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= 0001.3724.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... 663 0.0 gi|300310441|ref|YP_003774533.1| TRAP-type C4-dicarboxylate tran... 379 e-106 gi|300309847|ref|YP_003773939.1| TRAP-type C4-dicarboxylate tran... 375 e-105 gi|300310178|ref|YP_003774270.1| TRAP-type C4-dicarboxylate tran... 138 7e-34 gi|300312105|ref|YP_003776197.1| TRAP-type C4-dicarboxylate-bind... 122 5e-29 >gi|300313112|ref|YP_003777204.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 344 Score = 663 bits (1710), Expect = 0.0, Method: Compositional matrix adjust. Identities = 324/344 (94%), Positives = 334/344 (97%) Query: 1 MDHSTGKFTRRHFLKTASLASAAAATGLSSNAAHAAEFSFKYANNLPVTHPMNARAKEMA 60 M STGK TRR+FLKTAS+ASAAAATGL S +AHAAEF+FKYANNLPVTHPMNARAKEMA Sbjct: 1 MAQSTGKITRRNFLKTASVASAAAATGLVSTSAHAAEFTFKYANNLPVTHPMNARAKEMA 60 Query: 61 AAIAEQSKGRIELQLYPNNQLGTDTDMLSQVRAGAIDFFTLSPLILGTLVPSAQISGIGF 120 AAIAEQSKGRIELQLYPNNQLGTDTDMLSQVRAGAIDFFTLSPLILGTLVP+AQISGIGF Sbjct: 61 AAIAEQSKGRIELQLYPNNQLGTDTDMLSQVRAGAIDFFTLSPLILGTLVPAAQISGIGF 120 Query: 121 AFKDYSQVWPAMDGELGAHVRKQIESKSTLFAFEKIWDNGYRQITNSTRPIKTADDLKGM 180 AFKDYSQVWPAMDGELGAHVRKQIE++STLFAFEKIWDNGYRQITNST+PIK A+DLKGM Sbjct: 121 AFKDYSQVWPAMDGELGAHVRKQIEARSTLFAFEKIWDNGYRQITNSTKPIKVAEDLKGM 180 Query: 181 KLRVPPSPLWTSMFKAFDAAPTSINFAEVYSALQTKIVEGQENPMAIISTAKLYEVQKYC 240 KLRVPPSPLWTSMFKAFDAAPTSINFAEVYSALQTKIVEGQENPMAIISTAKLYEVQKYC Sbjct: 181 KLRVPPSPLWTSMFKAFDAAPTSINFAEVYSALQTKIVEGQENPMAIISTAKLYEVQKYC 240 Query: 241 SITNHMWDGFWFLGNKKSFERLPKDLQELMARIINEAAMNQRADVRKLNDSLVDEMKGKG 300 SITNHMWDGFWFLGNKKSFERLPKDLQELM RIINEA +NQRADVRKLNDSLVDEMKGKG Sbjct: 241 SITNHMWDGFWFLGNKKSFERLPKDLQELMTRIINEAGVNQRADVRKLNDSLVDEMKGKG 300 Query: 301 LVFNNADADSFRAKLRTAGFYAEWKKKFGDEPWALLEKYTGKLA 344 L FNNADADSFRAKLR AGFYAEWKKKFGDEPWALLEKYTGKLA Sbjct: 301 LAFNNADADSFRAKLRAAGFYAEWKKKFGDEPWALLEKYTGKLA 344 >gi|300310441|ref|YP_003774533.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 348 Score = 379 bits (973), Expect = e-106, Method: Compositional matrix adjust. Identities = 173/336 (51%), Positives = 245/336 (72%), Gaps = 1/336 (0%) Query: 9 TRRHFLKTASLASAAAATGLSSNAAHAAEFSFKYANNLPVTHPMNARAKEMAAAIAEQSK 68 +RR LK ++ +A + S A+AAEF++K+A +HP+N RA++ I E + Sbjct: 14 