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= 0038.0056.p (627 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310441|ref|YP_003774533.1| TRAP-type C4-dicarboxylate tran... 492 e-140 gi|300309847|ref|YP_003773939.1| TRAP-type C4-dicarboxylate tran... 479 e-136 gi|300313112|ref|YP_003777204.1| TRAP-type C4-dicarboxylate tran... 361 e-100 gi|300310440|ref|YP_003774532.1| TrapT dctQ-M fusion permease, d... 308 6e-85 gi|300313111|ref|YP_003777203.1| TRAP-type C4-dicarboxylate tran... 229 4e-61 >gi|300310441|ref|YP_003774533.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 348 Score = 492 bits (1267), Expect = e-140, Method: Compositional matrix adjust. Identities = 225/325 (69%), Positives = 282/325 (86%) Query: 8 QSGTTRRKLLTYGAAGAALPMSAWIAKYAHAAEFNYKFATGQDPTHPVNKRAQDAITRIK 67 ++ +RR+LL GA GAALP+ + +++ A+AAEFNYKFATGQDP+HPVNKRAQ AI RI+ Sbjct: 10 KTSVSRRQLLKAGAVGAALPLFSIMSRPANAAEFNYKFATGQDPSHPVNKRAQQAIDRIR 69 Query: 68 EATSGRVDIKLFPANQLGSDTDLLAQVRNGGVEFFNIAASILATLVPAAGIVNTGFAFSN 127 EAT GR+DIKLFPANQLGSDTDL++Q+RNGGVEFFN A+ +L+TLVPAAGIVNTGFAF + Sbjct: 70 EATGGRLDIKLFPANQLGSDTDLMSQIRNGGVEFFNQASVVLSTLVPAAGIVNTGFAFHD 129 Query: 128 YDEVWKAMDGDLGKYIFSQIDKVGVMSMSRAWNNGFRQITSGVKPIRTPDDLRGMKLRVP 187 Y EVW+AMDG LG Y+ +QI+KVG+++MS+ W+NGFRQIT+ KPI+T DL+G+KLRVP Sbjct: 130 YKEVWQAMDGPLGAYVRAQIEKVGLLTMSKPWDNGFRQITTSTKPIKTAADLKGLKLRVP 189 Query: 188 AAPILTSLFQSLGAGPTPINFNEVYSSLQTKLVEGQENPLPIIATARLYEVQKYCSMTSH 247 AAP+LTSLF +LGA PTPINFNEVYSSLQTKLVEGQENPL II+TARLYEVQK+C++++H Sbjct: 190 AAPMLTSLFSALGASPTPINFNEVYSSLQTKLVEGQENPLAIISTARLYEVQKFCTISNH 249 Query: 248 VWDAYLVLGNKRAFQKLPADVQAIVLREFDKAALDQRADIARLNDSLRQELSGKGLQFID 307 VWDAY +LGN+RAF+KLP D+Q IV RE DKAA D+RADIA L+ R +L GKG+Q I+ Sbjct: 250 VWDAYWILGNRRAFEKLPKDIQEIVRRELDKAATDERADIASLSGFARNDLQGKGVQIIE 309 Query: 308 VDKNAFRDALRKTTFYKDWKAKFGE 332 DKN+F++AL + +FYKD +AKFG+ Sbjct: 310 ADKNSFKEALARGSFYKDLRAKFGD 334 >gi|300309847|ref|YP_003773939.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 345 Score = 479 bits (1234), Expect = e-136, Method: Compositional matrix adjust. Identities = 219/329 (66%), Positives = 277/329 (84%) Query: 4 DTLTQSGTTRRKLLTYGAAGAALPMSAWIAKYAHAAEFNYKFATGQDPTHPVNKRAQDAI 63 D + TRR +L GA GAALP+ + +++ A AAEF+YKFATGQDP+HPVNKRAQ+AI Sbjct: 3 DERAKKQVTRRNMLKAGAVGAALPLFSILSRPASAAEFSYKFATGQDPSHPVNKRAQEAI 62 Query: 64 TRIKEATSGRVDIKLFPANQLGSDTDLLAQVRNGGVEFFNIAASILATLVPAAGIVNTGF 123 RI+ AT+GR++IKLFPANQLGSDTDL++QVRNGGVEFFN