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= 0257.0012.p (611 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310440|ref|YP_003774532.1| TrapT dctQ-M fusion permease, d... 696 0.0 gi|300313111|ref|YP_003777203.1| TRAP-type C4-dicarboxylate tran... 588 e-169 gi|300310180|ref|YP_003774272.1| TRAP-type C4-dicarboxylate tran... 160 2e-40 gi|300311996|ref|YP_003776088.1| TRAP-type C4-dicarboxylate tran... 99 9e-22 >gi|300310440|ref|YP_003774532.1| TrapT dctQ-M fusion permease, dicarboxylate transport protein [Herbaspirillum seropedicae SmR1] Length = 618 Score = 696 bits (1795), Expect = 0.0, Method: Compositional matrix adjust. Identities = 378/614 (61%), Positives = 475/614 (77%), Gaps = 4/614 (0%) Query: 1 LNRPVGN---MLGSVQYWLEKSVEVLTAGVLVAEVVLLFIGIIARSVLHSSLIWSDELAS 57 L +PV + + +++WL ++E+ A ++V EV +L G+I R + ++ + W+DELAS Sbjct: 6 LEQPVADERSLAARLEHWLGLAIEIPAAALVVGEVAVLLAGVIMRFIFNNPIPWADELAS 65 Query: 58 ILFLWLAMLGSALAVQRSCHMRLTFFVSKMSPRAQAWAETLAVGVTAVLLVMMIHPSFDY 117 ILFLWLA LG+A+A++R HMR T V MS R +AWAE LA+ V+L++++HP ++Y Sbjct: 66 ILFLWLANLGAAVALRRGTHMRTTVLVGFMSERGKAWAEALAIIAPCVMLLILMHPMWEY 125 Query: 118 VEDQGFVETPALGWSGMVRALAVPVGFLIAFVSCALRLMHHKKSDILTVAALLAVIAGAC 177 ED+ FV+TPALGW VRA AV VG + LR+ K D++ V ALLAV+AGA Sbjct: 126 AEDEMFVQTPALGWPNTVRAAAVAVGAALMIALSLLRISRQKLVDLVGVLALLAVVAGAM 185 Query: 178 YLGAPMFTAMGQSALPIFFIGLLGAAVMTGAPIAFAFAIATCAYLLTTTTTPVVIVVGRM 237 YLGA A+G L +FF +L +V+ G PIAF F +AT A++LT TT+P+ +V GR Sbjct: 186 YLGAAWLQAIGNWNLVVFFGLVLAVSVLLGIPIAFCFGLATVAFMLTVTTSPLAVVAGRF 245 Query: 238 DEGMSSLILLAVPMFVLLGQLVHATGLARVMVEFLAALVGHVRGGMSYVLLGAMLLVSGI 297 DEGMSSLILLAVP+F+LLG LV TG+A+ MV+FLA+L+GHVRGG++YVLLGAMLLVSGI Sbjct: 246 DEGMSSLILLAVPLFILLGHLVEMTGMAKAMVDFLASLLGHVRGGLNYVLLGAMLLVSGI 305 Query: 298 SGSKTADMAAVAPVLFPEMRKRGMQDSELISLLAASGAMSETIPPSLVLIAIASVTGISI 357 SG+KTADMAAVAPVL PEM++RG + ELISLLAASGAM+ETIPPSLVLI I SV G+SI Sbjct: 306 SGAKTADMAAVAPVLLPEMKRRGNHEGELISLLAASGAMAETIPPSLVLITIGSVAGVSI 365 Query: 358 AALFTAGIMPAFVLAIVLAVVAWWRAGSDHVATNRAPIKRVLKTFAIAVPALLLPFVIRT 417 AALFT GIMP VLA++LA++A WR+ RAP + VL+T IA+PALLLP +IRT Sbjct: 366 AALFTGGIMPGIVLAVLLAILARWRSAEIMEGIQRAPGRVVLRTLIIALPALLLPILIRT 425 Query: 418 AVVEGVATATEVSTIGIAYSLIVGLIIYRGSLKWHMALPILVQTAALSGAILFIVGAASA 477 AVVEGVATATEVSTIGIAYS++ GL++YR W P+LV TAALSGAILFI+G A+ Sbjct: 426 AVVEGVATATEVSTIGIAYSVVAGLLVYR-KFDWKRLYPMLVDTAALSGAILFIIGTATG 484 Query: 478 MGWALTQSGFSHDLAAMMTAVPGGATGFLLVSIAAFIVLGSVLEGIPAIVLFGPLLFPVA 537 M WALTQSGFSH LA MT+VPGG GFLLVSIAAFIVLGSVLEGIPA+VLF PLLFPVA Sbjct: 485 MSWALTQSGFSHALAEAMTSVPGGKYGFLLVSIAAFIVLGSVLEGIPAMVLFAPLLFPVA 544 Query: 538 RQLGIHEIHYAMVVILAMGLGVFAPPFGLCYYAACIIGEVKPEVALKRIWLYLGMLLLGL 597 + +G+HE+HYAMV+IL+MG+G+FAPPFGL YYAAC IG V P+VA+KRIW YLG L++GL Sbjct: 545 KAIGVHEVHYAMVIILSMGVGLFAPPFGLGYYAACTIGRVHPDVAVKRIWPYLGALVVGL 604 Query: 598 IAITFIPWISIGFL 611 + + F+PW SIGFL Sbjct: 605 LIVAFVPWFSIGFL 618 >gi|300313111|ref|YP_003777203.1| TRAP-type C4-dicarboxylate transport system dctQ-M fusion permease large permease [Herbaspirillum seropedicae SmR1] Length = 627 Score = 588 bits (1516), Expect = e-169, Method: Compositional matrix adjust. Identities = 331/585 (56%), Positives = 432/585 (73%), Gaps = 4/585 (0%) Query: 31 EVVLLFIGIIARSVLHSSLIWSDELASILFLWLAMLGSALAVQRSCHMRLTFFVSKMSPR 90 E V+L G+I R LH L+WSDELASILF+WL+MLG+ LA+ R HMRLT ++K S + Sbjct: 43 ETVVLLTGVIYRYALHDPLVWSDELASILFIWLSMLGAVLALDRGEHMRLTAIINKCSEK 102 Query: 91 AQAWAETLAVGVTAVLLVMMIHPSFDYVEDQGFVETPALGWSGMVRALAVPVGFLIAFVS 150 + W ET+A V + ++M+IHP+ D+ +Q + TPAL +RA A+PVG ++ ++ Sbjct: 103 GRIWLETVAALVVCIFVLMVIHPAVDHAVEQMPITTPALEIPDGLRAAALPVGAILMLLA 162 Query: 151 CALRLMHHKKSDILTVA-ALLAVIAGACYLGAPMFTAMGQSALPIFFIGLLGAAVMTGAP 209 R+ +L A A++AVI GA +L PM MG L +FF+ L+G V G P Sbjct: 163 AVSRMAAMTTMRLLLSALAVVAVIGGALWLAKPMLLGMGNYNLIVFFVLLIGVCVAGGIP 222 Query: 210 IAFAFAIATCAYLLTTTTTPVVIVVGRMDEGMSSLILLAVPMFVLLGQLVHATGLARVMV 269 IAFAF AT AYL TT P++IVV RMDEGMSSLILL+VP+FVLLG L+ +GLA+ ++ Sbjct: 223 IAFAFGTATMAYLALATTAPLMIVVSRMDEGMSSLILLSVPLFVLLGSLLEMSGLAKTLI 282 Query: 270 EFLAALVGHVRGGMSYVLLGAMLLVSGISGSKTADMAAVAPVLFPEMRKRGMQDSELISL 329 +F+AAL+GHVRGG+ YVLLGAM LVSGISGSK ADMAA+AP LFPEM+KRG + EL++L Sbjct: 283 DFMAALLGHVRGGLQYVLLGAMFLVSGISGSKAADMAAIAPALFPEMKKRGSKPEELVAL 342 Query: 330 LAASGAMSETIPPSLVLIAIASVTGISIAALFTAGIMPAFVLAIVLAVVAWWRAGSDHVA 389 L++SGAM+ETIPPSLVLI I +V +SI ALF G+MPA + I +AVV W RA + + Sbjct: 343 LSSSGAMTETIPPSLVLITIGAVCSVSITALFIGGLMPAAIATIAIAVVCWMRARREPMP 402 Query: 390 T-NRAPIKRVLKTFAIAVPALLLPFVIRTAVVEGVATATEVSTIGIAYSLIVGLI--IYR 446 RAP+ ++K A+PAL LP +IR