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= 0020.0443.p (618 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... 1186 0.0 gi|300313111|ref|YP_003777203.1| TRAP-type C4-dicarboxylate tran... 610 e-175 gi|300310180|ref|YP_003774272.1| TRAP-type C4-dicarboxylate tran... 168 1e-42 gi|300311996|ref|YP_003776088.1| TRAP-type C4-dicarboxylate tran... 137 3e-33 >gi|300310440|ref|YP_003774532.1| TrapT dctQ-M fusion permease, dicarboxylate transport protein [Herbaspirillum seropedicae SmR1] Length = 618 Score = 1186 bits (3068), Expect = 0.0, Method: Compositional matrix adjust. Identities = 616/618 (99%), Positives = 617/618 (99%) Query: 1 MSALSLEQPVADERSLAARLEHWLGLAIEIPAAALVVGEVAVLLAGVIMRFIFNSPIPWA 60 MSALSLEQPVADERSLAARLEHWLGLAIEIPAAALVVGEVAVLLAGVIMRFIFN+PIPWA Sbjct: 1 MSALSLEQPVADERSLAARLEHWLGLAIEIPAAALVVGEVAVLLAGVIMRFIFNNPIPWA 60 Query: 61 DELASILFLWLANLGAAVALRRGTHMRTTVLVGFMSERGKAWAEALAIIAPCVMLLILMH 120 DELASILFLWLANLGAAVALRRGTHMRTTVLVGFMSERGKAWAEALAIIAPCVMLLILMH Sbjct: 61 DELASILFLWLANLGAAVALRRGTHMRTTVLVGFMSERGKAWAEALAIIAPCVMLLILMH 120 Query: 121 PMWEYAEDEMFVQTPALGWPNTVRAAAVAVGAALMIALSLLRISRQKLVDLVGVLALLAV 180 PMWEYAEDEMFVQTPALGWPNTVRAAAVAVGAALMIALSLLRISRQKLVDLVGVLALLAV Sbjct: 121 PMWEYAEDEMFVQTPALGWPNTVRAAAVAVGAALMIALSLLRISRQKLVDLVGVLALLAV 180 Query: 181 VAGAMYLGAAWLQAIGNWNLVVFFGLVLVVSVLLGIPIAFCFGLATVAFMLTVTTSPLAV 240 VAGAMYLGAAWLQAIGNWNLVVFFGLVL VSVLLGIPIAFCFGLATVAFMLTVTTSPLAV Sbjct: 181 VAGAMYLGAAWLQAIGNWNLVVFFGLVLAVSVLLGIPIAFCFGLATVAFMLTVTTSPLAV 240 Query: 241 VAGRFDEGMSSLILLAVPLFILLGHLVEMTGMAKAMVDFLASLLGHVRGGLNYVLLGAML 300 VAGRFDEGMSSLILLAVPLFILLGHLVEMTGMAKAMVDFLASLLGHVRGGLNYVLLGAML Sbjct: 241 VAGRFDEGMSSLILLAVPLFILLGHLVEMTGMAKAMVDFLASLLGHVRGGLNYVLLGAML 300 Query: 301 LVSGISGAKTADMAAVAPVLLPEMKRRGNHEGELISLLAASGAMAETIPPSLVLITIGSV 360 LVSGISGAKTADMAAVAPVLLPEMKRRGNHEGELISLLAASGAMAETIPPSLVLITIGSV Sbjct: 301 LVSGISGAKTADMAAVAPVLLPEMKRRGNHEGELISLLAASGAMAETIPPSLVLITIGSV 360 Query: 361 AGVSIAALFTGGIMPGIVLAVLLAILARWRSAEIMEGIQRAPGRVVLRTLIIALPALLLP 420 AGVSIAALFTGGIMPGIVLAVLLAILARWRSAEIMEGIQRAPGRVVLRTLIIALPALLLP Sbjct: 361 AGVSIAALFTGGIMPGIVLAVLLAILARWRSAEIMEGIQRAPGRVVLRTLIIALPALLLP 420 Query: 421 ILIRTAVVEGVATATEVSTIGIAYSVVAGLLVYRKFDWKRLYPMLVDTAALSGAILFIIG 480 ILIRTAVVEGVATATEVSTIGIAYSVVAGLLVYRKFDWKRLYPMLVDTAALSGAILFIIG