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= 0020.0442.p (348 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310441|ref|YP_003774533.1| TRAP-type C4-dicarboxylate tran... 712 0.0 gi|300309847|ref|YP_003773939.1| TRAP-type C4-dicarboxylate tran... 634 0.0 gi|300313112|ref|YP_003777204.1| TRAP-type C4-dicarboxylate tran... 375 e-105 gi|300310178|ref|YP_003774270.1| TRAP-type C4-dicarboxylate tran... 128 8e-31 gi|300312105|ref|YP_003776197.1| TRAP-type C4-dicarboxylate-bind... 111 1e-25 >gi|300310441|ref|YP_003774533.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 348 Score = 712 bits (1839), Expect = 0.0, Method: Compositional matrix adjust. Identities = 347/348 (99%), Positives = 348/348 (100%) Query: 1 MNQDNSKPGKTSVSRRQLLKAGAVGAALPLFSIISRPANAAEFNYKFATGQDPSHPVNKR 60 MNQDNSKPGKTSVSRRQLLKAGAVGAALPLFSI+SRPANAAEFNYKFATGQDPSHPVNKR Sbjct: 1 MNQDNSKPGKTSVSRRQLLKAGAVGAALPLFSIMSRPANAAEFNYKFATGQDPSHPVNKR 60 Query: 61 AQQAIDRIREATGGRLDIKLFPANQLGSDTDLMSQIRNGGVEFFNQASVVLSTLVPAAGI 120 AQQAIDRIREATGGRLDIKLFPANQLGSDTDLMSQIRNGGVEFFNQASVVLSTLVPAAGI Sbjct: 61 AQQAIDRIREATGGRLDIKLFPANQLGSDTDLMSQIRNGGVEFFNQASVVLSTLVPAAGI 120 Query: 121 VNTGFAFHDYKEVWQAMDGPLGAYVRAQIEKVGLLTMSKPWDNGFRQITTSTKPIKTAAD 180 VNTGFAFHDYKEVWQAMDGPLGAYVRAQIEKVGLLTMSKPWDNGFRQITTSTKPIKTAAD Sbjct: 121 VNTGFAFHDYKEVWQAMDGPLGAYVRAQIEKVGLLTMSKPWDNGFRQITTSTKPIKTAAD 180 Query: 181 LKGLKLRVPAAPMLTSLFSALGASPTPINFNEVYSSLQTKLVEGQENPLAIISTARLYEV 240 LKGLKLRVPAAPMLTSLFSALGASPTPINFNEVYSSLQTKLVEGQENPLAIISTARLYEV Sbjct: 181 LKGLKLRVPAAPMLTSLFSALGASPTPINFNEVYSSLQTKLVEGQENPLAIISTARLYEV 240 Query: 241 QKFCTISNHVWDAYWILGNRRAFEKLPKDIQEIVRRELDKAATDERADIASLSGFARNDL 300 QKFCTISNHVWDAYWILGNRRAFEKLPKDIQEIVRRELDKAATDERADIASLSGFARNDL Sbjct: 241 QKFCTISNHVWDAYWILGNRRAFEKLPKDIQEIVRRELDKAATDERADIASLSGFARNDL 300 Query: 301 QGKGVQIIEADKNSFKEALARGSFYKDLRAKFGDDAWKLLQNSVGSLG 348 QGKGVQIIEADKNSFKEALARGSFYKDLRAKFGDDAWKLLQNSVGSLG Sbjct: 301 QGKGVQIIEADKNSFKEALARGSFYKDLRAKFGDDAWKLLQNSVGSLG 348 >gi|300309847|ref|YP_003773939.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 345 Score = 634 bits (1634), Expect = 0.0, Method: Compositional matrix adjust. Identities = 301/344 (87%), Positives = 326/344 (94%) Query: 5 NSKPGKTSVSRRQLLKAGAVGAALPLFSIISRPANAAEFNYKFATGQDPSHPVNKRAQQA 64 N + K V+RR +LKAGAVGAALPLFSI+SRPA+AAEF+YKFATGQDPSHPVNKRAQ+A Sbjct: 2 NDERAKKQVTRRNMLKAGAVGAALPLFSILSRPASAAEFSYKFATGQDPSHPVNKRAQEA 61 Query: 65 IDRIREATGGRLDIKLFPANQLGSDTDLMSQIRNGGVEFFNQASVVLSTLVPAAGIVNTG 124 IDRIR AT