AV+EGVATATEV+TIG+AY+++VGLI ++ Sbjct: 403 DVKRAPLSLIVKALIAAIPALALPMLIRVAVIEGVATATEVATIGVAYTVVVGLIMHLFM 462 Query: 447 GSLKWHMALPILVQTAALSGAILFIVGAASAMGWALTQSGFSHDLAAMMTAVPGGATGFL 506 L + P+L+++AALSGAIL I+G A+AM WALTQSGFS L A+M VPGG GFL Sbjct: 463 RHLSFKRLYPMLIESAALSGAILLIIGMATAMAWALTQSGFSAKLVALMQGVPGGGVGFL 522 Query: 507 LVSIAAFIVLGSVLEGIPAIVLFGPLLFPVARQLGIHEIHYAMVVILAMGLGVFAPPFGL 566 L++I FIVLGS+LEGIPAIVLFGPLLFPVAR LG+H++HYAMVVILAMG+G+FAPPFG+ Sbjct: 523 LITIVIFIVLGSLLEGIPAIVLFGPLLFPVARSLGVHDVHYAMVVILAMGIGLFAPPFGV 582 Query: 567 CYYAACIIGEVKPEVALKRIWLYLGMLLLGLIAITFIPWISIGFL 611 +YAAC IG+V P+ R+W YL L++ L+ + F+PWISIGFL Sbjct: 583 GFYAACAIGKVSPDGVFNRVWGYLAALVVALLVVAFVPWISIGFL 627 >gi|300310180|ref|YP_003774272.1| TRAP-type C4-dicarboxylate transport system large permease [Herbaspirillum seropedicae SmR1] Length = 426 Score = 160 bits (406), Expect = 2e-40, Method: Compositional matrix adjust. Identities = 108/375 (28%), Positives = 196/375 (52%), Gaps = 2/375 (0%) Query: 199 LLGAAVMTGAPIAFAFAIATCAYLLTTTTTPVVIVVGRMDEGMSSLILLAVPMFVLLGQL 258 LL A ++TG PI+ + + +L T T P+ V ++ G+ ++A+P F+L G Sbjct: 9 LLFALMLTGMPISISLGLTVLTFLFTMTEVPIQSVALKLFTGIEKFEIMAIPFFILAGNF 68 Query: 259 VHATGLARVMVEFLAALVGHVRGGMSYVLLGAMLLVSGISGSKTADMAAVAPVLFPEMRK 318 + G+AR M+ F ++VGH GG++ + A L + +SGS A + A+ ++ P M K Sbjct: 69 LTHGGVARRMINFATSMVGHWHGGLALAGVLACALFAAVSGSSPATVVAIGSIILPAMVK 128 Query: 319 RGMQDSELISLLAASGAMSETIPPSLVLIAIASVTGISIAALFTAGIMPAFVLAIVLAVV 378 +G + ++ SGA+ IPPS+V++ + T S+ LF AG++P +LA +L V Sbjct: 129 QGFPNRFGAGVITTSGALGILIPPSIVMVMYSVSTNTSVGKLFMAGVVPGLLLAFLLGVT 188 Query: 379 AWWRA-GSDHVATNRAPIKRVLKTFAIAVPALLLPFVIRTAVVEGVATATEVSTIGIAYS 437 W+ A +++ +A F + L L ++ + GV T TE + + Y+ Sbjct: 189 TWFLARKNNYPRLKKATWAERAAAFRKSGWGLFLIVIVMGGIYTGVFTPTEAAAMAAVYA 248 Query: 438 LIVGLIIYRGSLKWHMALPILVQTAALSGAILFIVGAASAMGWALTQSGFSHDLAAMMTA 497 + + +Y+ L +L+ +A++S +L+I+ A + +T +AA +T Sbjct: 249 FFIAVFVYK-DLTLKQVPKVLLDSASMSAMLLYIITNAVLFSFLVTSENIPQAMAAWITD 307 Query: 498 VPGGATGFLLVSIAAFIVLGSVLEGIPAIVLFGPLLFPVARQLGIHEIHYAMVVILAMGL 557 G FLLV ++ G+V+E +++ P+LFPVA +LGI +H+ +++++ M + Sbjct: 308 SGLGPITFLLVVNILLLLAGNVMEPSSIVLILAPILFPVAMKLGIDPVHFGILIVVNMEV 367 Query: 558 GVFAPPFGLCYYAAC 572 G+ PP GL Y A Sbjct: 368 GMCHPPVGLNLYVAS 382 >gi|300311996|ref|YP_003776088.1| TRAP-type C4-dicarboxylate transport system large permease [Herbaspirillum seropedicae SmR1] Length = 449 Score = 99.4 bits (246), Expect = 9e-22, Method: Compositional matrix adjust. Identities = 107/423 (25%), Positives = 196/423 (46%), Gaps = 25/423 (5%) Query: 206 TGAPIAFAFAIATCAYL-LTTTTTPVVIVVGRMDEGMSSLILLAVPMFVLLGQLVHATGL 264 +G PIAFA + ++ + + + + E ++S+ LL++P+F+L G + + Sbjct: 20 SGMPIAFALGVVATGFMYFFMPESSLDTITQNVYEEIASITLLSIPLFILKGAAIGKSPA 79 Query: 265 ARVMVEFLAALVGHVRGGMSYVLLGAMLLVSGISGSKTADMAAVAPVLFPEMRKRGMQDS 324 + + + A + V GG+ + A L + ++GS A +A+ PEMR+RG Sbjct: 80 GKDLYSAIHAWLNKVPGGLGIANVFACALFAAMAGSSPATCSAIGSAGIPEMRRRGYSPG 139 Query: 325 ELISLLAASGAMSETIPPSLVLIAIASVTGISIAALFTAGIMPAFVLAIVLAVVAWWRAG 384 ++AA G + +PPS+ +I A S+ LF AGI P +L ++ A A +RA Sbjct: 140 FAAGIIAAGGTLGILLPPSITMILYAVAAEQSLGRLFLAGIGPGVLLVLLFAGYAVYRAR 199 Query: 385 SDHV---------ATNRAPIKRVLKTFAIAVPAL--LLPFVI-----RTAVVEGVATATE 428 ++ A + T A V L +LPF+I A+ G+AT +E Sbjct: 200 KEYRLAHAVYSAGGAKSAYLDDEHFTLAQKVEMLPRVLPFLILLIGVMVALYGGLATPSE 259 Query: 429 VSTIGIAYSLIVGLIIYRGSLKWHMALPILVQTAALSGAILFIVGAASAMGWALTQSGFS 488 + +G +L++ ++YR +A P L T SG +L I+G + + ++ S Sbjct: 260 TAGLGALLALVLIAVVYRIYKPREIA-PFLSSTIKESGMLLLIIGMSLLYSYVMSYLHIS 318 Query: 489 HDLAAMMTAVPGGATGFLLVSIAAFIVLGSVLEGIPAIVLFGPLLFPVARQLGIHEIHYA 548 A + + L V + IVLG L + I++ P++ P + G I + Sbjct: 319 QSAAQWVVDLHLSKWLLLAVILGMVIVLGFFLPPVSIILMTAPIILPPLKAAGFDLIWFG 378 Query: 549 MVVILAMGLGVFAPPFGLCYYAACIIGEVKPEVAL----KRIWLYLGMLLLGLIAITFIP 604 +V+ + M +G+ PP GL + +I + P++AL K +L ++ L ++ + P Sbjct: 379 IVMTVVMEMGLIHPPVGLNLF---VIKNIAPDIALGDVIKGTIPFLALMFLAVLLLCMFP 435 Query: 605 WIS 607 I+ Sbjct: 436 GIA 438 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 0.140 0.417 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: 1,671,893 Number of extensions: 65239 Number of successful extensions: 453 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 440 Number of HSP's successfully gapped: 4 Length of query: 611 Length of database: 1,619,870 Length adjustment: 91 Effective length of query: 520 Effective length of database: 1,188,985 Effective search space: 618272200 Effective search space used: 618272200 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: 133 (55.8 bits)