +++ AP+LFPVA +G+ VH+ Sbjct: 495 SHALAEAMTSVPGGKYGFLLVSIAAFIVLGSVLEGIPAMVLFAPLLFPVAKAIGVHEVHY 554 Query: 358 GILIVVNMEVGMCHPPVGLNLYVASGITKMGITELTIAVMPWLLTMLGFLALVTYWPALS 417 ++I+++M VG+ PP GL Y A I ++ + P+L ++ L +V + P S Sbjct: 555 AMVIILSMGVGLFAPPFGLGYYAACTIGRVHPDVAVKRIWPYLGALVVGLLIVAFVPWFS 614 Query: 418 L 418 + Sbjct: 615 I 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 = 161 bits (407), Expect = 1e-40, Method: Compositional matrix adjust. Identities = 107/389 (27%), Positives = 206/389 (52%), Gaps = 4/389 (1%) Query: 2 NALIIFVLLFALMLTG-MPISISLGLTVLTFLFTMTEVPIQSVALKLFTGIEKFEIMAIP 60 N ++ FVLL + + G +PI+ + G + +L T P+ V ++ G+ ++++P Sbjct: 204 NLIVFFVLLIGVCVAGGIPIAFAFGTATMAYLALATTAPLMIVVSRMDEGMSSLILLSVP 263 Query: 61 FFILAGNFLTHGGVARRMINFATSMVGHWHGGLALAGVLACALFAAVSGSSPATVVAIGS 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 LAFLLGVTTWFLARKNNYPRLKKATWAERAAAFRKSGWGLFLIVIVMGGIYTGVFTPTEA 240 + V W AR+ P +K+A + A + L L +++ + GV T TE Sbjct: 384 ATIAIAVVCWMRARREPMPDVKRAPLSLIVKALIAAIPALALPMLIRVAVIEGVATATEV 443 Query: 241 AAMAAVYAFFIAVFVY---KDLTLKQVPKVLLDSASMSAMLLYIITNAVLFSFLVTSENI 297 A + Y + + ++ + L+ K++ +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 0.427 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: 1,124,931 Number of extensions: 42119 Number of successful extensions: 215 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 207 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)