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= 0007.0033.p (451 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... 791 0.0 gi|300310180|ref|YP_003774272.1| TRAP-type C4-dicarboxylate tran... 213 3e-56 gi|300310440|ref|YP_003774532.1| TrapT dctQ-M fusion permease, d... 128 1e-30 gi|300313111|ref|YP_003777203.1| TRAP-type C4-dicarboxylate tran... 98 1e-21 >gi|300311996|ref|YP_003776088.1| TRAP-type C4-dicarboxylate transport system large permease [Herbaspirillum seropedicae SmR1] Length = 449 Score = 791 bits (2042), Expect = 0.0, Method: Compositional matrix adjust. Identities = 412/449 (91%), Positives = 434/449 (96%) Query: 3 LTPLVLGSLYGIVTILVMCSGMPIAFALGVVATSFMYFFMPASSLDTVTQNVYEEIASIT 62 ++PL LG LYG+VTI+VMCSGMPIAFALGVVAT FMYFFMP SSLDT+TQNVYEEIASIT Sbjct: 1 MSPLTLGVLYGVVTIVVMCSGMPIAFALGVVATGFMYFFMPESSLDTITQNVYEEIASIT 60 Query: 63 LLSIPLFILKGAAIGKSPAGKDLYSAIHAWLNRVPGGLGIANVFACALFAAMAGSSPATC 122 LLSIPLFILKGAAIGKSPAGKDLYSAIHAWLN+VPGGLGIANVFACALFAAMAGSSPATC Sbjct: 61 LLSIPLFILKGAAIGKSPAGKDLYSAIHAWLNKVPGGLGIANVFACALFAAMAGSSPATC 120 Query: 123 SAIGSAGIPEMRRRGYSPGFAAGIIAAGGTLGILLPPSITMILYAVAAEQSLGRLFLAGI 182 SAIGSAGIPEMRRRGYSPGFAAGIIAAGGTLGILLPPSITMILYAVAAEQSLGRLFLAGI Sbjct: 121 SAIGSAGIPEMRRRGYSPGFAAGIIAAGGTLGILLPPSITMILYAVAAEQSLGRLFLAGI 180 Query: 183 GPGVLLVILFAGYAVFRAHKEYKMAHAIYTGGGAKSAYLDDEHFTLAQKVEMLPRVLPFL 242 GPGVLLV+LFAGYAV+RA KEY++AHA+Y+ GGAKSAYLDDEHFTLAQKVEMLPRVLPFL Sbjct: 181 GPGVLLVLLFAGYAVYRARKEYRLAHAVYSAGGAKSAYLDDEHFTLAQKVEMLPRVLPFL 240 Query: 243 ILLIGVMIALYGGFATPSETAGLGALLAIVLIAVVYRIYKPRELVPFLNSTIKESGMLLL 302 ILLIGVM+ALYGG ATPSETAGLGALLA+VLIAVVYRIYKPRE+ PFL+STIKESGMLLL Sbjct: 241 ILLIGVMVALYGGLATPSETAGLGALLALVLIAVVYRIYKPREIAPFLSSTIKESGMLLL 300 Query: 303 IIGMSLLYSYVMSYLHISQSAAQWVVDMHLSKWLLLAVILLMVIVLGFFLPPVSIILMTA 362 IIGMSLLYSYVMSYLHISQSAAQWVVD+HLSKWLLLAVIL MVIVLGFFLPPVSIILMTA Sbjct: 301 IIGMSLLYSYVMSYLHISQSAAQWVVDLHLSKWLLLAVILGMVIVLGFFLPPVSIILMTA 360 Query: 363 PIILPPLREAGFDLIWFGIVMTVVMEMGLIHPPVGLNLFVIKNIAPDIPLSEVIKGTIPF 422 PIILPPL+ AGFDLIWFGIVMTVVMEMGLIHPPVGLNLFVIKNIAPDI L +VIKGTIPF Sbjct: 361 PIILPPLKAAGFDLIWFGIVMTVVMEMGLIHPPVGLNLFVIKNIAPDIALGDVIKGTIPF 420 Query: 423 LALMFLAVILLCFFPGIATGLPDIIMGVK 451 LALMFLAV+LLC FPGIAT LPD++MG K Sbjct: 421 LALMFLAVLLLCMFPGIATLLPDLLMGAK 449 >gi|300310180|ref|YP_003774272.1| TRAP-type C4-dicarboxylate transport system large permease [Herbaspirillum seropedicae SmR1] Length = 426 Score = 213 bits (541), Expect = 3e-56, Method: Compositional matrix adjust. Identities = 144/429 (33%), Positives = 240/429 (55%), Gaps = 17/429 (3%) Query: 19 VMCSGMPIAFALGVVATSFMYFFMPASSLDTVTQNVYEEIASITLLSIPLFILKGAAIGK 