SRRQLLKAGAVGAALPLFSIMSRPANAAEFNYKFATGQDPSHPVNKRAQQAIDRIREATG 73 Query: 69 GRIELQLYPNNQLGTDTDMLSQVRAGAIDFFTLSPLILGTLVPSAQISGIGFAFKDYSQV 128 GR++++L+P NQLG+DTD++SQ+R G ++FF + ++L TLVP+A I GFAF DY +V Sbjct: 74 GRLDIKLFPANQLGSDTDLMSQIRNGGVEFFNQASVVLSTLVPAAGIVNTGFAFHDYKEV 133 Query: 129 WPAMDGELGAHVRKQIESKSTLFAFEKIWDNGYRQITNSTRPIKTADDLKGMKLRVPPSP 188 W AMDG LGA+VR QIE K L K WDNG+RQIT ST+PIKTA DLKG+KLRVP +P Sbjct: 134 WQAMDGPLGAYVRAQIE-KVGLLTMSKPWDNGFRQITTSTKPIKTAADLKGLKLRVPAAP 192 Query: 189 LWTSMFKAFDAAPTSINFAEVYSALQTKIVEGQENPMAIISTAKLYEVQKYCSITNHMWD 248 + TS+F A A+PT INF EVYS+LQTK+VEGQENP+AIISTA+LYEVQK+C+I+NH+WD Sbjct: 193 MLTSLFSALGASPTPINFNEVYSSLQTKLVEGQENPLAIISTARLYEVQKFCTISNHVWD 252 Query: 249 GFWFLGNKKSFERLPKDLQELMARIINEAAMNQRADVRKLNDSLVDEMKGKGLVFNNADA 308 +W LGN+++FE+LPKD+QE++ R +++AA ++RAD+ L+ ++++GKG+ AD Sbjct: 253 AYWILGNRRAFEKLPKDIQEIVRRELDKAATDERADIASLSGFARNDLQGKGVQIIEADK 312 Query: 309 DSFRAKLRTAGFYAEWKKKFGDEPWALLEKYTGKLA 344 +SF+ L FY + + KFGD+ W LL+ G L Sbjct: 313 NSFKEALARGSFYKDLRAKFGDDAWKLLQNSVGSLG 348 >gi|300309847|ref|YP_003773939.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 345 Score = 375 bits (963), Expect = e-105, Method: Compositional matrix adjust. Identities = 175/338 (51%), Positives = 240/338 (71%), Gaps = 1/338 (0%) Query: 7 KFTRRHFLKTASLASAAAATGLSSNAAHAAEFSFKYANNLPVTHPMNARAKEMAAAIAEQ 66 + TRR+ LK ++ +A + S A AAEFS+K+A +HP+N RA+E I Sbjct: 9 QVTRRNMLKAGAVGAALPLFSILSRPASAAEFSYKFATGQDPSHPVNKRAQEAIDRIRNA 68 Query: 67 SKGRIELQLYPNNQLGTDTDMLSQVRAGAIDFFTLSPLILGTLVPSAQISGIGFAFKDYS 126 + GR+E++L+P NQLG+DTD++SQVR G ++FF + +L TLVP+A I GFAF DY Sbjct: 69 TNGRLEIKLFPANQLGSDTDLMSQVRNGGVEFFNQANTVLSTLVPAAGIVNTGFAFHDYG 128 Query: 127 QVWPAMDGELGAHVRKQIESKSTLFAFEKIWDNGYRQITNSTRPIKTADDLKGMKLRVPP 186 VW AMDG LGAHVR QIE K L K WDNG+RQIT ST+P++ 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 WDGFWFLGNKKSFERLPKDLQELMARIINEAAMNQRADVRKLNDSLVDEMKGKGLVFNNA 306 WD +W LGN+++FE+LPKD+QE++ R +++AA ++RAD+ + +++ KGL A Sbjct: 248 WDAYWILGNRRAFEKLPKDIQEIVRRELDKAASDERADIAAFSGFARNDLASKGLQIVEA 307 Query: 307 DADSFRAKLRTAGFYAEWKKKFGDEPWALLEKYTGKLA 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 = 138 bits (348), Expect = 7e-34, Method: Compositional matrix adjust. Identities = 97/322 (30%), Positives = 171/322 (53%), Gaps = 30/322 (9%) Query: 