Sbjct: 421 ILIRTAVVEGVATATEVSTIGIAYSVVAGLLVYRKFDWKRLYPMLVDTAALSGAILFIIG 480 Query: 481 TATGMSWALTQSGFSHALAEAMTSVPGGKYGFLLVSIAAFIVLGSVLEGIPAMVLFAPLL 540 TATGMSWALTQSGFSHALAEAMTSVPGGKYGFLLVSIAAFIVLGSVLEGIPAMVLFAPLL Sbjct: 481 TATGMSWALTQSGFSHALAEAMTSVPGGKYGFLLVSIAAFIVLGSVLEGIPAMVLFAPLL 540 Query: 541 FPVAKAIGVHEVHYAMVIILSMGVGLFAPPFGLGYYAACTIGRVHPDVAVKRIWPYLGAL 600 FPVAKAIGVHEVHYAMVIILSMGVGLFAPPFGLGYYAACTIGRVHPDVAVKRIWPYLGAL Sbjct: 541 FPVAKAIGVHEVHYAMVIILSMGVGLFAPPFGLGYYAACTIGRVHPDVAVKRIWPYLGAL 600 Query: 601 VVGLLIVAFVPWFSIGFL 618 VVGLLIVAFVPWFSIGFL Sbjct: 601 VVGLLIVAFVPWFSIGFL 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 = 610 bits (1572), Expect = e-175, Method: Compositional matrix adjust. Identities = 344/585 (58%), Positives = 453/585 (77%), Gaps = 5/585 (0%) Query: 39 EVAVLLAGVIMRFIFNSPIPWADELASILFLWLANLGAAVALRRGTHMRTTVLVGFMSER 98 E VLL GVI R+ + P+ W+DELASILF+WL+ LGA +AL RG HMR T ++ SE+ Sbjct: 43 ETVVLLTGVIYRYALHDPLVWSDELASILFIWLSMLGAVLALDRGEHMRLTAIINKCSEK 102 Query: 99 GKAWAEALAIIAPCVMLLILMHPMWEYAEDEMFVQTPALGWPNTVRAAAVAVGAALMIAL 158 G+ W E +A + C+ +L+++HP ++A ++M + TPAL P+ +RAAA+ VGA LM+ Sbjct: 103 GRIWLETVAALVVCIFVLMVIHPAVDHAVEQMPITTPALEIPDGLRAAALPVGAILMLLA 162 Query: 159 SLLRISRQKLVDLV-GVLALLAVVAGAMYLGAAWLQAIGNWNLVVFFGLVLVVSVLLGIP 217 ++ R++ + L+ LA++AV+ GA++L L +GN+NL+VFF L++ V V GIP Sbjct: 163 AVSRMAAMTTMRLLLSALAVVAVIGGALWLAKPMLLGMGNYNLIVFFVLLIGVCVAGGIP 222 Query: 218 IAFCFGLATVAFMLTVTTSPLAVVAGRFDEGMSSLILLAVPLFILLGHLVEMTGMAKAMV 277 IAF FG AT+A++ TT+PL +V R DEGMSSLILL+VPLF+LLG L+EM+G+AK ++ Sbjct: 223 IAFAFGTATMAYLALATTAPLMIVVSRMDEGMSSLILLSVPLFVLLGSLLEMSGLAKTLI 282 Query: 278 DFLASLLGHVRGGLNYVLLGAMLLVSGISGAKTADMAAVAPVLLPEMKRRGNHEGELISL 337 DF+A+LLGHVRGGL YVLLGAM LVSGISG+K ADMAA+AP L PEMK+RG+ EL++L Sbjct: 283 DFMAALLGHVRGGLQYVLLGAMFLVSGISGSKAADMAAIAPALFPEMKKRGSKPEELVAL 342 Query: 338 LAASGAMAETIPPSLVLITIGSVAGVSIAALFTGGIMPGIVLAVLLAILARWRS-AEIME 396 L++SGAM ETIPPSLVLITIG+V VSI ALF GG+MP + + +A++ R+ E M Sbjct: 343 LSSSGAMTETIPPSLVLITIGAVCSVSITALFIGGLMPAAIATIAIAVVCWMRARREPMP 402 Query: 397 GIQRAPGRVVLRTLIIALPALLLPILIRTAVVEGVATATEVSTIGIAYSVVAGLLVY--- 453 ++RAP ++++ LI A+PAL LP+LIR AV+EGVATATEV+TIG+AY+VV GL+++ Sbjct: 403 DVKRAPLSLIVKALIAAIPALALPMLIRVAVIEGVATATEVATIGVAYTVVVGLIMHLFM 462 Query: 454 