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= 0001.0026.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... 873 0.0 gi|300310180|ref|YP_003774272.1| TRAP-type C4-dicarboxylate tran... 213 2e-56 gi|300310440|ref|YP_003774532.1| TrapT dctQ-M fusion permease, d... 131 9e-32 gi|300313111|ref|YP_003777203.1| TRAP-type C4-dicarboxylate tran... 96 8e-21 >gi|300311996|ref|YP_003776088.1| TRAP-type C4-dicarboxylate transport system large permease [Herbaspirillum seropedicae SmR1] Length = 449 Score = 873 bits (2255), Expect = 0.0, Method: Compositional matrix adjust. Identities = 449/449 (100%), Positives = 449/449 (100%) Query: 1 MSPLTLGVLYGVVTIVVMCSGMPIAFALGVVATGFMYFFMPESSLDTITQNVYEEIASIT 60 MSPLTLGVLYGVVTIVVMCSGMPIAFALGVVATGFMYFFMPESSLDTITQNVYEEIASIT Sbjct: 1 MSPLTLGVLYGVVTIVVMCSGMPIAFALGVVATGFMYFFMPESSLDTITQNVYEEIASIT 60 Query: 61 LLSIPLFILKGAAIGKSPAGKDLYSAIHAWLNKVPGGLGIANVFACALFAAMAGSSPATC 120 LLSIPLFILKGAAIGKSPAGKDLYSAIHAWLNKVPGGLGIANVFACALFAAMAGSSPATC Sbjct: 61 LLSIPLFILKGAAIGKSPAGKDLYSAIHAWLNKVPGGLGIANVFACALFAAMAGSSPATC 120 Query: 121 SAIGSAGIPEMRRRGYSPGFAAGIIAAGGTLGILLPPSITMILYAVAAEQSLGRLFLAGI 180 SAIGSAGIPEMRRRGYSPGFAAGIIAAGGTLGILLPPSITMILYAVAAEQSLGRLFLAGI Sbjct: 121 SAIGSAGIPEMRRRGYSPGFAAGIIAAGGTLGILLPPSITMILYAVAAEQSLGRLFLAGI 180 Query: 181 GPGVLLVLLFAGYAVYRARKEYRLAHAVYSAGGAKSAYLDDEHFTLAQKVEMLPRVLPFL 240 GPGVLLVLLFAGYAVYRARKEYRLAHAVYSAGGAKSAYLDDEHFTLAQKVEMLPRVLPFL Sbjct: 181 GPGVLLVLLFAGYAVYRARKEYRLAHAVYSAGGAKSAYLDDEHFTLAQKVEMLPRVLPFL 240 Query: 241 ILLIGVMVALYGGLATPSETAGLGALLALVLIAVVYRIYKPREIAPFLSSTIKESGMLLL 300 ILLIGVMVALYGGLATPSETAGLGALLALVLIAVVYRIYKPREIAPFLSSTIKESGMLLL Sbjct: 241 ILLIGVMVALYGGLATPSETAGLGALLALVLIAVVYRIYKPREIAPFLSSTIKESGMLLL 300 Query: 301 IIGMSLLYSYVMSYLHISQSAAQWVVDLHLSKWLLLAVILGMVIVLGFFLPPVSIILMTA 360 IIGMSLLYSYVMSYLHISQSAAQWVVDLHLSKWLLLAVILGMVIVLGFFLPPVSIILMTA Sbjct: 301 IIGMSLLYSYVMSYLHISQSAAQWVVDLHLSKWLLLAVILGMVIVLGFFLPPVSIILMTA 360 Query: 361 PIILPPLKAAGFDLIWFGIVMTVVMEMGLIHPPVGLNLFVIKNIAPDIALGDVIKGTIPF 420 PIILPPLKAAGFDLIWFGIVMTVVMEMGLIHPPVGLNLFVIKNIAPDIALGDVIKGTIPF Sbjct: 361 PIILPPLKAAGFDLIWFGIVMTVVMEMGLIHPPVGLNLFVIKNIAPDIALGDVIKGTIPF 420 Query: 421 LALMFLAVLLLCMFPGIATLLPDLLMGAK 449 LALMFLAVLLLCMFPGIATLLPDLLMGAK 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 (543), Expect = 2e-56, Method: Compositional matrix adjust. Identities = 147/436 (33%), Positives = 243/436 (55%), Gaps = 21/436 (4%) Query: 12 VVTIVVMCSGMPIAFALGVVATGFMYFFMPESSLDTITQNVYEEIASITLLSIPLFILKG 71 V+ +M +GMPI+ +LG+ F+ F M E + ++ ++ I +++IP FIL G Sbjct: 8 VLLFALMLTGMPISISLGLTVLTFL-FTMTEVPIQSVALKLFTGIEKFEIMAIPFFILAG 66 Query: 72 AAIGKSPAGKDLYSAIHAWLNKVPGGLGIANVFACALFAAMAGSSPATCSAIGSAGIPEM 131 + + + + + + GGL +A V ACALFAA++GSSPAT AIGS +P M Sbjct: 67 NFLTHGGVARRMINFATSMVGHWHGGLALAGVLACALFAAVSGSSPATVVAIGSIILPAM 126 Query: 132 RRRGYSPGFAAGIIAAGGTLGILLPPSITMILYAVAAEQSLGRLFLAGIGPGVLLVLLFA 191 ++G+ F AG+I G LGIL+PPSI M++Y+V+ S+G+LF+AG+ PG+LL L Sbjct: 127 VKQGFPNRFGAGVITTSGALGILIPPSIVMVMYSVSTNTSVGKLFMAGVVPGLLLAFLLG 186 Query: 192 GYAVYRARKEY--RLAHAVYSAGGAKSAYLDDEHFTLAQKVEMLPRVLPFLILLIGVMVA 249 + ARK RL A ++ ++A + L FLI++ VM Sbjct: 187 VTTWFLARKNNYPRLKKATWA---ERAAAFRKSGWGL------------FLIVI--VMGG 229 Query: 250 