14 LKTASLASAAAATGLSSNA----AHAAEFSFKYANNLPVTHPMNARAKEMAAAIAEQ-SK 68 LK+ LA AAA +S+NA +FS AN+ P +A E +AE+ +K Sbjct: 3 LKSILLAMTAAAI-VSTNAFAQQPIVIKFSHVVANDTP-----KGKAAERFKELAEKATK 56 Query: 69 GRIELQLYPNNQLGTDTDMLSQVRAGAIDFFTLSPLILGTL-VPSAQISGIGFAFKDYSQ 127 GR+++++YPN+ L D + L ++ GA+ S G L V ++ + + F Sbjct: 57 GRVKIEVYPNSTLYKDKEELEALQLGAVQMLAPSLAKFGPLGVKEFEVFDLPYIFPTKEV 116 Query: 128 VWPAMDGELGAHVRKQIESKS-TLFAFEKIWDNGYRQITNSTRPIKTADDLKGMKLRVPP 186 ++ +G +G + K++E K T A+ WDNG++ + ++ +P+ D +G+K+R+ Sbjct: 117 LYRVTEGPIGKDLFKKLEPKGITGLAY---WDNGFK-VMSANKPLHHPADFRGLKMRIQS 172 Query: 187 SPLWTSMFKAFDAAPTSINFAEVYSALQTKIVEGQENPMAIISTAKLYEVQKYCSITNHM 246 S + + +A A P + F+EVY ALQT +V+G ENP + + T K++EVQK+ +++NH Sbjct: 173 SKVLDAQMRALGANPQVLAFSEVYQALQTGVVDGTENPPSNLYTQKMHEVQKHVTVSNHG 232 Query: 247 WDGFWFLGNKKSFERLPKDLQELMARIINEAAMNQRADVRKLNDSLVD--EMKGKGLVFN 304 + G+ + NKK ++ LP D++ + + +A A ++ ND+ + E GK V+ Sbjct: 233 YLGYAVIVNKKFWDGLPSDIRTQLEGAMKDATKYANAIAQQENDAALAAVEKTGKTTVYR 292 Query: 305 NADADSFRAKLRTAGFYAEWKK 326 DA+ AEW+K Sbjct: 293 LTDAEK-----------AEWRK 303 >gi|300312105|ref|YP_003776197.1| TRAP-type C4-dicarboxylate-binding periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 344 Score = 122 bits (306), Expect = 5e-29, Method: Compositional matrix adjust. Identities = 83/298 (27%), Positives = 151/298 (50%), Gaps = 20/298 (6%) Query: 14 LKTASLASAAAATGLSSNAAHAAE--------FSFKYANNLPVTHPMNARAKEMAAAIAE 65 L+TA A A GL AA A + FS AN+ P + E +AE Sbjct: 6 LRTALAACAFVTLGLPQPAALAQQPQQPIIIKFSHVVANDTP-----KGKGAERFKELAE 60 Query: 66 Q-SKGRIELQLYPNNQLGTDTDMLSQVRAGAIDFFTLSPLILGTL-VPSAQISGIGFAFK 123 + ++GR+++++YPN+ L D + L ++ G++ S G L ++ + + F Sbjct: 61 KATQGRVKVEVYPNSTLYKDKEELEALQLGSVQMLAPSLAKFGPLGAREFEVFDLPYIFP 120 Query: 124 DYSQVWPAMDGELGAHVRKQIESKSTL-FAFEKIWDNGYRQITNSTRPIKTADDLKGMKL 182 D + + +G +G + +++E K A+ WDNG + +T + RP+ 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 TNHMWDGFWFLGNKKSFERLPKDLQELMARIINEAAMNQRADVRKLNDSLVDEMKGKG 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 0.318 0.131 0.385 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: 910,667 Number of extensions: 33294 Number of successful extensions: 97 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 90 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)