GRL+IKLFPANQLGSDTDLMSQ+RNGGVEFFNQA+ VLSTLVPAAGIVNTG Sbjct: 62 IDRIRNATNGRLEIKLFPANQLGSDTDLMSQVRNGGVEFFNQANTVLSTLVPAAGIVNTG 121 Query: 125 FAFHDYKEVWQAMDGPLGAYVRAQIEKVGLLTMSKPWDNGFRQITTSTKPIKTAADLKGL 184 FAFHDY VW+AMDGPLGA+VRAQIEKVGLLTMSKPWDNGFRQITTSTKP++ A D+KGL Sbjct: 122 FAFHDYGAVWKAMDGPLGAHVRAQIEKVGLLTMSKPWDNGFRQITTSTKPVRNAGDVKGL 181 Query: 185 KLRVPAAPMLTSLFSALGASPTPINFNEVYSSLQTKLVEGQENPLAIISTARLYEVQKFC 244 KLRVPAAPMLTSLFSALGASPTPINFNEVYSSLQTKLVEGQENPLAIISTARLYEVQKFC Sbjct: 182 KLRVPAAPMLTSLFSALGASPTPINFNEVYSSLQTKLVEGQENPLAIISTARLYEVQKFC 241 Query: 245 TISNHVWDAYWILGNRRAFEKLPKDIQEIVRRELDKAATDERADIASLSGFARNDLQGKG 304 TISNHVWDAYWILGNRRAFEKLPKDIQEIVRRELDKAA+DERADIA+ SGFARNDL KG Sbjct: 242 TISNHVWDAYWILGNRRAFEKLPKDIQEIVRRELDKAASDERADIAAFSGFARNDLASKG 301 Query: 305 VQIIEADKNSFKEALARGSFYKDLRAKFGDDAWKLLQNSVGSLG 348 +QI+EADK+SFKEALAR +FYKD+RAKFG+DAWKLL+ SVG+LG Sbjct: 302 LQIVEADKDSFKEALARANFYKDMRAKFGEDAWKLLEGSVGALG 345 >gi|300313112|ref|YP_003777204.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 344 Score = 375 bits (962), Expect = e-105, Method: Compositional matrix adjust. Identities = 173/337 (51%), Positives = 244/337 (72%), Gaps = 1/337 (0%) Query: 13 VSRRQLLKAGAVGAALPLFSIISRPANAAEFNYKFATGQDPSHPVNKRAQQAIDRIREAT 72 ++RR LK +V +A ++S A+AAEF +K+A +HP+N RA++ I E + Sbjct: 8 ITRRNFLKTASVASAAAATGLVSTSAHAAEFTFKYANNLPVTHPMNARAKEMAAAIAEQS 67 Query: 73 GGRLDIKLFPANQLGSDTDLMSQIRNGGVEFFNQASVVLSTLVPAAGIVNTGFAFHDYKE 132 GR++++L+P NQLG+DTD++SQ+R G ++FF + ++L TLVPAA I GFAF DY + Sbjct: 68 KGRIELQLYPNNQLGTDTDMLSQVRAGAIDFFTLSPLILGTLVPAAQISGIGFAFKDYSQ 127 Query: 133 VWQAMDGPLGAYVRAQIE-KVGLLTMSKPWDNGFRQITTSTKPIKTAADLKGLKLRVPAA 191 VW AMDG LGA+VR QIE + L K WDNG+RQIT STKPIK A DLKG+KLRVP + Sbjct: 128 VWPAMDGELGAHVRKQIEARSTLFAFEKIWDNGYRQITNSTKPIKVAEDLKGMKLRVPPS 187 Query: 192 PMLTSLFSALGASPTPINFNEVYSSLQTKLVEGQENPLAIISTARLYEVQKFCTISNHVW 251 P+ TS+F A A+PT INF EVYS+LQTK+VEGQENP+AIISTA+LYEVQK+C+I+NH+W Sbjct: 188 PLWTSMFKAFDAAPTSINFAEVYSALQTKIVEGQENPMAIISTAKLYEVQKYCSITNHMW 247 Query: 252 DAYWILGNRRAFEKLPKDIQEIVRRELDKAATDERADIASLSGFARNDLQGKGVQIIEAD 311 D +W LGN+++FE+LPKD+QE++ R +++A ++RAD+ L+ ++++GKG+ AD Sbjct: 248 DGFWFLGNKKSFERLPKDLQELMTRIINEAGVNQRADVRKLNDSLVDEMKGKGLAFNNAD 307 Query: 312 KNSFKEALARGSFYKDLRAKFGDDAWKLLQNSVGSLG 348 +SF+ L FY + + KFGD+ W LL+ G L Sbjct: 308 ADSFRAKLRAAGFYAEWKKKFGDEPWALLEKYTGKLA 344 >gi|300310178|ref|YP_003774270.