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= 0011.0028.p (345 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300309847|ref|YP_003773939.1| TRAP-type C4-dicarboxylate tran... 707 0.0 gi|300310441|ref|YP_003774533.1| TRAP-type C4-dicarboxylate tran... 634 0.0 gi|300313112|ref|YP_003777204.1| TRAP-type C4-dicarboxylate tran... 373 e-104 gi|300310178|ref|YP_003774270.1| TRAP-type C4-dicarboxylate tran... 129 3e-31 gi|300312105|ref|YP_003776197.1| TRAP-type C4-dicarboxylate-bind... 113 2e-26 >gi|300309847|ref|YP_003773939.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 345 Score = 707 bits (1824), Expect = 0.0, Method: Compositional matrix adjust. Identities = 344/345 (99%), Positives = 345/345 (100%) Query: 1 MNDERAKKQVTRRNILKAGAVGAALPLFSILSRPASAAEFSYKFATGQDPSHPVNKRAQE 60 MNDERAKKQVTRRN+LKAGAVGAALPLFSILSRPASAAEFSYKFATGQDPSHPVNKRAQE Sbjct: 1 MNDERAKKQVTRRNMLKAGAVGAALPLFSILSRPASAAEFSYKFATGQDPSHPVNKRAQE 60 Query: 61 AIDRIRNATNGRLEIKLFPANQLGSDTDLMSQVRNGGVEFFNQANTVLSTLVPAAGIVNT 120 AIDRIRNATNGRLEIKLFPANQLGSDTDLMSQVRNGGVEFFNQANTVLSTLVPAAGIVNT Sbjct: 61 AIDRIRNATNGRLEIKLFPANQLGSDTDLMSQVRNGGVEFFNQANTVLSTLVPAAGIVNT 120 Query: 121 GFAFHDYGAVWKAMDGPLGAHVRAQIEKVGLLTMSKPWDNGFRQITTSTKPVRNAGDVKG 180 GFAFHDYGAVWKAMDGPLGAHVRAQIEKVGLLTMSKPWDNGFRQITTSTKPVRNAGDVKG Sbjct: 121 GFAFHDYGAVWKAMDGPLGAHVRAQIEKVGLLTMSKPWDNGFRQITTSTKPVRNAGDVKG 180 Query: 181 LKLRVPAAPMLTSLFSALGASPTPINFNEVYSSLQTKLVEGQENPLAIISTARLYEVQKF 240 LKLRVPAAPMLTSLFSALGASPTPINFNEVYSSLQTKLVEGQENPLAIISTARLYEVQKF Sbjct: 181 LKLRVPAAPMLTSLFSALGASPTPINFNEVYSSLQTKLVEGQENPLAIISTARLYEVQKF 240 Query: 241 CTISNHVWDAYWILGNRRAFEKLPKDIQEIVRRELDKAASDERADIAAFSGFARNDLASK 300 CTISNHVWDAYWILGNRRAFEKLPKDIQEIVRRELDKAASDERADIAAFSGFARNDLASK Sbjct: 241 CTISNHVWDAYWILGNRRAFEKLPKDIQEIVRRELDKAASDERADIAAFSGFARNDLASK 300 Query: 301 GLQIVEADKDSFKEALARANFYKDMRAKFGEDAWKLLEGSVGALG 345 GLQIVEADKDSFKEALARANFYKDMRAKFGEDAWKLLEGSVGALG Sbjct: 301 GLQIVEADKDSFKEALARANFYKDMRAKFGEDAWKLLEGSVGALG 345 >gi|300310441|ref|YP_003774533.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 348 Score = 634 bits (1634), Expect = 0.0, Method: Compositional matrix adjust. Identities = 301/344 (87%), Positives = 326/344 (94%) Query: 2 NDERAKKQVTRRNILKAGAVGAALPLFSILSRPASAAEFSYKFATGQDPSHPVNKRAQEA 61 N + K V+RR +LKAGAVGAALPLFSI+SRPA+AAEF+YKFATGQDPSHPVNKRAQ+A Sbjct: 5 NSKPGKTSVSRRQLLKAGAVGAALPLFSIMSRPANAAEFNYKFATGQDPSHPVNKRAQQA 64 Query: 62 IDRIRNATNGRLEIKLFPANQLGSDTDLMSQVRNGGVEFFNQANTVLSTLVPAAGIVNTG 121 IDRIR AT GRL+IKLFPANQLGSDTDLMSQ+RNGGVEFFNQA+ VLSTLVPAAGIVNTG Sbjct: 65 IDRIREATGGRLDIKLFPANQLGSDTDLMSQIRNGGVEFFNQASVVLSTLVPAAGIVNTG 124 Query: 122 