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= 0003.0083.p (258 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313112|ref|YP_003777204.1| TRAP-type C4-dicarboxylate tran... 523 e-150 gi|300310441|ref|YP_003774533.1| TRAP-type C4-dicarboxylate tran... 312 2e-86 gi|300309847|ref|YP_003773939.1| TRAP-type C4-dicarboxylate tran... 308 3e-85 gi|300310178|ref|YP_003774270.1| TRAP-type C4-dicarboxylate tran... 109 3e-25 gi|300312105|ref|YP_003776197.1| TRAP-type C4-dicarboxylate-bind... 96 2e-21 >gi|300313112|ref|YP_003777204.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 344 Score = 523 bits (1348), Expect = e-150, Method: Compositional matrix adjust. Identities = 249/258 (96%), Positives = 255/258 (98%) Query: 1 MLSQVRAGAIDFFTLSPLILGTLVPAAQISGIGFAFKDYSQVWPAMDGELGAHVRKQIEA 60 MLSQVRAGAIDFFTLSPLILGTLVPAAQISGIGFAFKDYSQVWPAMDGELGAHVRKQIEA Sbjct: 87 MLSQVRAGAIDFFTLSPLILGTLVPAAQISGIGFAFKDYSQVWPAMDGELGAHVRKQIEA 146 Query: 61 KSTLFAFEKIWDNGYRQITNSTKPIKAADDLKGMKLRVPPSPLWTSMFKAFDAAPTSINF 120 +STLFAFEKIWDNGYRQITNSTKPIK A+DLKGMKLRVPPSPLWTSMFKAFDAAPTSINF Sbjct: 147 RSTLFAFEKIWDNGYRQITNSTKPIKVAEDLKGMKLRVPPSPLWTSMFKAFDAAPTSINF 206 Query: 121 AEVYSALQTKIVEGQENPMAIISTAKLYEVQKYCSITNHMWDGFWFLGNKKSFERLPKDL 180 AEVYSALQTKIVEGQENPMAIISTAKLYEVQKYCSITNHMWDGFWFLGNKKSFERLPKDL Sbjct: 207 AEVYSALQTKIVEGQENPMAIISTAKLYEVQKYCSITNHMWDGFWFLGNKKSFERLPKDL 266 Query: 181 QDLMARLINEAAMNQRADVRKLNDSLVDEMKGKGLAFNNADADSFRAKLRSAGFYAEWKK 240 Q+LM R+INEA +NQRADVRKLNDSLVDEMKGKGLAFNNADADSFRAKLR+AGFYAEWKK Sbjct: 267 QELMTRIINEAGVNQRADVRKLNDSLVDEMKGKGLAFNNADADSFRAKLRAAGFYAEWKK 326 Query: 241 KFGDEPWALLEKYTGKLA 258 KFGDEPWALLEKYTGKLA Sbjct: 327 KFGDEPWALLEKYTGKLA 344 >gi|300310441|ref|YP_003774533.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 348 Score = 312 bits (800), Expect = 2e-86, Method: Compositional matrix adjust. Identities = 142/258 (55%), Positives = 193/258 (74%), Gaps = 1/258 (0%) Query: 1 MLSQVRAGAIDFFTLSPLILGTLVPAAQISGIGFAFKDYSQVWPAMDGELGAHVRKQIEA 60 ++SQ+R G ++FF + ++L TLVPAA I GFAF DY +VW AMDG LGA+VR QIE Sbjct: 92 LMSQIRNGGVEFFNQASVVLSTLVPAAGIVNTGFAFHDYKEVWQAMDGPLGAYVRAQIE- 150 Query: 61 KSTLFAFEKIWDNGYRQITNSTKPIKAADDLKGMKLRVPPSPLWTSMFKAFDAAPTSINF 120 K L K WDNG+RQIT STKPIK A DLKG+KLRVP +P+ TS+F A A+PT INF Sbjct: 151 KVGLLTMSKPWDNGFRQITTSTKPIKTAADLKGLKLRVPAAPMLTSLFSALGASPTPINF 210 Query: 121 AEVYSALQTKIVEGQENPMAIISTAKLYEVQKYCSITNHMWDGFWFLGNKKSFERLPKDL 180 EVYS+LQTK+VEGQENP+AIISTA+LYEVQK+C+I+NH+WD +W LGN+++FE+LPKD+ Sbjct: 211 NEVYSSLQTKLVEGQENPLAIISTARLYEVQKFCTISNHVWDAYWILGNRRAFEKLPKDI 270 Query: 181 QDLMARLINEAAMNQRADVRKLNDSLVDEMKGKGLAFNNADADSFRAKLRSAGFYAEWKK 240 Q+++ R +++AA ++RAD+ L+ ++++GKG+ AD +SF+ L FY + + Sbjct: 271 QEIVRRELDKAATDERADIASLSGFARNDLQGKGVQIIEADKNSFKEALARGSFYKDLRA 330 Query: 241 KFGDEPWALLEKYTGKLA 258 KFGD+ W LL+ G L Sbjct: 331 KFGDDAWKLLQNSVGSLG 348 >gi|300309847|ref|YP_003773939.