78 +M +GMPI+ +LG+ +F+ F M + +V ++ I +++IP FIL G + Sbjct: 13 LMLTGMPISISLGLTVLTFL-FTMTEVPIQSVALKLFTGIEKFEIMAIPFFILAGNFLTH 71 Query: 79 SPAGKDLYSAIHAWLNRVPGGLGIANVFACALFAAMAGSSPATCSAIGSAGIPEMRRRGY 138 + + + + + GGL +A V ACALFAA++GSSPAT AIGS +P M ++G+ Sbjct: 72 GGVARRMINFATSMVGHWHGGLALAGVLACALFAAVSGSSPATVVAIGSIILPAMVKQGF 131 Query: 139 SPGFAAGIIAAGGTLGILLPPSITMILYAVAAEQSLGRLFLAGIGPGVLLVILFAGYAVF 198 F AG+I G LGIL+PPSI M++Y+V+ S+G+LF+AG+ PG+LL L F Sbjct: 132 PNRFGAGVITTSGALGILIPPSIVMVMYSVSTNTSVGKLFMAGVVPGLLLAFLLGVTTWF 191 Query: 199 RAHKEYKMAHAIYTGGGAKSAYLDDEHFTLAQKVEMLPRVLPFLILLIGVMIALYGGFAT 258 A K+ Y + T A++ + L L++ VM +Y G T Sbjct: 192 LAR---------------KNNYPRLKKATWAERAAAFRKSGWGLFLIVIVMGGIYTGVFT 236 Query: 259 PSETAGLGALLAIVLIAVVYRIYKPRELVPFLNSTIKESGMLLLIIGMSLLYSYVMSYLH 318 P+E A + A+ A + VY+ +++ L + S MLL II ++L+S++++ + Sbjct: 237 PTEAAAMAAVYAFFIAVFVYKDLTLKQVPKVLLDSASMSAMLLYIITNAVLFSFLVTSEN 296 Query: 319 ISQSAAQWVVDMHLSKWLLLAVILLMVIVLGFFLPPVSIILMTAPIILPPLREAGFDLIW 378 I Q+ A W+ D L L V+ +++++ G + P SI+L+ API+ P + G D + Sbjct: 297 IPQAMAAWITDSGLGPITFLLVVNILLLLAGNVMEPSSIVLILAPILFPVAMKLGIDPVH 356 Query: 379 FGIVMTVVMEMGLIHPPVGLNLFVIKNIAPDIPLSEVIKGTIPFLALMFLAVILLCFFPG 438 FGI++ V ME+G+ HPPVGLNL+V I + ++E+ +P+L M + L+ ++P Sbjct: 357 FGILIVVNMEVGMCHPPVGLNLYVASGIT-KMGITELTIAVMPWLLTMLGFLALVTYWPA 415 Query: 439 IATGLPDII 447 ++ LP++I Sbjct: 416 LSLWLPNLI 424 >gi|300310440|ref|YP_003774532.1| TrapT dctQ-M fusion permease, dicarboxylate transport protein [Herbaspirillum seropedicae SmR1] Length = 618 Score = 128 bits (321), Expect = 1e-30, Method: Compositional matrix adjust. Identities = 118/434 (27%), Positives = 207/434 (47%), Gaps = 24/434 (5%) Query: 12 YGIVTILVMCSGMPIAFALGVVATSFMYFFMPASSLDTVTQNVYEEIASITLLSIPLFIL 71 +G+V + + G+PIAF G+ +FM + S L V E ++S+ LL++PLFIL Sbjct: 204 FGLVLAVSVLLGIPIAFCFGLATVAFM-LTVTTSPLAVVAGRFDEGMSSLILLAVPLFIL 262 Query: 72 KGAAIGKSPAGKDLYSAIHAWLNRVPGGLGIANVFACALFAAMAGSSPATCSAIGSAGIP 131 G + + K + + + L V GGL + A L + ++G+ A +A+ +P Sbjct: 263 LGHLVEMTGMAKAMVDFLASLLGHVRGGLNYVLLGAMLLVSGISGAKTADMAAVAPVLLP 322 Query: 132 EMRRRGYSPGFAAGIIAAGGTLGILLPPSITMILYAVAAEQSLGRLFLAGIGPGVLLVIL 191 EM+RRG G ++AA G + +PPS+ +I A S+ LF GI PG++L +L Sbjct: 323 EMKRRGNHEGELISLLAASGAMAETIPPSLVLITIGSVAGVSIAALFTGGIMPGIVLAVL 382 Query: 192 FAGYAVFRAHKEYKMAHAIYTGGGAKSAYLDDEHFTLAQKVEMLPRVLPFLILLIGVMIA 251 A A +R+ ++ I G + A + +L R A Sbjct: 383 LAILARWRSA---EIMEGIQRAPG-RVVLRTLIIALPALLLPILIRT------------A 426 Query: 252 LYGGFATPSETAGLGALLAIVLIAVVYRIYKPRELVPFLNSTIKESGMLLLIIGMSLLYS 311 + G AT +E + +G ++V +VYR + + L P L T SG +L IIG + S Sbjct: 427 