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= 0029.0271.p (344 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... 710 0.0 gi|300310441|ref|YP_003774533.1| TRAP-type C4-dicarboxylate tran... 381 e-107 gi|300309847|ref|YP_003773939.1| TRAP-type C4-dicarboxylate tran... 380 e-106 gi|300310178|ref|YP_003774270.1| TRAP-type C4-dicarboxylate tran... 139 4e-34 gi|300312105|ref|YP_003776197.1| TRAP-type C4-dicarboxylate-bind... 117 1e-27 >gi|300313112|ref|YP_003777204.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 344 Score = 710 bits (1833), Expect = 0.0, Method: Compositional matrix adjust. Identities = 343/344 (99%), Positives = 344/344 (100%) Query: 1 MAQSTGKITRRNFLKTASVASAAAATGLVSTSAHAAEFTFKYANNLPVTHPMNARAKEMA 60 MAQSTGKITRRNFLKTASVASAAAATGLVSTSAHAAEFTFKYANNLPVTHPMNARAKEMA Sbjct: 1 MAQSTGKITRRNFLKTASVASAAAATGLVSTSAHAAEFTFKYANNLPVTHPMNARAKEMA 60 Query: 61 AAIAEQSKGRIELQLYPNNQLGTDTDMLSQVRAGAIDFFTLSPLILGTLVPAAQISGIGF 120 AAIAEQSKGRIELQLYPNNQLGTDTDMLSQVRAGAIDFFTLSPLILGTLVPAAQISGIGF Sbjct: 61 AAIAEQSKGRIELQLYPNNQLGTDTDMLSQVRAGAIDFFTLSPLILGTLVPAAQISGIGF 120 Query: 121 AFKDYSQVWPAMDGELGAHVRKQIEAKSTLFAFEKIWDNGYRQITNSTKPIKVAEDLKGM 180 AFKDYSQVWPAMDGELGAHVRKQIEA+STLFAFEKIWDNGYRQITNSTKPIKVAEDLKGM Sbjct: 121 AFKDYSQVWPAMDGELGAHVRKQIEARSTLFAFEKIWDNGYRQITNSTKPIKVAEDLKGM 180 Query: 181 KLRVPPSPLWTSMFKAFDAAPTSINFAEVYSALQTKIVEGQENPMAIISTAKLYEVQKYC 240 KLRVPPSPLWTSMFKAFDAAPTSINFAEVYSALQTKIVEGQENPMAIISTAKLYEVQKYC Sbjct: 181 KLRVPPSPLWTSMFKAFDAAPTSINFAEVYSALQTKIVEGQENPMAIISTAKLYEVQKYC 240 Query: 241 SITNHMWDGFWFLGNKKSFERLPKDLQELMTRIINEAGVNQRADVRKLNDSLVDEMKGKG 300 SITNHMWDGFWFLGNKKSFERLPKDLQELMTRIINEAGVNQRADVRKLNDSLVDEMKGKG Sbjct: 241 SITNHMWDGFWFLGNKKSFERLPKDLQELMTRIINEAGVNQRADVRKLNDSLVDEMKGKG 300 Query: 301 LAFNNADADSFRAKLRAAGFYAEWKKKFGDEPWALLEKYTGKLA 344 LAFNNADADSFRAKLRAAGFYAEWKKKFGDEPWALLEKYTGKLA Sbjct: 301 LAFNNADADSFRAKLRAAGFYAEWKKKFGDEPWALLEKYTGKLA 344 >gi|300310441|ref|YP_003774533.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 348 Score = 381 bits (979), Expect = e-107, Method: Compositional matrix adjust. Identities = 174/337 (51%), Positives = 244/337 (72%), Gaps = 1/337 (0%) Query: 8 ITRRNFLKTASVASAAAATGLVSTSAHAAEFTFKYANNLPVTHPMNARAKEMAAAIAEQS 67 ++RR LK +V +A ++S A+AAEF +K+A +HP+N RA++ I E + Sbjct: 13 VSRRQLLKAGAVGAALPLFSIMSRPANAAEFNYKFATGQDPSHPVNKRAQQAIDRIREAT 72 Query: 68 KGRIELQLYPNNQLGTDTDMLSQVRAGAIDFFTLSPLILGTLVPAAQISGIGFAFKDYSQ 127 GR++++L+P NQLG+DTD++SQ+R G ++FF + ++L TLVPAA I GFAF DY + Sbjct: 73 GGRLDIKLFPANQLGSDTDLMSQIRNGGVEFFNQASVVLSTLVPAAGIVNTGFAFHDYKE 132 Query: 128 VWPAMDGELGAHVRKQIEAKSTLFAFEKIWDNGYRQITNSTKPIKVAEDLKGMKLRVPPS 