A ++L+TLVPAAGIVNTGF Sbjct: 63 DRIRNATNGRLEIKLFPANQLGSDTDLMSQVRNGGVEFFNQANTVLSTLVPAAGIVNTGF 122 Query: 124 AFSNYDEVWKAMDGDLGKYIFSQIDKVGVMSMSRAWNNGFRQITSGVKPIRTPDDLRGMK 183 AF +Y VWKAMDG LG ++ +QI+KVG+++MS+ W+NGFRQIT+ KP+R D++G+K Sbjct: 123 AFHDYGAVWKAMDGPLGAHVRAQIEKVGLLTMSKPWDNGFRQITTSTKPVRNAGDVKGLK 182 Query: 184 LRVPAAPILTSLFQSLGAGPTPINFNEVYSSLQTKLVEGQENPLPIIATARLYEVQKYCS 243 LRVPAAP+LTSLF +LGA PTPINFNEVYSSLQTKLVEGQENPL II+TARLYEVQK+C+ Sbjct: 183 LRVPAAPMLTSLFSALGASPTPINFNEVYSSLQTKLVEGQENPLAIISTARLYEVQKFCT 242 Query: 244 MTSHVWDAYLVLGNKRAFQKLPADVQAIVLREFDKAALDQRADIARLNDSLRQELSGKGL 303 +++HVWDAY +LGN+RAF+KLP D+Q IV RE DKAA D+RADIA + R +L+ KGL Sbjct: 243 ISNHVWDAYWILGNRRAFEKLPKDIQEIVRRELDKAASDERADIAAFSGFARNDLASKGL 302 Query: 304 QFIDVDKNAFRDALRKTTFYKDWKAKFGE 332 Q ++ DK++F++AL + FYKD +AKFGE Sbjct: 303 QIVEADKDSFKEALARANFYKDMRAKFGE 331 >gi|300313112|ref|YP_003777204.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 344 Score = 361 bits (926), Expect = e-100, Method: Compositional matrix adjust. Identities = 162/323 (50%), Positives = 235/323 (72%), Gaps = 1/323 (0%) Query: 12 TRRKLLTYGAAGAALPMSAWIAKYAHAAEFNYKFATGQDPTHPVNKRAQDAITRIKEATS 71 TRR L + +A + ++ AHAAEF +K+A THP+N RA++ I E + Sbjct: 9 TRRNFLKTASVASAAAATGLVSTSAHAAEFTFKYANNLPVTHPMNARAKEMAAAIAEQSK 68 Query: 72 GRVDIKLFPANQLGSDTDLLAQVRNGGVEFFNIAASILATLVPAAGIVNTGFAFSNYDEV 131 GR++++L+P NQLG+DTD+L+QVR G ++FF ++ IL TLVPAA I GFAF +Y +V Sbjct: 69 GRIELQLYPNNQLGTDTDMLSQVRAGAIDFFTLSPLILGTLVPAAQISGIGFAFKDYSQV 128 Query: 132 WKAMDGDLGKYIFSQID-KVGVMSMSRAWNNGFRQITSGVKPIRTPDDLRGMKLRVPAAP 190 W AMDG+LG ++ QI+ + + + + W+NG+RQIT+ KPI+ +DL+GMKLRVP +P Sbjct: 129 WPAMDGELGAHVRKQIEARSTLFAFEKIWDNGYRQITNSTKPIKVAEDLKGMKLRVPPSP 188 Query: 191 ILTSLFQSLGAGPTPINFNEVYSSLQTKLVEGQENPLPIIATARLYEVQKYCSMTSHVWD 250 + TS+F++ A PT INF EVYS+LQTK+VEGQENP+ II+TA+LYEVQKYCS+T+H+WD Sbjct: 189 LWTSMFKAFDAAPTSINFAEVYSALQTKIVEGQENPMAIISTAKLYEVQKYCSITNHMWD 248 Query: 251 AYLVLGNKRAFQKLPADVQAIVLREFDKAALDQRADIARLNDSLRQELSGKGLQFIDVDK 310 + LGNK++F++LP D+Q ++ R ++A ++QRAD+ +LNDSL E+ GKGL F + D Sbjct: 249 GFWFLGNKKSFERLPKDLQELMTRIINEAGVNQRADVRKLNDSLVDEMKGKGLAFNNADA 308 Query: 311 NAFRDALRKTTFYKDWKAKFGEQ 333 ++FR LR FY +WK KFG++ Sbjct: 309 DSFRAKLRAAGFYAEWKKKFGDE 331 >gi|300310440|ref|YP_003774532.1| TrapT dctQ-M fusion permease, dicarboxylate transport protein [Herbaspirillum seropedicae SmR1] Length = 618 Score = 308 bits (790), Expect = 6e-85, Method: Compositional matrix