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 334 Score = 128 bits (321), Expect = 8e-31, Method: Compositional matrix adjust. Identities = 71/230 (30%), Positives = 134/230 (58%), Gaps = 7/230 (3%) Query: 56 PVNKRAQQAIDRIREATGGRLDIKLFPANQLGSDTDLMSQIRNGGVEFFNQASVVLSTL- 114 P K A++ + +AT GR+ I+++P + L D + + ++ G V+ + L Sbjct: 39 PKGKAAERFKELAEKATKGRVKIEVYPNSTLYKDKEELEALQLGAVQMLAPSLAKFGPLG 98 Query: 115 VPAAGIVNTGFAFHDYKEVWQAMDGPLGAYVRAQIEKVGLLTMSKPWDNGFRQITTSTKP 174 V + + + F + +++ +GP+G + ++E G+ ++ WDNGF+ + ++ KP Sbjct: 99 VKEFEVFDLPYIFPTKEVLYRVTEGPIGKDLFKKLEPKGITGLAY-WDNGFK-VMSANKP 156 Query: 175 IKTAADLKGLKLRVPAAPMLTSLFSALGASPTPINFNEVYSSLQTKLVEGQENPLAIIST 234 + AD +GLK+R+ ++ +L + ALGA+P + F+EVY +LQT +V+G ENP + + T Sbjct: 157 LHHPADFRGLKMRIQSSKVLDAQMRALGANPQVLAFSEVYQALQTGVVDGTENPPSNLYT 216 Query: 235 ARLYEVQKFCTISNHVWDAYWILGNRRAFEKLPKDIQEIVRRELDKAATD 284 +++EVQK T+SNH + Y ++ N++ ++ LP DI R +L+ A D Sbjct: 217 QKMHEVQKHVTVSNHGYLGYAVIVNKKFWDGLPSDI----RTQLEGAMKD 262 >gi|300312105|ref|YP_003776197.1| TRAP-type C4-dicarboxylate-binding periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 344 Score = 111 bits (277), Expect = 1e-25, Method: Compositional matrix adjust. Identities = 63/230 (27%), Positives = 128/230 (55%), Gaps = 9/230 (3%) Query: 56 PVNKRAQQAIDRIREATGGRLDIKLFPANQLGSDTDLMSQIRNGGVEFFNQASVVLSTLV 115 P K A++ + +AT GR+ ++++P + L D + + ++ G V+ + L+ Sbjct: 47 PKGKGAERFKELAEKATQGRVKVEVYPNSTLYKDKEELEALQLGSVQMLAPS---LAKFG 103 Query: 116 PAAG----IVNTGFAFHDYKEVWQAMDGPLGAYVRAQIEKVGLLTMSKPWDNGFRQITTS 171 P + + + F D + + +GP+G + ++E G+ ++ WDNG + + T+ Sbjct: 104 PLGAREFEVFDLPYIFPDKAVLKRVTEGPIGQGLFQKLEGKGIKGLAY-WDNGMK-VMTA 161 Query: 172 TKPIKTAADLKGLKLRVPAAPMLTSLFSALGASPTPINFNEVYSSLQTKLVEGQENPLAI 231 +P+ AD + LK+R+ ++ +L F AL A+P + F+EVY ++QT +V+G EN + Sbjct: 162 NRPLHKVADFRALKMRIQSSKVLDEQFRALKANPQVLAFSEVYQAMQTGVVDGSENTPSN 221 Query: 232 ISTARLYEVQKFCTISNHVWDAYWILGNRRAFEKLPKDIQEIVRRELDKA 281 + T +++EVQ T+S+H + Y ++ N++ +E LP DI+ + + +A Sbjct: 222 VYTQKMHEVQSNLTVSDHGYIGYAVIVNKKFWEALPADIRSQLEAAMKQA 271 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 0.317 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: 1,082,357 Number of extensions: 44643 Number of successful extensions: 133 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 127 Number of HSP's successfully gapped: 6 Length of query: 348 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 262 Effective length of database: 1,212,660 Effective search space: 317716920 Effective search space used: 317716920 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)