FAFHDYGAVWKAMDGPLGAHVRAQIEKVGLLTMSKPWDNGFRQITTSTKPVRNAGDVKGL 181 FAFHDY VW+AMDGPLGA+VRAQIEKVGLLTMSKPWDNGFRQITTSTKP++ A D+KGL Sbjct: 125 FAFHDYKEVWQAMDGPLGAYVRAQIEKVGLLTMSKPWDNGFRQITTSTKPIKTAADLKGL 184 Query: 182 KLRVPAAPMLTSLFSALGASPTPINFNEVYSSLQTKLVEGQENPLAIISTARLYEVQKFC 241 KLRVPAAPMLTSLFSALGASPTPINFNEVYSSLQTKLVEGQENPLAIISTARLYEVQKFC Sbjct: 185 KLRVPAAPMLTSLFSALGASPTPINFNEVYSSLQTKLVEGQENPLAIISTARLYEVQKFC 244 Query: 242 TISNHVWDAYWILGNRRAFEKLPKDIQEIVRRELDKAASDERADIAAFSGFARNDLASKG 301 TISNHVWDAYWILGNRRAFEKLPKDIQEIVRRELDKAA+DERADIA+ SGFARNDL KG Sbjct: 245 TISNHVWDAYWILGNRRAFEKLPKDIQEIVRRELDKAATDERADIASLSGFARNDLQGKG 304 Query: 302 LQIVEADKDSFKEALARANFYKDMRAKFGEDAWKLLEGSVGALG 345 +QI+EADK+SFKEALAR +FYKD+RAKFG+DAWKLL+ SVG+LG Sbjct: 305 VQIIEADKNSFKEALARGSFYKDLRAKFGDDAWKLLQNSVGSLG 348 >gi|300313112|ref|YP_003777204.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 344 Score = 373 bits (957), Expect = e-104, Method: Compositional matrix adjust. Identities = 176/338 (52%), Positives = 241/338 (71%), Gaps = 1/338 (0%) Query: 9 QVTRRNILKAGAVGAALPLFSILSRPASAAEFSYKFATGQDPSHPVNKRAQEAIDRIRNA 68 ++TRRN LK +V +A ++S A AAEF++K+A +HP+N RA+E I Sbjct: 7 KITRRNFLKTASVASAAAATGLVSTSAHAAEFTFKYANNLPVTHPMNARAKEMAAAIAEQ 66 Query: 69 TNGRLEIKLFPANQLGSDTDLMSQVRNGGVEFFNQANTVLSTLVPAAGIVNTGFAFHDYG 128 + GR+E++L+P NQLG+DTD++SQVR G ++FF + +L TLVPAA I GFAF DY Sbjct: 67 SKGRIELQLYPNNQLGTDTDMLSQVRAGAIDFFTLSPLILGTLVPAAQISGIGFAFKDYS 126 Query: 129 AVWKAMDGPLGAHVRAQIE-KVGLLTMSKPWDNGFRQITTSTKPVRNAGDVKGLKLRVPA 187 VW AMDG LGAHVR QIE + L K WDNG+RQIT STKP++ A D+KG+KLRVP Sbjct: 127 QVWPAMDGELGAHVRKQIEARSTLFAFEKIWDNGYRQITNSTKPIKVAEDLKGMKLRVPP 186 Query: 188 APMLTSLFSALGASPTPINFNEVYSSLQTKLVEGQENPLAIISTARLYEVQKFCTISNHV 247 +P+ TS+F A A+PT INF EVYS+LQTK+VEGQENP+AIISTA+LYEVQK+C+I+NH+ Sbjct: 187 SPLWTSMFKAFDAAPTSINFAEVYSALQTKIVEGQENPMAIISTAKLYEVQKYCSITNHM 246 Query: 248 WDAYWILGNRRAFEKLPKDIQEIVRRELDKAASDERADIAAFSGFARNDLASKGLQIVEA 307 WD +W LGN+++FE+LPKD+QE++ R +++A ++RAD+ + +++ KGL A Sbjct: 247 WDGFWFLGNKKSFERLPKDLQELMTRIINEAGVNQRADVRKLNDSLVDEMKGKGLAFNNA 306 Query: 308 DKDSFKEALARANFYKDMRAKFGEDAWKLLEGSVGALG 345 D DSF+ L A FY + + KFG++ W LLE G L Sbjct: 307 DADSFRAKLRAAGFYAEWKKKFGDEPWALLEKYTGKLA 344 >gi|300310178|ref|YP_003774270.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 334 Score = 129 bits (325), Expect = 3e-31, Method: Compositional matrix adjust. Identities = 84/303 (27%), Positives = 160/303 (52%), Gaps = 19/303 (6%) Query: 53 PVNKRAQEAIDRIRNATNGRLEIKLFPANQLGSDTDLMSQVRNGGVEFFNQANTVLSTL- 111 P K A+ + AT GR++I+++P + L D + + ++ G V+ + L Sbjct: 39 PKGKAAERFKELAEKATKGRVKIEVYPNSTLYKDKEELEALQLGAVQMLAPSLAKFGPLG 98 Query: 112 