LYGGLATPSETAGLGALLALVLIAVVYRIYKPREIAPFLSSTIKESGMLLLIIGMSLLYS 309 +Y G+ TP+E A + A+ A + VY+ +++ L + S MLL II ++L+S Sbjct: 230 IYTGVFTPTEAAAMAAVYAFFIAVFVYKDLTLKQVPKVLLDSASMSAMLLYIITNAVLFS 289 Query: 310 YVMSYLHISQSAAQWVVDLHLSKWLLLAVILGMVIVLGFFLPPVSIILMTAPIILPPLKA 369 ++++ +I Q+ A W+ D L L V+ ++++ G + P SI+L+ API+ P Sbjct: 290 FLVTSENIPQAMAAWITDSGLGPITFLLVVNILLLLAGNVMEPSSIVLILAPILFPVAMK 349 Query: 370 AGFDLIWFGIVMTVVMEMGLIHPPVGLNLFVIKNIAPDIALGDVIKGTIPFLALMFLAVL 429 G D + FGI++ V ME+G+ HPPVGLNL+V I + + ++ +P+L M + Sbjct: 350 LGIDPVHFGILIVVNMEVGMCHPPVGLNLYVASGIT-KMGITELTIAVMPWLLTMLGFLA 408 Query: 430 LLCMFPGIATLLPDLL 445 L+ +P ++ LP+L+ Sbjct: 409 LVTYWPALSLWLPNLI 424 >gi|300310440|ref|YP_003774532.1| TrapT dctQ-M fusion permease, dicarboxylate transport protein [Herbaspirillum seropedicae SmR1] Length = 618 Score = 131 bits (330), Expect = 9e-32, Method: Compositional matrix adjust. Identities = 121/434 (27%), Positives = 209/434 (48%), Gaps = 24/434 (5%) Query: 5 TLGVLYGVVTIVVMCSGMPIAFALGVVATGFMYFFMPESSLDTITQNVYEEIASITLLSI 64 L V +G+V 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 LLVLLFAGYAVYRARKEYRLAHAVYSAGGAKSAYLDDEHFTLAQKVEMLPRVLPFLILLI 244 +L +L A A +R+ + + + A G + A + +L R Sbjct: 378 VLAVLLAILARWRSAE---IMEGIQRAPG-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 SLLYSYVMSYLHISQSAAQWVVDLHLSKWLLLAVILGMVIVLGFFLPPVSIILMTAPIIL 364 + S+ ++ S + A+ + + K+ L V + 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 = 95.5 bits (236), Expect = 8e-21, Method: Compositional matrix adjust. Identities = 105/398 (26%), Positives = 187/398 (46%), Gaps = 22/398 (5%) Query: 16 VVMCSGMPIAFALGVVATGFMYFFMPESSLDTITQNVYEEIASITLLSIPLFILKGAAIG 75 V + G+PIAFA G ++ + L + + E ++S+ LLS+PLF+L G+ + Sbjct: 215 VCVAGGIPIAFAFGTATMAYLAL-ATTAPLMIVVSRMDEGMSSLILLSVPLFVLLGSLLE 273 Query: 76 KSPAGKDLYSAIHAWLNKVPGGLGIANVFACALFAAMAGSSPATCSAIGSAGIPEMRRRG 135 S K L + A L V GGL + A L + ++GS A +AI A PEM++RG Sbjct: 274 MSGLAKTLIDFMAALLGHVRGGLQYVLLGAMFLVSGISGSKAADMAAIAPALFPEMKKRG 333 Query: 136 YSPGFAAGIIAAGGTLGILLPPSITMILYAVAAEQSLGRLFLAGIGPGVLLVLLFAGYAV 195 P ++++ G + +PPS+ +I S+ LF+ G+ P + + A Sbjct: 334 SKPEELVALLSSSGAMTETIPPSLVLITIGAVCSVSITALFIGGLMPAAIATIAIAVVCW 393 Query: 196 YRARKEYRLAHAVYSAGGAKSAYLDDEHFTLAQKVEMLPRVLPFLILLIGVMVALYGGLA 255 RAR+E D + L+ V+ L +P L L + + VA+ G+A Sbjct: 394 MRARRE---------------PMPDVKRAPLSLIVKALIAAIPALALPMLIRVAVIEGVA 438 Query: 256 TPSETAGLGALLALVLIAVVY---RIYKPREIAPFLSSTIKESGMLLLIIGMSLLYSYVM 312 T +E A +G +V+ +++ R + + P L + SG +LLIIGM+ ++ + Sbjct: 439 TATEVATIGVAYTVVVGLIMHLFMRHLSFKRLYPMLIESAALSGAILLIIGMATAMAWAL 498 Query: 313 SYLHISQSAAQWVVDLHLSKWLLLAVILGMVIVLGFFLPPVSIILMTAPIILPPLKAAGF 372 + S + + L + + + IVLG L + I++ P++ P ++ G Sbjct: 499 TQSGFSAKLVALMQGVPGGGVGFLLITIVIFIVLGSLLEGIPAIVLFGPLLFPVARSLGV 558 Query: 373 DLIWFGIVMTVVMEMGLIHPPVGLNLF---VIKNIAPD 407 + + +V+ + M +GL PP G+ + I ++PD Sbjct: 559 HDVHYAMVVILAMGIGLFAPPFGVGFYAACAIGKVSPD 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 0.427 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: 1,271,659 Number of extensions: 49492 Number of successful extensions: 308 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 298 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)