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= 0030.0061.p (338 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310178|ref|YP_003774270.1| TRAP-type C4-dicarboxylate tran... 657 0.0 gi|300312105|ref|YP_003776197.1| TRAP-type C4-dicarboxylate-bind... 525 e-150 gi|300313112|ref|YP_003777204.1| TRAP-type C4-dicarboxylate tran... 131 9e-32 gi|300309847|ref|YP_003773939.1| TRAP-type C4-dicarboxylate tran... 129 5e-31 gi|300310441|ref|YP_003774533.1| TRAP-type C4-dicarboxylate tran... 125 3e-30 >gi|300310178|ref|YP_003774270.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 334 Score = 657 bits (1694), Expect = 0.0, Method: Compositional matrix adjust. Identities = 318/338 (94%), Positives = 329/338 (97%), Gaps = 4/338 (1%) Query: 1 MKLKSIVFALAAATVVNAGLVASAFAQQPIIIKFSHVVANDTPKGKAAERFKELAEKATK 60 MKLKSI+ A+ AA +V+ +AFAQQPI+IKFSHVVANDTPKGKAAERFKELAEKATK Sbjct: 1 MKLKSILLAMTAAAIVST----NAFAQQPIVIKFSHVVANDTPKGKAAERFKELAEKATK 56 Query: 61 GRVKVEVYPNSTLYKDKEELEALQLGAVQMLAPSLAKFGPLGVKEFEVFDLPYIFPSKDV 120 GRVK+EVYPNSTLYKDKEELEALQLGAVQMLAPSLAKFGPLGVKEFEVFDLPYIFP+K+V Sbjct: 57 GRVKIEVYPNSTLYKDKEELEALQLGAVQMLAPSLAKFGPLGVKEFEVFDLPYIFPTKEV 116 Query: 121 LYRVTEGPIGKDLFKKLEPKGITGLAYWDNGFKVMSANKPLHQPSDFRGLKMRIQSSKVL 180 LYRVTEGPIGKDLFKKLEPKGITGLAYWDNGFKVMSANKPLH P+DFRGLKMRIQSSKVL Sbjct: 117 LYRVTEGPIGKDLFKKLEPKGITGLAYWDNGFKVMSANKPLHHPADFRGLKMRIQSSKVL 176 Query: 181 DAQMRALGANPQVLAFSEVYQALQTGVVDGTENPPSNLYTQKMHEVQKHVTVSNHGYLGY 240 DAQMRALGANPQVLAFSEVYQALQTGVVDGTENPPSNLYTQKMHEVQKHVTVSNHGYLGY Sbjct: 177 DAQMRALGANPQVLAFSEVYQALQTGVVDGTENPPSNLYTQKMHEVQKHVTVSNHGYLGY 236 Query: 241 AVIVNKKFWDGLPSDVRTQLEGAMKDATKYANAIAQQENDAALAAVEKTGKTTVYRLTDA 300 AVIVNKKFWDGLPSD+RTQLEGAMKDATKYANAIAQQENDAALAAVEKTGKTTVYRLTDA Sbjct: 237 AVIVNKKFWDGLPSDIRTQLEGAMKDATKYANAIAQQENDAALAAVEKTGKTTVYRLTDA 296 Query: 301 EKAEWRKALLPVQQQMASRIGKDLIDAVNKESAALGQK 338 EKAEWRKALLPVQQQMASRIGKDLIDAVNKESAALGQK Sbjct: 297 EKAEWRKALLPVQQQMASRIGKDLIDAVNKESAALGQK 334 >gi|300312105|ref|YP_003776197.1| TRAP-type C4-dicarboxylate-binding periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 344 Score = 525 bits (1351), Expect = e-150, Method: Compositional matrix adjust. Identities = 256/342 (74%), Positives = 290/342 (84%), Gaps = 4/342 (1%) Query: 1 MKLKSIVFALAAATVVNAGLVASAF----AQQPIIIKFSHVVANDTPKGKAAERFKELAE 56 M + + ALAA V GL A QQPIIIKFSHVVANDTPKGK AERFKELAE Sbjct: 1 MTILPLRTALAACAFVTLGLPQPAALAQQPQQPIIIKFSHVVANDTPKGKGAERFKELAE 60 Query: 57 KATKGRVKVEVYPNSTLYKDKEELEALQLGAVQMLAPSLAKFGPLGVKEFEVFDLPYIFP 116 