adjust. Identities = 160/210 (76%), Positives = 181/210 (86%) Query: 336 VAVVLAAIAAALYLGGSQLQAMGNWNLAFFFIALLGAGVLAGVPIAFCFGLVTIAYLLCT 395 V +LA +A A+YLG + LQA+GNWNL FF +L VL G+PIAFCFGL T+A++L Sbjct: 174 VLALLAVVAGAMYLGAAWLQAIGNWNLVVFFGLVLAVSVLLGIPIAFCFGLATVAFMLTV 233 Query: 396 TSTPLEVVPGRINEGMSSLILLAVPLFILLGQLIEMTQMAKAMVAFLASLLGHVRGGLSY 455 T++PL VV GR +EGMSSLILLAVPLFILLG L+EMT MAKAMV FLASLLGHVRGGL+Y Sbjct: 234 TTSPLAVVAGRFDEGMSSLILLAVPLFILLGHLVEMTGMAKAMVDFLASLLGHVRGGLNY 293 Query: 456 VLLGAIMLVSGISGAKTADMAAVAPVLFPEMKKRGMEEGELVSLLAASGAMAETIPPSLV 515 VLLGA++LVSGISGAKTADMAAVAPVL PEMK+RG EGEL+SLLAASGAMAETIPPSLV Sbjct: 294 VLLGAMLLVSGISGAKTADMAAVAPVLLPEMKRRGNHEGELISLLAASGAMAETIPPSLV 353 Query: 516 LITIGSVTGVSIAALFTGGLLPGIVLAXLF 545 LITIGSV GVSIAALFTGG++PGIVLA L Sbjct: 354 LITIGSVAGVSIAALFTGGIMPGIVLAVLL 383 >gi|300313111|ref|YP_003777203.1| TRAP-type C4-dicarboxylate transport system dctQ-M fusion permease large permease [Herbaspirillum seropedicae SmR1] Length = 627 Score = 229 bits (585), Expect = 4e-61, Method: Compositional matrix adjust. Identities = 128/199 (64%), Positives = 157/199 (78%) Query: 339 VLAAIAAALYLGGSQLQAMGNWNLAFFFIALLGAGVLAGVPIAFCFGLVTIAYLLCTTST 398 V+A I AL+L L MGN+NL FF+ L+G V G+PIAF FG T+AYL T+ Sbjct: 182 VVAVIGGALWLAKPMLLGMGNYNLIVFFVLLIGVCVAGGIPIAFAFGTATMAYLALATTA 241 Query: 399 PLEVVPGRINEGMSSLILLAVPLFILLGQLIEMTQMAKAMVAFLASLLGHVRGGLSYVLL 458 PL +V R++EGMSSLILL+VPLF+LLG L+EM+ +AK ++ F+A+LLGHVRGGL YVLL Sbjct: 242 PLMIVVSRMDEGMSSLILLSVPLFVLLGSLLEMSGLAKTLIDFMAALLGHVRGGLQYVLL 301 Query: 459 GAIMLVSGISGAKTADMAAVAPVLFPEMKKRGMEEGELVSLLAASGAMAETIPPSLVLIT 518 GA+ LVSGISG+K ADMAA+AP LFPEMKKRG + ELV+LL++SGAM ETIPPSLVLIT Sbjct: 302 GAMFLVSGISGSKAADMAAIAPALFPEMKKRGSKPEELVALLSSSGAMTETIPPSLVLIT 361 Query: 519 IGSVTGVSIAALFTGGLLP 537 IG+V VSI ALF GGL+P Sbjct: 362 IGAVCSVSITALFIGGLMP 380 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 0.322 0.135 0.400 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: 1,827,518 Number of extensions: 74920 Number of successful extensions: 303 Number of sequences better than 1.0e-08: 10 Number of HSP's gapped: 296 Number of HSP's successfully gapped: 10 Length of query: 627 Length of database: 1,619,870 Length adjustment: 91 Effective length of query: 536 Effective length of database: 1,188,985 Effective search space: 637295960 Effective search space used: 637295960 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 133 (55.8 bits)