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 345 Score = 308 bits (789), Expect = 3e-85, Method: Compositional matrix adjust. Identities = 142/258 (55%), Positives = 189/258 (73%), Gaps = 1/258 (0%) Query: 1 MLSQVRAGAIDFFTLSPLILGTLVPAAQISGIGFAFKDYSQVWPAMDGELGAHVRKQIEA 60 ++SQVR G ++FF + +L TLVPAA I GFAF DY VW AMDG LGAHVR QIE Sbjct: 89 LMSQVRNGGVEFFNQANTVLSTLVPAAGIVNTGFAFHDYGAVWKAMDGPLGAHVRAQIE- 147 Query: 61 KSTLFAFEKIWDNGYRQITNSTKPIKAADDLKGMKLRVPPSPLWTSMFKAFDAAPTSINF 120 K L K WDNG+RQIT STKP++ A D+KG+KLRVP +P+ TS+F A A+PT INF Sbjct: 148 KVGLLTMSKPWDNGFRQITTSTKPVRNAGDVKGLKLRVPAAPMLTSLFSALGASPTPINF 207 Query: 121 AEVYSALQTKIVEGQENPMAIISTAKLYEVQKYCSITNHMWDGFWFLGNKKSFERLPKDL 180 EVYS+LQTK+VEGQENP+AIISTA+LYEVQK+C+I+NH+WD +W LGN+++FE+LPKD+ Sbjct: 208 NEVYSSLQTKLVEGQENPLAIISTARLYEVQKFCTISNHVWDAYWILGNRRAFEKLPKDI 267 Query: 181 QDLMARLINEAAMNQRADVRKLNDSLVDEMKGKGLAFNNADADSFRAKLRSAGFYAEWKK 240 Q+++ R +++AA ++RAD+ + +++ KGL AD DSF+ L A FY + + Sbjct: 268 QEIVRRELDKAASDERADIAAFSGFARNDLASKGLQIVEADKDSFKEALARANFYKDMRA 327 Query: 241 KFGDEPWALLEKYTGKLA 258 KFG++ W LLE G L Sbjct: 328 KFGEDAWKLLEGSVGALG 345 >gi|300310178|ref|YP_003774270.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 334 Score = 109 bits (272), Expect = 3e-25, Method: Compositional matrix adjust. Identities = 70/243 (28%), Positives = 127/243 (52%), Gaps = 19/243 (7%) Query: 2 LSQVRAGAIDFFTLSPLILGTL-VPAAQISGIGFAFKDYSQVWPAMDGELGAHVRKQIEA 60 L ++ GA+ S G L V ++ + + F ++ +G +G + K++E Sbjct: 76 LEALQLGAVQMLAPSLAKFGPLGVKEFEVFDLPYIFPTKEVLYRVTEGPIGKDLFKKLEP 135 Query: 61 KS-TLFAFEKIWDNGYRQITNSTKPIKAADDLKGMKLRVPPSPLWTSMFKAFDAAPTSIN 119 K T A+ WDNG++ + ++ KP+ D +G+K+R+ S + + +A A P + Sbjct: 136 KGITGLAY---WDNGFK-VMSANKPLHHPADFRGLKMRIQSSKVLDAQMRALGANPQVLA 191 Query: 120 FAEVYSALQTKIVEGQENPMAIISTAKLYEVQKYCSITNHMWDGFWFLGNKKSFERLPKD 179 F+EVY ALQT +V+G ENP + + T K++EVQK+ +++NH + G+ + NKK ++ LP D Sbjct: 192 FSEVYQALQTGVVDGTENPPSNLYTQKMHEVQKHVTVSNHGYLGYAVIVNKKFWDGLPSD 251 Query: 180 LQDLMARLINEAAMNQRADVRKLNDSLVD--EMKGKGLAFNNADADSFRAKLRSAGFYAE 237 ++ + + +A A ++ ND+ + E GK + DA+ AE Sbjct: 252 IRTQLEGAMKDATKYANAIAQQENDAALAAVEKTGKTTVYRLTDAEK-----------AE 300 Query: 238 WKK 240 W+K Sbjct: 301 WRK 303 >gi|300312105|ref|YP_003776197.1| TRAP-type C4-dicarboxylate-binding periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 344 Score = 96.3 bits (238), Expect = 2e-21, Method: Compositional matrix adjust. Identities = 52/182 (28%), Positives = 99/182 (54%), Gaps = 5/182 (2%) Query: 34 FAFKDYSQVWPAMDGELGAHVRKQIEAKSTL-FAFEKIWDNGYRQITNSTKPIKAADDLK 92 + F D + + +G +G + +++E K A+ WDNG + +T + +P+ D + Sbjct: 117 YIFPDKAVLKRVTEGPIGQGLFQKLEGKGIKGLAY---WDNGMKVMT-ANRPLHKVADFR 172 Query: 93 GMKLRVPPSPLWTSMFKAFDAAPTSINFAEVYSALQTKIVEGQENPMAIISTAKLYEVQK 152 +K+R+ S + F+A A P + F+EVY A+QT +V+G EN + + T K++EVQ Sbjct: 173 ALKMRIQSSKVLDEQFRALKANPQVLAFSEVYQAMQTGVVDGSENTPSNVYTQKMHEVQS 232 Query: 153 YCSITNHMWDGFWFLGNKKSFERLPKDLQDLMARLINEAAMNQRADVRKLNDSLVDEMKG 212 ++++H + G+ + NKK +E LP D++ + + +A + +K ND + +K Sbjct: 233 NLTVSDHGYIGYAVIVNKKFWEALPADIRSQLEAAMKQATLYANTIAQKENDDALAAIKA 292 Query: 213 KG 214 G Sbjct: 293 SG 294 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 0.319 0.134 0.402 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: 760,445 Number of extensions: 28619 Number of successful extensions: 82 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 79 Number of HSP's successfully gapped: 6 Length of query: 258 Length of database: 1,619,870 Length adjustment: 83 Effective length of query: 175 Effective length of database: 1,226,865 Effective search space: 214701375 Effective search space used: 214701375 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 (21.8 bits) S2: 129 (54.3 bits)