VVEGVATATEVSTIGIAYSVVAGLLVYRKFDWKRLYPMLVDTAALSGAILFIIGTATGMS 486 Query: 312 YVMSYLHISQSAAQWVVDMHLSKWLLLAVILLMVIVLGFFLPPVSIILMTAPIILPPLRE 371 + ++ S + A+ + + K+ L V + IVLG L + +++ AP++ P + Sbjct: 487 WALTQSGFSHALAEAMTSVPGGKYGFLLVSIAAFIVLGSVLEGIPAMVLFAPLLFPVAKA 546 Query: 372 AGFDLIWFGIVMTVVMEMGLIHPPVGLNLF---VIKNIAPDIPLSEVIKGTIPFLALMFL 428 G + + +V+ + M +GL PP GL + I + PD+ +K P+L + + Sbjct: 547 IGVHEVHYAMVIILSMGVGLFAPPFGLGYYAACTIGRVHPDV----AVKRIWPYLGALVV 602 Query: 429 AVILLCFFPGIATG 442 ++++ F P + G Sbjct: 603 GLLIVAFVPWFSIG 616 >gi|300313111|ref|YP_003777203.1| TRAP-type C4-dicarboxylate transport system dctQ-M fusion permease large permease [Herbaspirillum seropedicae SmR1] Length = 627 Score = 97.8 bits (242), Expect = 1e-21, Method: Compositional matrix adjust. Identities = 107/393 (27%), Positives = 184/393 (46%), Gaps = 22/393 (5%) Query: 23 GMPIAFALGVVATSFMYFFMPASSLDTVTQNVYEEIASITLLSIPLFILKGAAIGKSPAG 82 G+PIAFA G +++ A L V + E ++S+ LLS+PLF+L G+ + S Sbjct: 220 GIPIAFAFGTATMAYLALATTAP-LMIVVSRMDEGMSSLILLSVPLFVLLGSLLEMSGLA 278 Query: 83 KDLYSAIHAWLNRVPGGLGIANVFACALFAAMAGSSPATCSAIGSAGIPEMRRRGYSPGF 142 K L + A L V GGL + A L + ++GS A +AI A PEM++RG P Sbjct: 279 KTLIDFMAALLGHVRGGLQYVLLGAMFLVSGISGSKAADMAAIAPALFPEMKKRGSKPEE 338 Query: 143 AAGIIAAGGTLGILLPPSITMILYAVAAEQSLGRLFLAGIGPGVLLVILFAGYAVFRAHK 202 ++++ G + +PPS+ +I S+ LF+ G+ P + I A RA + Sbjct: 339 LVALLSSSGAMTETIPPSLVLITIGAVCSVSITALFIGGLMPAAIATIAIAVVCWMRARR 398 Query: 203 EYKMAHAIYTGGGAKSAYLDDEHFTLAQKVEMLPRVLPFLILLIGVMIALYGGFATPSET 262 E D + L+ V+ L +P L L + + +A+ G AT +E Sbjct: 399 E---------------PMPDVKRAPLSLIVKALIAAIPALALPMLIRVAVIEGVATATEV 443 Query: 263 AGLGALLAIVLIAVVY---RIYKPRELVPFLNSTIKESGMLLLIIGMSLLYSYVMSYLHI 319 A +G +V+ +++ R + L P L + SG +LLIIGM+ ++ ++ Sbjct: 444 ATIGVAYTVVVGLIMHLFMRHLSFKRLYPMLIESAALSGAILLIIGMATAMAWALTQSGF 503 Query: 320 SQSAAQWVVDMHLSKWLLLAVILLMVIVLGFFLPPVSIILMTAPIILPPLREAGFDLIWF 379 S + + L + +++ IVLG L + I++ P++ P R G + + Sbjct: 504 SAKLVALMQGVPGGGVGFLLITIVIFIVLGSLLEGIPAIVLFGPLLFPVARSLGVHDVHY 563 Query: 380 GIVMTVVMEMGLIHPPVGLNLF---VIKNIAPD 409 +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 0.431 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: 1,274,003 Number of extensions: 49888 Number of successful extensions: 262 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 250 Number of HSP's successfully gapped: 4 Length of query: 451 Length of database: 1,619,870 Length adjustment: 88 Effective length of query: 363 Effective length of database: 1,203,190 Effective search space: 436757970 Effective search space used: 436757970 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)