KAT+GRVKVEVYPNSTLYKDKEELEALQLG+VQMLAPSLAKFGPLG +EFEVFDLPYIFP Sbjct: 61 KATQGRVKVEVYPNSTLYKDKEELEALQLGSVQMLAPSLAKFGPLGAREFEVFDLPYIFP 120 Query: 117 SKDVLYRVTEGPIGKDLFKKLEPKGITGLAYWDNGFKVMSANKPLHQPSDFRGLKMRIQS 176 K VL RVTEGPIG+ LF+KLE KGI GLAYWDNG KVM+AN+PLH+ +DFR LKMRIQS Sbjct: 121 DKAVLKRVTEGPIGQGLFQKLEGKGIKGLAYWDNGMKVMTANRPLHKVADFRALKMRIQS 180 Query: 177 SKVLDAQMRALGANPQVLAFSEVYQALQTGVVDGTENPPSNLYTQKMHEVQKHVTVSNHG 236 SKVLD Q RAL ANPQVLAFSEVYQA+QTGVVDG+EN PSN+YTQKMHEVQ ++TVS+HG Sbjct: 181 SKVLDEQFRALKANPQVLAFSEVYQAMQTGVVDGSENTPSNVYTQKMHEVQSNLTVSDHG 240 Query: 237 YLGYAVIVNKKFWDGLPSDVRTQLEGAMKDATKYANAIAQQENDAALAAVEKTGKTTVYR 296 Y+GYAVIVNKKFW+ LP+D+R+QLE AMK AT YAN IAQ+END ALAA++ +GKT VY Sbjct: 241 YIGYAVIVNKKFWEALPADIRSQLEAAMKQATLYANTIAQKENDDALAAIKASGKTRVYT 300 Query: 297 LTDAEKAEWRKALLPVQQQMASRIGKDLIDAVNKESAALGQK 338 L++ EKAEWR+ALLPV + MA+R+G DLI+A+ KES A G K Sbjct: 301 LSEQEKAEWRRALLPVHKSMAARVGADLIEAIYKESEAAGVK 342 >gi|300313112|ref|YP_003777204.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 344 Score = 131 bits (329), Expect = 9e-32, Method: Compositional matrix adjust. Identities = 83/304 (27%), Positives = 158/304 (51%), Gaps = 19/304 (6%) Query: 19 GLVASAFAQQPIIIKFSHVVANDTPKGKAAERFKELAEKATKGRVKVEVYPNSTLYKDKE 78 GLV+++ K+++ + P A+ + +KGR+++++YPN+ L D + Sbjct: 27 GLVSTSAHAAEFTFKYANNLPVTHPMNARAKEMAAAIAEQSKGRIELQLYPNNQLGTDTD 86 Query: 79 ELEALQLGAVQMLAPSLAKFGPLGVKEFEVFDLPYIFPSKDVLYRVTEGPIGKDLFKKLE 138 L ++ GA+ S G L V ++ + + F ++ +G +G + K++E Sbjct: 87 MLSQVRAGAIDFFTLSPLILGTL-VPAAQISGIGFAFKDYSQVWPAMDGELGAHVRKQIE 145 Query: 139 PKGITGLAY---WDNGFK-VMSANKPLHQPSDFRGLKMRIQSSKVLDAQMRALGANPQVL 194 + T A+ WDNG++ + ++ KP+ D +G+K+R+ S + + +A A P + Sbjct: 146 ARS-TLFAFEKIWDNGYRQITNSTKPIKVAEDLKGMKLRVPPSPLWTSMFKAFDAAPTSI 204 Query: 195 AFSEVYQALQTGVVDGTENPPSNLYTQKMHEVQKHVTVSNHGYLGYAVIVNKKFWDGLPS 254 F+EVY ALQT +V+G ENP + + T K++EVQK+ +++NH + G+ + NKK ++ LP Sbjct: 205 NFAEVYSALQTKIVEGQENPMAIISTAKLYEVQKYCSITNHMWDGFWFLGNKKSFERLPK 264 Query: 255 DVRTQLEGAMKDATKYANAIAQQENDAALAAVEKTGKTTVYRLTDAEK-----------A 303 D++ + + +A A ++ ND+ + E GK + DA+ A Sbjct: 265 DLQELMTRIINEAGVNQRADVRKLNDSLVD--EMKGKGLAFNNADADSFRAKLRAAGFYA 322 Query: 304 EWRK 307 EW+K Sbjct: 323 EWKK 326 >gi|300309847|ref|YP_003773939.