VPAAGIVNTGFAFHDYGAVWKAMDGPLGAHVRAQIEKVGLLTMSKPWDNGFRQITTSTKP 171 V + + + F +++ +GP+G + ++E G+ ++ WDNGF+ + ++ KP Sbjct: 99 VKEFEVFDLPYIFPTKEVLYRVTEGPIGKDLFKKLEPKGITGLAY-WDNGFK-VMSANKP 156 Query: 172 VRNAGDVKGLKLRVPAAPMLTSLFSALGASPTPINFNEVYSSLQTKLVEGQENPLAIIST 231 + + D +GLK+R+ ++ +L + ALGA+P + F+EVY +LQT +V+G ENP + + T Sbjct: 157 LHHPADFRGLKMRIQSSKVLDAQMRALGANPQVLAFSEVYQALQTGVVDGTENPPSNLYT 216 Query: 232 ARLYEVQKFCTISNHVWDAYWILGNRRAFEKLPKDIQEIVRRELDKAASDERADIAAFSG 291 +++EVQK T+SNH + Y ++ N++ ++ LP DI R +L+ A D A + Sbjct: 217 QKMHEVQKHVTVSNHGYLGYAVIVNKKFWDGLPSDI----RTQLEGAMKDATKYANAIAQ 272 Query: 292 FARNDLASKGLQ---------IVEADKDSFKEALARANFYKDMRAKFGEDAWKLLEGSVG 342 ND A ++ + +A+K +++AL + M ++ G+D + Sbjct: 273 -QENDAALAAVEKTGKTTVYRLTDAEKAEWRKALLPVQ--QQMASRIGKDLIDAVNKESA 329 Query: 343 ALG 345 ALG Sbjct: 330 ALG 332 >gi|300312105|ref|YP_003776197.1| TRAP-type C4-dicarboxylate-binding periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 344 Score = 113 bits (283), Expect = 2e-26, Method: Compositional matrix adjust. Identities = 76/292 (26%), Positives = 150/292 (51%), Gaps = 23/292 (7%) Query: 53 PVNKRAQEAIDRIRNATNGRLEIKLFPANQLGSDTDLMSQVRNGGVEFFNQANTVLSTLV 112 P K A+ + AT GR++++++P + L D + + ++ G V+ + L+ Sbjct: 47 PKGKGAERFKELAEKATQGRVKVEVYPNSTLYKDKEELEALQLGSVQMLAPS---LAKFG 103 Query: 113 PAAG----IVNTGFAFHDYGAVWKAMDGPLGAHVRAQIEKVGLLTMSKPWDNGFRQITTS 168 P + + + F D + + +GP+G + ++E G+ ++ WDNG + + T+ Sbjct: 104 PLGAREFEVFDLPYIFPDKAVLKRVTEGPIGQGLFQKLEGKGIKGLAY-WDNGMK-VMTA 161 Query: 169 TKPVRNAGDVKGLKLRVPAAPMLTSLFSALGASPTPINFNEVYSSLQTKLVEGQENPLAI 228 +P+ D + LK+R+ ++ +L F AL A+P + F+EVY ++QT +V+G EN + Sbjct: 162 NRPLHKVADFRALKMRIQSSKVLDEQFRALKANPQVLAFSEVYQAMQTGVVDGSENTPSN 221 Query: 229 ISTARLYEVQKFCTISNHVWDAYWILGNRRAFEKLPKDIQEIVRRELDKA-------ASD 281 + T +++EVQ T+S+H + Y ++ N++ +E LP DI+ + + +A A Sbjct: 222 VYTQKMHEVQSNLTVSDHGYIGYAVIVNKKFWEALPADIRSQLEAAMKQATLYANTIAQK 281 Query: 282 ERAD-IAAFSGFARNDLASKGLQIVEADKDSFKEALARANFYKDMRAKFGED 332 E D +AA + + + + E +K ++ AL +K M A+ G D Sbjct: 282 ENDDALAAIKASGKTRVYT----LSEQEKAEWRRAL--LPVHKSMAARVGAD 327 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 0.318 0.133 0.383 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: 1,062,158 Number of extensions: 43682 Number of successful extensions: 114 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 109 Number of HSP's successfully gapped: 6 Length of query: 345 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 259 Effective length of database: 1,212,660 Effective search space: 314078940 Effective search space used: 314078940 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 (21.7 bits) S2: 131 (55.1 bits)