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= 0023.0006.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... 456 e-130 gi|300310441|ref|YP_003774533.1| TRAP-type C4-dicarboxylate tran... 293 1e-80 gi|300309847|ref|YP_003773939.1| TRAP-type C4-dicarboxylate tran... 289 2e-79 gi|300310178|ref|YP_003774270.1| TRAP-type C4-dicarboxylate tran... 111 5e-26 gi|300312105|ref|YP_003776197.1| TRAP-type C4-dicarboxylate-bind... 98 7e-22 >gi|300313112|ref|YP_003777204.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 344 Score = 456 bits (1173), Expect = e-130, Method: Compositional matrix adjust. Identities = 212/258 (82%), Positives = 234/258 (90%) Query: 1 MLSQVRAGAIDFFTISPEVLGTLVSAGQISGVGFAFKDYNQVWAAMDGDLGAYVRKQIAA 60 MLSQVRAGAIDFFT+SP +LGTLV A QISG+GFAFKDY+QVW AMDG+LGA+VRKQI A Sbjct: 87 MLSQVRAGAIDFFTLSPLILGTLVPAAQISGIGFAFKDYSQVWPAMDGELGAHVRKQIEA 146 Query: 61 TTSLFAFERCWDNGYRQVTTSTRPITRPEDFKGMKLRVPPSPLWTSMFRAFDAAPASINF 120 ++LFAFE+ WDNGYRQ+T ST+PI ED KGMKLRVPPSPLWTSMF+AFDAAP SINF Sbjct: 147 RSTLFAFEKIWDNGYRQITNSTKPIKVAEDLKGMKLRVPPSPLWTSMFKAFDAAPTSINF 206 Query: 121 AEVYSALQTKIVEGQENPMAIISTAKLYEVQKYCSMTNHMWDGFWFLANKKSFERLPKDL 180 AEVYSALQTKIVEGQENPMAIISTAKLYEVQKYCS+TNHMWDGFWFL NKKSFERLPKDL Sbjct: 207 AEVYSALQTKIVEGQENPMAIISTAKLYEVQKYCSITNHMWDGFWFLGNKKSFERLPKDL 266 Query: 181 QEIVTRNVNEAGIKQRADVKALNDSLATEMKGKGLAFNDTDNEAFRAKLRSAGFYAEWHK 240 QE++TR +NEAG+ QRADV+ LNDSL EMKGKGLAFN+ D ++FRAKLR+AGFYAEW K Sbjct: 267 QELMTRIINEAGVNQRADVRKLNDSLVDEMKGKGLAFNNADADSFRAKLRAAGFYAEWKK 326 Query: 241 KFGPEAWALLEKYTGKLA 258 KFG E WALLEKYTGKLA Sbjct: 327 KFGDEPWALLEKYTGKLA 344 >gi|300310441|ref|YP_003774533.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 348 Score = 293 bits (750), Expect = 1e-80, Method: Compositional matrix adjust. Identities = 132/258 (51%), Positives = 180/258 (69%), Gaps = 1/258 (0%) Query: 1 MLSQVRAGAIDFFTISPEVLGTLVSAGQISGVGFAFKDYNQVWAAMDGDLGAYVRKQIAA 60 ++SQ+R G ++FF + VL TLV A I GFAF DY +VW AMDG LGAYVR QI Sbjct: 92 LMSQIRNGGVEFFNQASVVLSTLVPAAGIVNTGFAFHDYKEVWQAMDGPLGAYVRAQIE- 150 Query: 61 TTSLFAFERCWDNGYRQVTTSTRPITRPEDFKGMKLRVPPSPLWTSMFRAFDAAPASINF 120 L + WDNG+RQ+TTST+PI D KG+KLRVP +P+ TS+F A A+P INF Sbjct: 151 KVGLLTMSKPWDNGFRQITTSTKPIKTAADLKGLKLRVPAAPMLTSLFSALGASPTPINF 210 Query: 121 AEVYSALQTKIVEGQENPMAIISTAKLYEVQKYCSMTNHMWDGFWFLANKKSFERLPKDL 180 EVYS+LQTK+VEGQENP+AIISTA+LYEVQK+C+++NH+WD +W L N+++FE+LPKD+ Sbjct: 211 NEVYSSLQTKLVEGQENPLAIISTARLYEVQKFCTISNHVWDAYWILGNRRAFEKLPKDI 270 Query: 181 QEIVTRNVNEAGIKQRADVKALNDSLATEMKGKGLAFNDTDNEAFRAKLRSAGFYAEWHK 240 QEIV R +++A +RAD+ +L+ +++GKG+ + D +F+ L FY + Sbjct: 271 QEIVRRELDKAATDERADIASLSGFARNDLQGKGVQIIEADKNSFKEALARGSFYKDLRA 330 Query: 241 KFGPEAWALLEKYTGKLA 258 KFG +AW 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 = 289 bits (739), Expect = 2e-79, Method: Compositional matrix adjust. Identities = 133/257 (51%), Positives = 178/257 (69%), Gaps = 1/257 (0%) Query: 1 MLSQVRAGAIDFFTISPEVLGTLVSAGQISGVGFAFKDYNQVWAAMDGDLGAYVRKQIAA 60 ++SQVR G ++FF + VL TLV A I GFAF DY VW AMDG LGA+VR QI Sbjct: 89 