187 VW AMDG LGA+VR QIE K L K WDNG+RQIT STKPIK A DLKG+KLRVP + Sbjct: 133 VWQAMDGPLGAYVRAQIE-KVGLLTMSKPWDNGFRQITTSTKPIKTAADLKGLKLRVPAA 191 Query: 188 PLWTSMFKAFDAAPTSINFAEVYSALQTKIVEGQENPMAIISTAKLYEVQKYCSITNHMW 247 P+ TS+F A A+PT INF EVYS+LQTK+VEGQENP+AIISTA+LYEVQK+C+I+NH+W Sbjct: 192 PMLTSLFSALGASPTPINFNEVYSSLQTKLVEGQENPLAIISTARLYEVQKFCTISNHVW 251 Query: 248 DGFWFLGNKKSFERLPKDLQELMTRIINEAGVNQRADVRKLNDSLVDEMKGKGLAFNNAD 307 D +W LGN+++FE+LPKD+QE++ R +++A ++RAD+ L+ ++++GKG+ AD Sbjct: 252 DAYWILGNRRAFEKLPKDIQEIVRRELDKAATDERADIASLSGFARNDLQGKGVQIIEAD 311 Query: 308 ADSFRAKLRAAGFYAEWKKKFGDEPWALLEKYTGKLA 344 +SF+ L FY + + KFGD+ W LL+ G L Sbjct: 312 KNSFKEALARGSFYKDLRAKFGDDAWKLLQNSVGSLG 348 >gi|300309847|ref|YP_003773939.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 345 Score = 380 bits (975), Expect = e-106, Method: Compositional matrix adjust. Identities = 177/338 (52%), Positives = 241/338 (71%), Gaps = 1/338 (0%) Query: 7 KITRRNFLKTASVASAAAATGLVSTSAHAAEFTFKYANNLPVTHPMNARAKEMAAAIAEQ 66 ++TRRN LK +V +A ++S A AAEF++K+A +HP+N RA+E I Sbjct: 9 QVTRRNMLKAGAVGAALPLFSILSRPASAAEFSYKFATGQDPSHPVNKRAQEAIDRIRNA 68 Query: 67 SKGRIELQLYPNNQLGTDTDMLSQVRAGAIDFFTLSPLILGTLVPAAQISGIGFAFKDYS 126 + GR+E++L+P NQLG+DTD++SQVR G ++FF + +L TLVPAA I GFAF DY Sbjct: 69 TNGRLEIKLFPANQLGSDTDLMSQVRNGGVEFFNQANTVLSTLVPAAGIVNTGFAFHDYG 128 Query: 127 QVWPAMDGELGAHVRKQIEAKSTLFAFEKIWDNGYRQITNSTKPIKVAEDLKGMKLRVPP 186 VW AMDG LGAHVR QIE K L K WDNG+RQIT STKP++ A D+KG+KLRVP Sbjct: 129 AVWKAMDGPLGAHVRAQIE-KVGLLTMSKPWDNGFRQITTSTKPVRNAGDVKGLKLRVPA 187 Query: 187 SPLWTSMFKAFDAAPTSINFAEVYSALQTKIVEGQENPMAIISTAKLYEVQKYCSITNHM 246 +P+ TS+F A A+PT INF EVYS+LQTK+VEGQENP+AIISTA+LYEVQK+C+I+NH+ Sbjct: 188 APMLTSLFSALGASPTPINFNEVYSSLQTKLVEGQENPLAIISTARLYEVQKFCTISNHV 247 Query: 247 WDGFWFLGNKKSFERLPKDLQELMTRIINEAGVNQRADVRKLNDSLVDEMKGKGLAFNNA 306 WD +W LGN+++FE+LPKD+QE++ R +++A ++RAD+ + +++ KGL A Sbjct: 248 WDAYWILGNRRAFEKLPKDIQEIVRRELDKAASDERADIAAFSGFARNDLASKGLQIVEA 307 Query: 307 DADSFRAKLRAAGFYAEWKKKFGDEPWALLEKYTGKLA 344 D DSF+ L A FY + + KFG++ W LLE G L Sbjct: 308 DKDSFKEALARANFYKDMRAKFGEDAWKLLEGSVGALG 345 >gi|300310178|ref|YP_003774270.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 334 Score = 139 bits (350), Expect = 4e-34, Method: Compositional matrix adjust. Identities = 95/323 (29%), Positives = 170/323 (52%), Gaps = 30/323 (9%) Query: 14 LKTASVASAAAATGLVSTSAHAAE-----FTFKYANNLPVTHPMNARAKEMAAAIAEQ-S 67 +K S+ A A +VST+A A + F+ AN+ P +A E +AE+ + Sbjct: 1 MKLKSILLAMTAAAIVSTNAFAQQPIVIKFSHVVANDTP-----KGKAAERFKELAEKAT 55 Query: 68 KGRIELQLYPNNQLGTDTDMLSQVRAGAIDFFTLSPLILGTL-VPAAQISGIGFAFKDYS 126 KGR+++++YPN+ L D + L ++ GA+ S G L V ++ + + F Sbjct: 56 KGRVKIEVYPNSTLYKDKEELEALQLGAVQMLAPSLAKFGPLGVKEFEVFDLPYIFPTKE 115 Query: 127 QVWPAMDGELGAHVRKQIEAKS-TLFAFEKIWDNGYRQITNSTKPIKVAEDLKGMKLRVP 185 ++ +G +G + K++E K T A+ WDNG++ + ++ KP+ D +G+K+R+ Sbjct: 116 VLYRVTEGPIGKDLFKKLEPKGITGLAY---WDNGFK-VMSANKPLHHPADFRGLKMRIQ 171 Query: 186 PSPLWTSMFKAFDAAPTSINFAEVYSALQTKIVEGQENPMAIISTAKLYEVQKYCSITNH 245 S + + +A A P + F+EVY ALQT +V+G ENP + + T K++EVQK+ +++NH Sbjct: 172 SSKVLDAQMRALGANPQVLAFSEVYQALQTGVVDGTENPPSNLYTQKMHEVQKHVTVSNH 231 Query: 246 MWDGFWFLGNKKSFERLPKDLQELMTRIINEAGVNQRADVRKLNDSLVD--EMKGKGLAF 303 + G+ + NKK ++ LP D++ + + +A A ++ ND+ + E GK + Sbjct: 232 GYLGYAVIVNKKFWDGLPSDIRTQLEGAMKDATKYANAIAQQENDAALAAVEKTGKTTVY 291 Query: 304 NNADADSFRAKLRAAGFYAEWKK 326 DA+ AEW+K Sbjct: 292 RLTDAEK-----------AEWRK 303 >gi|300312105|ref|YP_003776197.1| TRAP-type C4-dicarboxylate-binding periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 344 Score = 117 bits (293), Expect = 1e-27, Method: Compositional matrix adjust. Identities = 80/298 (26%), Positives = 151/298 (50%), Gaps = 20/298 (6%) Query: 14 LKTASVASAAAATGLVSTSAHAAE--------FTFKYANNLPVTHPMNARAKEMAAAIAE 65 L+TA A A GL +A A + F+ AN+ P + E +AE Sbjct: 6 LRTALAACAFVTLGLPQPAALAQQPQQPIIIKFSHVVANDTP-----KGKGAERFKELAE 60 Query: 66 Q-SKGRIELQLYPNNQLGTDTDMLSQVRAGAIDFFTLSPLILGTL-VPAAQISGIGFAFK 123 + ++GR+++++YPN+ L D + L ++ G++ S G L ++ + + F Sbjct: 61 KATQGRVKVEVYPNSTLYKDKEELEALQLGSVQMLAPSLAKFGPLGAREFEVFDLPYIFP 120 Query: 124 DYSQVWPAMDGELGAHVRKQIEAKSTL-FAFEKIWDNGYRQITNSTKPIKVAEDLKGMKL 182 D + + +G +G + +++E K A+ WDNG + +T + +P+ D + +K+ Sbjct: 121 DKAVLKRVTEGPIGQGLFQKLEGKGIKGLAY---WDNGMKVMT-ANRPLHKVADFRALKM 176 Query: 183 RVPPSPLWTSMFKAFDAAPTSINFAEVYSALQTKIVEGQENPMAIISTAKLYEVQKYCSI 242 R+ S + F+A A P + F+EVY A+QT +V+G EN + + T K++EVQ ++ Sbjct: 177 RIQSSKVLDEQFRALKANPQVLAFSEVYQAMQTGVVDGSENTPSNVYTQKMHEVQSNLTV 236 Query: 243 TNHMWDGFWFLGNKKSFERLPKDLQELMTRIINEAGVNQRADVRKLNDSLVDEMKGKG 300 ++H + G+ + NKK +E LP D++ + + +A + +K ND + +K G Sbjct: 237 SDHGYIGYAVIVNKKFWEALPADIRSQLEAAMKQATLYANTIAQKENDDALAAIKASG 294 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 0.131 0.382 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: 917,168 Number of extensions: 34384 Number of successful extensions: 106 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 99 Number of HSP's successfully gapped: 6 Length of query: 344 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 258 Effective length of database: 1,212,660 Effective search space: 312866280 Effective search space used: 312866280 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)