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 345 Score = 129 bits (323), Expect = 5e-31, Method: Compositional matrix adjust. Identities = 83/303 (27%), Positives = 159/303 (52%), Gaps = 19/303 (6%) Query: 43 PKGKAAERFKELAEKATKGRVKVEVYPNSTLYKDKEELEALQLGAVQMLAPSLAKFGPLG 102 P K A+ + AT GR++++++P + L D + + ++ G V+ + L Sbjct: 53 PVNKRAQEAIDRIRNATNGRLEIKLFPANQLGSDTDLMSQVRNGGVEFFNQANTVLSTL- 111 Query: 103 VKEFEVFDLPYIFPSKDVLYRVTEGPIGKDLFKKLEPKGITGLAY-WDNGFK-VMSANKP 160 V + + + F +++ +GP+G + ++E G+ ++ WDNGF+ + ++ KP Sbjct: 112 VPAAGIVNTGFAFHDYGAVWKAMDGPLGAHVRAQIEKVGLLTMSKPWDNGFRQITTSTKP 171 Query: 161 LHQPSDFRGLKMRIQSSKVLDAQMRALGANPQVLAFSEVYQALQTGVVDGTENPPSNLYT 220 + D +GLK+R+ ++ +L + ALGA+P + F+EVY +LQT +V+G ENP + + T Sbjct: 172 VRNAGDVKGLKLRVPAAPMLTSLFSALGASPTPINFNEVYSSLQTKLVEGQENPLAIIST 231 Query: 221 QKMHEVQKHVTVSNHGYLGYAVIVNKKFWDGLPSD----VRTQLEGAMKDATKYANAIAQ 276 +++EVQK T+SNH + Y ++ N++ ++ LP D VR +L+ A D A + Sbjct: 232 ARLYEVQKFCTISNHVWDAYWILGNRRAFEKLPKDIQEIVRRELDKAASDERADIAAFSG 291 Query: 277 -QENDAALAAVEKTGKTTVYRLTDAEKAEWRKALLPVQ--QQMASRIGKDLIDAVNKESA 333 ND A ++ + +A+K +++AL + M ++ G+D + Sbjct: 292 FARNDLASKGLQ---------IVEADKDSFKEALARANFYKDMRAKFGEDAWKLLEGSVG 342 Query: 334 ALG 336 ALG Sbjct: 343 ALG 345 >gi|300310441|ref|YP_003774533.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 348 Score = 125 bits (315), Expect = 3e-30, Method: Compositional matrix adjust. Identities = 69/230 (30%), Positives = 133/230 (57%), Gaps = 7/230 (3%) Query: 43 PKGKAAERFKELAEKATKGRVKVEVYPNSTLYKDKEELEALQLGAVQMLAPSLAKFGPLG 102 P K A++ + +AT GR+ ++++P + L D + + ++ G V+ + L Sbjct: 56 PVNKRAQQAIDRIREATGGRLDIKLFPANQLGSDTDLMSQIRNGGVEFFNQASVVLSTL- 114 Query: 103 VKEFEVFDLPYIFPSKDVLYRVTEGPIGKDLFKKLEPKGITGLAY-WDNGFK-VMSANKP 160 V + + + F +++ +GP+G + ++E G+ ++ WDNGF+ + ++ KP Sbjct: 115 VPAAGIVNTGFAFHDYKEVWQAMDGPLGAYVRAQIEKVGLLTMSKPWDNGFRQITTSTKP 174 Query: 161 LHQPSDFRGLKMRIQSSKVLDAQMRALGANPQVLAFSEVYQALQTGVVDGTENPPSNLYT 220 + +D +GLK+R+ ++ +L + ALGA+P + F+EVY +LQT +V+G ENP + + T Sbjct: 175 IKTAADLKGLKLRVPAAPMLTSLFSALGASPTPINFNEVYSSLQTKLVEGQENPLAIIST 234 Query: 221 QKMHEVQKHVTVSNHGYLGYAVIVNKKFWDGLPSD----VRTQLEGAMKD 266 +++EVQK T+SNH + Y ++ N++ ++ LP D VR +L+ A D Sbjct: 235 ARLYEVQKFCTISNHVWDAYWILGNRRAFEKLPKDIQEIVRRELDKAATD 284 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 0.315 0.131 0.367 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: 966,484 Number of extensions: 38451 Number of successful extensions: 158 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 151 Number of HSP's successfully gapped: 6 Length of query: 338 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 252 Effective length of database: 1,212,660 Effective search space: 305590320 Effective search space used: 305590320 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 131 (55.1 bits)