LMSQVRNGGVEFFNQANTVLSTLVPAAGIVNTGFAFHDYGAVWKAMDGPLGAHVRAQIE- 147 Query: 61 TTSLFAFERCWDNGYRQVTTSTRPITRPEDFKGMKLRVPPSPLWTSMFRAFDAAPASINF 120 L + WDNG+RQ+TTST+P+ D KG+KLRVP +P+ TS+F A A+P INF Sbjct: 148 KVGLLTMSKPWDNGFRQITTSTKPVRNAGDVKGLKLRVPAAPMLTSLFSALGASPTPINF 207 Query: 121 AEVYSALQTKIVEGQENPMAIISTAKLYEVQKYCSMTNHMWDGFWFLANKKSFERLPKDL 180 EVYS+LQTK+VEGQENP+AIISTA+LYEVQK+C+++NH+WD +W L N+++FE+LPKD+ Sbjct: 208 NEVYSSLQTKLVEGQENPLAIISTARLYEVQKFCTISNHVWDAYWILGNRRAFEKLPKDI 267 Query: 181 QEIVTRNVNEAGIKQRADVKALNDSLATEMKGKGLAFNDTDNEAFRAKLRSAGFYAEWHK 240 QEIV R +++A +RAD+ A + ++ KGL + D ++F+ L A FY + Sbjct: 268 QEIVRRELDKAASDERADIAAFSGFARNDLASKGLQIVEADKDSFKEALARANFYKDMRA 327 Query: 241 KFGPEAWALLEKYTGKL 257 KFG +AW LLE G L Sbjct: 328 KFGEDAWKLLEGSVGAL 344 >gi|300310178|ref|YP_003774270.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 334 Score = 111 bits (278), Expect = 5e-26, Method: Compositional matrix adjust. Identities = 74/248 (29%), Positives = 125/248 (50%), Gaps = 21/248 (8%) Query: 2 LSQVRAGAIDFFTISPEVLGTL-VSAGQISGVGFAFKDYNQVWAAMDGDLGAYVRKQI-- 58 L ++ GA+ S G L V ++ + + F ++ +G +G + K++ Sbjct: 76 LEALQLGAVQMLAPSLAKFGPLGVKEFEVFDLPYIFPTKEVLYRVTEGPIGKDLFKKLEP 135 Query: 59 AATTSLFAFERCWDNGYRQVTTSTRPITRPEDFKGMKLRVPPSPLWTSMFRAFDAAPASI 118 T L WDNG++ V ++ +P+ P DF+G+K+R+ S + + RA A P + Sbjct: 136 KGITGL----AYWDNGFK-VMSANKPLHHPADFRGLKMRIQSSKVLDAQMRALGANPQVL 190 Query: 119 NFAEVYSALQTKIVEGQENPMAIISTAKLYEVQKYCSMTNHMWDGFWFLANKKSFERLPK 178 F+EVY ALQT +V+G ENP + + T K++EVQK+ +++NH + G+ + NKK ++ LP Sbjct: 191 AFSEVYQALQTGVVDGTENPPSNLYTQKMHEVQKHVTVSNHGYLGYAVIVNKKFWDGLPS 250 Query: 179 DLQEIVTRNVNEAGIKQRADVKALNDS--LATEMKGKGLAFNDTDNEAFRAKLRSAGFYA 236 D++ + + +A A + ND+ A E GK + TD E A Sbjct: 251 DIRTQLEGAMKDATKYANAIAQQENDAALAAVEKTGKTTVYRLTDAEK-----------A 299 Query: 237 EWHKKFGP 244 EW K P Sbjct: 300 EWRKALLP 307 >gi|300312105|ref|YP_003776197.1| TRAP-type C4-dicarboxylate-binding periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 344 Score = 97.8 bits (242), Expect = 7e-22, Method: Compositional matrix adjust. Identities = 53/162 (32%), Positives = 90/162 (55%), Gaps = 1/162 (0%) Query: 71 WDNGYRQVTTSTRPITRPEDFKGMKLRVPPSPLWTSMFRAFDAAPASINFAEVYSALQTK 130 WDNG + V T+ RP+ + DF+ +K+R+ S + FRA A P + F+EVY A+QT Sbjct: 152 WDNGMK-VMTANRPLHKVADFRALKMRIQSSKVLDEQFRALKANPQVLAFSEVYQAMQTG 210 Query: 131 IVEGQENPMAIISTAKLYEVQKYCSMTNHMWDGFWFLANKKSFERLPKDLQEIVTRNVNE 190 +V+G EN + + T K++EVQ ++++H + G+ + NKK +E LP D++ + + + Sbjct: 211 VVDGSENTPSNVYTQKMHEVQSNLTVSDHGYIGYAVIVNKKFWEALPADIRSQLEAAMKQ 270 Query: 191 AGIKQRADVKALNDSLATEMKGKGLAFNDTDNEAFRAKLRSA 232 A + + ND +K G T +E +A+ R A Sbjct: 271 ATLYANTIAQKENDDALAAIKASGKTRVYTLSEQEKAEWRRA 312 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 0.132 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: 767,423 Number of extensions: 28864 Number of successful extensions: 72 Number of sequences better than 1.0e-08: 5 Number of HSP's gapped: 71 Number of HSP's successfully gapped: 5 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)