RKFDWKRLYPMLVDTAALSGAILFIIGTATGMSWALTQSGFSHALAEAMTSVPGGKYGFL 513 R +KRLYPML+++AALSGAIL IIG AT M+WALTQSGFS L M VPGG GFL Sbjct: 463 RHLSFKRLYPMLIESAALSGAILLIIGMATAMAWALTQSGFSAKLVALMQGVPGGGVGFL 522 Query: 514 LVSIAAFIVLGSVLEGIPAMVLFAPLLFPVAKAIGVHEVHYAMVIILSMGVGLFAPPFGL 573 L++I FIVLGS+LEGIPA+VLF PLLFPVA+++GVH+VHYAMV+IL+MG+GLFAPPFG+ Sbjct: 523 LITIVIFIVLGSLLEGIPAIVLFGPLLFPVARSLGVHDVHYAMVVILAMGIGLFAPPFGV 582 Query: 574 GYYAACTIGRVHPDVAVKRIWPYLGALVVGLLIVAFVPWFSIGFL 618 G+YAAC IG+V PD R+W YL ALVV LL+VAFVPW SIGFL Sbjct: 583 GFYAACAIGKVSPDGVFNRVWGYLAALVVALLVVAFVPWISIGFL 627 >gi|300310180|ref|YP_003774272.1| TRAP-type C4-dicarboxylate transport system large permease [Herbaspirillum seropedicae SmR1] Length = 426 Score = 168 bits (425), Expect = 1e-42, Method: Compositional matrix adjust. Identities = 121/408 (29%), Positives = 215/408 (52%), Gaps = 7/408 (1%) Query: 212 VLLGIPIAFCFGLATVAFMLTVTTSPLAVVAGRFDEGMSSLILLAVPLFILLGHLVEMTG 271 +L G+PI+ GL + F+ T+T P+ VA + G+ ++A+P FIL G+ + G Sbjct: 14 MLTGMPISISLGLTVLTFLFTMTEVPIQSVALKLFTGIEKFEIMAIPFFILAGNFLTHGG 73 Query: 272 MAKAMVDFLASLLGHVRGGLNYVLLGAMLLVSGISGAKTADMAAVAPVLLPEMKRRGNHE 331 +A+ M++F S++GH GGL + A L + +SG+ A + A+ ++LP M ++G Sbjct: 74 VARRMINFATSMVGHWHGGLALAGVLACALFAAVSGSSPATVVAIGSIILPAMVKQGFPN 133 Query: 332 GELISLLAASGAMAETIPPSLVLITIGSVAGVSIAALFTGGIMPGIVLAVLLAI----LA 387 ++ SGA+ IPPS+V++ S+ LF G++PG++LA LL + LA Sbjct: 134 RFGAGVITTSGALGILIPPSIVMVMYSVSTNTSVGKLFMAGVVPGLLLAFLLGVTTWFLA 193 Query: 388 RWRSAEIMEGIQRAPGRVVLRTLIIALPALLLPILIRTAVVEGVATATEVSTIGIAYSVV 447 R + ++ A R + L L +++ + GV T TE + + Y+ Sbjct: 194 RKNNYPRLKKATWAERAAAFRK---SGWGLFLIVIVMGGIYTGVFTPTEAAAMAAVYAFF 250 Query: 448 AGLLVYRKFDWKRLYPMLVDTAALSGAILFIIGTATGMSWALTQSGFSHALAEAMTSVPG 507 + VY+ K++ +L+D+A++S +L+II A S+ +T A+A +T Sbjct: 251 IAVFVYKDLTLKQVPKVLLDSASMSAMLLYIITNAVLFSFLVTSENIPQAMAAWITDSGL 310 Query: 508 GKYGFLLVSIAAFIVLGSVLEGIPAMVLFAPLLFPVAKAIGVHEVHYAMVIILSMGVGLF 567 G FLLV ++ G+V+E +++ AP+LFPVA +G+ VH+ ++I+++M VG+ Sbjct: 311 GPITFLLVVNILLLLAGNVMEPSSIVLILAPILFPVAMKLGIDPVHFGILIVVNMEVGMC 370 Query: 568 APPFGLGYYAACTIGRVHPDVAVKRIWPYLGALVVGLLIVAFVPWFSI 615 PP GL Y A I ++ + P+L ++ L +V + P S+ Sbjct: 371 HPPVGLNLYVASGITKMGITELTIAVMPWLLTMLGFLALVTYWPALSL 418 >gi|300311996|ref|YP_003776088.1| TRAP-type C4-dicarboxylate