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= 0013.0141.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|300312105|ref|YP_003776197.1| TRAP-type C4-dicarboxylate-bind... 555 e-159 gi|300310178|ref|YP_003774270.1| TRAP-type C4-dicarboxylate tran... 529 e-151 gi|300313112|ref|YP_003777204.1| TRAP-type C4-dicarboxylate tran... 126 2e-30 gi|300309847|ref|YP_003773939.1| TRAP-type C4-dicarboxylate tran... 124 1e-29 gi|300310441|ref|YP_003774533.1| TRAP-type C4-dicarboxylate tran... 121 7e-29 >gi|300312105|ref|YP_003776197.1| TRAP-type C4-dicarboxylate-binding periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 344 Score = 555 bits (1429), Expect = e-159, Method: Compositional matrix adjust. Identities = 266/337 (78%), Positives = 296/337 (87%), Gaps = 3/337 (0%) Query: 5 LFAAATTAALLAFALQTTPALAQQT---IVIKFSHVVANNTPKGKGAERFKQLAEERTKG 61 L A A + L ALAQQ I+IKFSHVVAN+TPKGKGAERFK+LAE+ T+G Sbjct: 6 LRTALAACAFVTLGLPQPAALAQQPQQPIIIKFSHVVANDTPKGKGAERFKELAEKATQG 65 Query: 62 RVKVEVYPNSQLYKDKEELEALQLGAVQMLAPSLAKFGPLGVKEYEVFDLPYIFPNRAVL 121 RVKVEVYPNS LYKDKEELEALQLG+VQMLAPSLAKFGPLG +E+EVFDLPYIFP++AVL Sbjct: 66 RVKVEVYPNSTLYKDKEELEALQLGSVQMLAPSLAKFGPLGAREFEVFDLPYIFPDKAVL 125 Query: 122 ARITEGPIGQNLFRKLEAKGIKGLAYWDNGMKVMTANKPLHKVDDFRGMKMRIQSSKVLD 181 R+TEGPIGQ LF+KLE KGIKGLAYWDNGMKVMTAN+PLHKV DFR +KMRIQSSKVLD Sbjct: 126 KRVTEGPIGQGLFQKLEGKGIKGLAYWDNGMKVMTANRPLHKVADFRALKMRIQSSKVLD 185 Query: 182 EQFRALKANPQVLAFSEVYQAMQTGVVDGSENTPSNIYSQKVHEVQSQLTVSDHGYIGYA 241 EQFRALKANPQVLAFSEVYQAMQTGVVDGSENTPSN+Y+QK+HEVQS LTVSDHGYIGYA Sbjct: 186 EQFRALKANPQVLAFSEVYQAMQTGVVDGSENTPSNVYTQKMHEVQSNLTVSDHGYIGYA 245 Query: 242 VIVNKKFWESLPPDVRGQLESAMKDATRYANAIAQQENEDALAAIKASGKTKVYYLTDAE 301 VIVNKKFWE+LP D+R QLE+AMK AT YAN IAQ+EN+DALAAIKASGKT+VY L++ E Sbjct: 246 VIVNKKFWEALPADIRSQLEAAMKQATLYANTIAQKENDDALAAIKASGKTRVYTLSEQE 305 Query: 302 KAEWRKALLPVHKSMESRVGKDLIQEIYKETANLGAK 338 KAEWR+ALLPVHKSM +RVG DLI+ IYKE+ G K Sbjct: 306 KAEWRRALLPVHKSMAARVGADLIEAIYKESEAAGVK 342 >gi|300310178|ref|YP_003774270.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 334 Score = 529 bits (1363), Expect = e-151, Method: Compositional matrix adjust. Identities = 252/326 (77%), Positives = 286/326 (87%) Query: 13 ALLAFALQTTPALAQQTIVIKFSHVVANNTPKGKGAERFKQLAEERTKGRVKVEVYPNSQ 72 A+ A A+ +T A AQQ IVIKFSHVVAN+TPKGK AERFK+LAE+ TKGRVK+EVYPNS Sbjct: 9 AMTAAAIVSTNAFAQQPIVIKFSHVVANDTPKGKAAERFKELAEKATKGRVKIEVYPNST 68 Query: 73 LYKDKEELEALQLGAVQMLAPSLAKFGPLGVKEYEVFDLPYIFPNRAVLARITEGPIGQN 132 LYKDKEELEALQLGAVQMLAPSLAKFGPLGVKE+EVFDLPYIFP + VL R+TEGPIG++ Sbjct: 69 LYKDKEELEALQLGAVQMLAPSLAKFGPLGVKEFEVFDLPYIFPTKEVLYRVTEGPIGKD 128 Query: 133 LFRKLEAKGIKGLAYWDNGMKVMTANKPLHKVDDFRGMKMRIQSSKVLDEQFRALKANPQ 192 LF+KLE KGI GLAYWDNG KVM+ANKPLH DFRG+KMRIQSSKVLD Q RAL ANPQ Sbjct: 129 LFKKLEPKGITGLAYWDNGFKVMSANKPLHHPADFRGLKMRIQSSKVLDAQMRALGANPQ 188 Query: 193 VLAFSEVYQAMQTGVVDGSENTPSNIYSQKVHEVQSQLTVSDHGYIGYAVIVNKKFWESL 252 VLAFSEVYQA+QTGVVDG+EN PSN+Y+QK+HEVQ +TVS+HGY+GYAVIVNKKFW+ L Sbjct: 189 VLAFSEVYQALQTGVVDGTENPPSNLYTQKMHEVQKHVTVSNHGYLGYAVIVNKKFWDGL 248 Query: 253 PPDVRGQLESAMKDATRYANAIAQQENEDALAAIKASGKTKVYYLTDAEKAEWRKALLPV 312 P D+R QLE AMKDAT+YANAIAQQEN+ ALAA++ +GKT VY LTDAEKAEWRKALLPV Sbjct: 249 PSDIRTQLEGAMKDATKYANAIAQQENDAALAAVEKTGKTTVYRLTDAEKAEWRKALLPV 308 Query: 313 HKSMESRVGKDLIQEIYKETANLGAK 338 + M SR+GKDLI + KE+A LG K Sbjct: 309 QQQMASRIGKDLIDAVNKESAALGQK 334 >gi|300313112|ref|YP_003777204.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 344 Score = 126 bits (317), Expect = 2e-30, Method: Compositional matrix adjust. Identities = 85/294 (28%), Positives = 157/294 (53%), Gaps = 23/294 (7%) Query: 33 KFSHVVANNTPKGKGAE-RFKQLAE---ERTKGRVKVEVYPNSQLYKDKEELEALQLGAV 88 +F+ ANN P R K++A E++KGR+++++YPN+QL D + L ++ GA+ Sbjct: 37 EFTFKYANNLPVTHPMNARAKEMAAAIAEQSKGRIELQLYPNNQLGTDTDMLSQVRAGAI 96 Query: 89 QMLAPSLAKFGPLGVKEYEVFDLPYIFPNRAVLARITEGPIGQNLFRKLEAKGIKGLAY- 147 S G L V ++ + + F + + + +G +G ++ +++EA+ A+ Sbjct: 97 DFFTLSPLILGTL-VPAAQISGIGFAFKDYSQVWPAMDGELGAHVRKQIEARSTL-FAFE 154 Query: 148 --WDNGMKVMT-ANKPLHKVDDFRGMKMRIQSSKVLDEQFRALKANPQVLAFSEVYQAMQ 204 WDNG + +T + KP+ +D +GMK+R+ S + F+A A P + F+EVY A+Q Sbjct: 155 KIWDNGYRQITNSTKPIKVAEDLKGMKLRVPPSPLWTSMFKAFDAAPTSINFAEVYSALQ 214 Query: 205 TGVVDGSENTPSNIYSQKVHEVQSQLTVSDHGYIGYAVIVNKKFWESLPPDVRGQLESAM 264 T +V+G EN + I + K++EVQ ++++H + G+ + NKK +E LP D++ + + Sbjct: 215 TKIVEGQENPMAIISTAKLYEVQKYCSITNHMWDGFWFLGNKKSFERLPKDLQELMTRII 274 Query: 265 KDATRYANAIAQQENEDALAAIKASGKTKVYYLTDAEK-----------AEWRK 307 +A A ++ N+ + +K GK + DA+ AEW+K Sbjct: 275 NEAGVNQRADVRKLNDSLVDEMK--GKGLAFNNADADSFRAKLRAAGFYAEWKK 326 >gi|300309847|ref|YP_003773939.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 345 Score = 124 bits (311), Expect = 1e-29, Method: Compositional matrix adjust. Identities = 92/340 (27%), Positives = 174/340 (51%), Gaps = 18/340 (5%) Query: 5 LFAAATTAALLAFALQTTPALAQQTIVIKFSHVVANNTPKGKGAERFKQLAEERTKGRVK 64 L A A AAL F++ + PA A + KF+ + P K A+ T GR++ Sbjct: 16 LKAGAVGAALPLFSILSRPASAAE-FSYKFATGQDPSHPVNKRAQEAIDRIRNATNGRLE 74 Query: 65 VEVYPNSQLYKDKEELEALQLGAVQMLAPSLAKFGPLGVKEYEVFDLPYIFPNRAVLARI 124 ++++P +QL D + + ++ G V+ + L V + + + F + + + Sbjct: 75 IKLFPANQLGSDTDLMSQVRNGGVEFFNQANTVLSTL-VPAAGIVNTGFAFHDYGAVWKA 133 Query: 125 TEGPIGQNLFRKLEAKGIKGLAY-WDNGMK-VMTANKPLHKVDDFRGMKMRIQSSKVLDE 182 +GP+G ++ ++E G+ ++ WDNG + + T+ KP+ D +G+K+R+ ++ +L Sbjct: 134 MDGPLGAHVRAQIEKVGLLTMSKPWDNGFRQITTSTKPVRNAGDVKGLKLRVPAAPMLTS 193 Query: 183 QFRALKANPQVLAFSEVYQAMQTGVVDGSENTPSNIYSQKVHEVQSQLTVSDHGYIGYAV 242 F AL A+P + F+EVY ++QT +V+G EN + I + +++EVQ T+S+H + Y + Sbjct: 194 LFSALGASPTPINFNEVYSSLQTKLVEGQENPLAIISTARLYEVQKFCTISNHVWDAYWI 253 Query: 243 IVNKKFWESLPPD----VRGQLESAMKDATRYANAIAQQENEDALAAIKASGKTKVYYLT 298 + N++ +E LP D VR +L+ A D A + D LA +K + Sbjct: 254 LGNRRAFEKLPKDIQEIVRRELDKAASDERADIAAFSGFARND-LA-------SKGLQIV 305 Query: 299 DAEKAEWRKAL--LPVHKSMESRVGKDLIQEIYKETANLG 336 +A+K +++AL +K M ++ G+D + + LG Sbjct: 306 EADKDSFKEALARANFYKDMRAKFGEDAWKLLEGSVGALG 345 >gi|300310441|ref|YP_003774533.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 348 Score = 121 bits (304), Expect = 7e-29, Method: Compositional matrix adjust. Identities = 89/340 (26%), Positives = 173/340 (50%), Gaps = 18/340 (5%) Query: 5 LFAAATTAALLAFALQTTPALAQQTIVIKFSHVVANNTPKGKGAERFKQLAEERTKGRVK 64 L A A AAL F++ + PA A + KF+ + P K A++ E T GR+ Sbjct: 19 LKAGAVGAALPLFSIMSRPANAAE-FNYKFATGQDPSHPVNKRAQQAIDRIREATGGRLD 77 Query: 65 VEVYPNSQLYKDKEELEALQLGAVQMLAPSLAKFGPLGVKEYEVFDLPYIFPNRAVLARI 124 ++++P +QL D + + ++ G V+ + L V + + + F + + + Sbjct: 78 IKLFPANQLGSDTDLMSQIRNGGVEFFNQASVVLSTL-VPAAGIVNTGFAFHDYKEVWQA 136 Query: 125 TEGPIGQNLFRKLEAKGIKGLAY-WDNGMK-VMTANKPLHKVDDFRGMKMRIQSSKVLDE 182 +GP+G + ++E G+ ++ WDNG + + T+ KP+ D +G+K+R+ ++ +L Sbjct: 137 MDGPLGAYVRAQIEKVGLLTMSKPWDNGFRQITTSTKPIKTAADLKGLKLRVPAAPMLTS 196 Query: 183 QFRALKANPQVLAFSEVYQAMQTGVVDGSENTPSNIYSQKVHEVQSQLTVSDHGYIGYAV 242 F AL A+P + F+EVY ++QT +V+G EN + I + +++EVQ T+S+H + Y + Sbjct: 197 LFSALGASPTPINFNEVYSSLQTKLVEGQENPLAIISTARLYEVQKFCTISNHVWDAYWI 256 Query: 243 IVNKKFWESLPPD----VRGQLESAMKDATRYANAIAQQENEDALAAIKASGKTKVYYLT 298 + N++ +E LP D VR +L+ A D +++ D + K + Sbjct: 257 LGNRRAFEKLPKDIQEIVRRELDKAATDERADIASLSGFARNDL--------QGKGVQII 308 Query: 299 DAEKAEWRKALL--PVHKSMESRVGKDLIQEIYKETANLG 336 +A+K +++AL +K + ++ G D + + +LG Sbjct: 309 EADKNSFKEALARGSFYKDLRAKFGDDAWKLLQNSVGSLG 348 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 0.130 0.362 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: 869,981 Number of extensions: 32736 Number of successful extensions: 128 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 122 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)