transport system large permease [Herbaspirillum seropedicae SmR1] Length = 449 Score = 137 bits (345), Expect = 3e-33, Method: Compositional matrix adjust. Identities = 124/434 (28%), Positives = 213/434 (49%), Gaps = 24/434 (5%) Query: 199 NLVVFFGLVLVVSVLLGIPIAFCFGLATVAFM-LTVTTSPLAVVAGRFDEGMSSLILLAV 257 L V +G+V +V + G+PIAF G+ FM + S L + E ++S+ LL++ Sbjct: 5 TLGVLYGVVTIVVMCSGMPIAFALGVVATGFMYFFMPESSLDTITQNVYEEIASITLLSI 64 Query: 258 PLFILLGHLVEMTGMAKAMVDFLASLLGHVRGGLNYVLLGAMLLVSGISGAKTADMAAVA 317 PLFIL G + + K + + + L V GGL + A L + ++G+ A +A+ Sbjct: 65 PLFILKGAAIGKSPAGKDLYSAIHAWLNKVPGGLGIANVFACALFAAMAGSSPATCSAIG 124 Query: 318 PVLLPEMKRRGNHEGELISLLAASGAMAETIPPSLVLITIGSVAGVSIAALFTGGIMPGI 377 +PEM+RRG G ++AA G + +PPS+ +I A S+ LF GI PG+ Sbjct: 125 SAGIPEMRRRGYSPGFAAGIIAAGGTLGILLPPSITMILYAVAAEQSLGRLFLAGIGPGV 184 Query: 378 VLAVLLAILARWRSAE---IMEGIQRAPGRVV-------------LRTLIIALPALLLPI 421 +L +L A A +R+ + + + A G + L LP L+L I Sbjct: 185 LLVLLFAGYAVYRARKEYRLAHAVYSAGGAKSAYLDDEHFTLAQKVEMLPRVLPFLILLI 244 Query: 422 LIRTAVVEGVATATEVSTIGIAYSVVAGLLVYRKFDWKRLYPMLVDTAALSGAILFIIGT 481 + A+ G+AT +E + +G ++V +VYR + + + P L T SG +L IIG Sbjct: 245 GVMVALYGGLATPSETAGLGALLALVLIAVVYRIYKPREIAPFLSSTIKESGMLLLIIGM 304 Query: 482 ATGMSWALTQSGFSHALAEAMTSVPGGKYGFLLVSIAAFIVLGSVLEGIPAMVLFAPLLF 541 + S+ ++ S + A+ + + K+ L V + IVLG L + +++ AP++ Sbjct: 305 SLLYSYVMSYLHISQSAAQWVVDLHLSKWLLLAVILGMVIVLGFFLPPVSIILMTAPIIL 364 Query: 542 PVAKAIGVHEVHYAMVIILSMGVGLFAPPFGLGYYAACTIGRVHPDVA----VKRIWPYL 597 P KA G + + +V+ + M +GL PP GL + I + PD+A +K P+L Sbjct: 365 PPLKAAGFDLIWFGIVMTVVMEMGLIHPPVGLNLF---VIKNIAPDIALGDVIKGTIPFL 421 Query: 598 GALVVGLLIVAFVP 611 + + +L++ P Sbjct: 422 ALMFLAVLLLCMFP 435 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 0.141 0.420 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: 1,533,389 Number of extensions: 57344 Number of successful extensions: 396 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 384 Number of HSP's successfully gapped: 4 Length of query: 618 Length of database: 1,619,870 Length adjustment: 91 Effective length of query: 527 Effective length of database: 1,188,985 Effective search space: 626595095 Effective search space used: 626595095 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: 133 (55.8 bits)