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= 0001.0706.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|300310178|ref|YP_003774270.1| TRAP-type C4-dicarboxylate tran... 649 0.0 gi|300312105|ref|YP_003776197.1| TRAP-type C4-dicarboxylate-bind... 518 e-148 gi|300309847|ref|YP_003773939.1| TRAP-type C4-dicarboxylate tran... 134 8e-33 gi|300313112|ref|YP_003777204.1| TRAP-type C4-dicarboxylate tran... 134 1e-32 gi|300310441|ref|YP_003774533.1| TRAP-type C4-dicarboxylate tran... 129 3e-31 >gi|300310178|ref|YP_003774270.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 334 Score = 649 bits (1675), Expect = 0.0, Method: Compositional matrix adjust. Identities = 315/338 (93%), Positives = 327/338 (96%), Gaps = 4/338 (1%) Query: 1 MKLKSIVFAMATAAVVNVGLAASALAQQPIIIKFSHVVANDTPKGKAAERFKELAEKATK 60 MKLKSI+ AM AA+V+ +A AQQPI+IKFSHVVANDTPKGKAAERFKELAEKATK Sbjct: 1 MKLKSILLAMTAAAIVST----NAFAQQPIVIKFSHVVANDTPKGKAAERFKELAEKATK 56 Query: 61 GRVKVEVYPNSTLYKDKEELEALQLGAVQMLAPSLAKFGPLGVKEFEVFDLPYIFPSKEV 120 GRVK+EVYPNSTLYKDKEELEALQLGAVQMLAPSLAKFGPLGVKEFEVFDLPYIFP+KEV Sbjct: 57 GRVKIEVYPNSTLYKDKEELEALQLGAVQMLAPSLAKFGPLGVKEFEVFDLPYIFPTKEV 116 Query: 121 LYRVTEGPIGRELFKKLEPKGITGLAYWDNGFKVMSANKPLRHPNDFRGLKMRIQSSKVL 180 LYRVTEGPIG++LFKKLEPKGITGLAYWDNGFKVMSANKPL HP DFRGLKMRIQSSKVL Sbjct: 117 LYRVTEGPIGKDLFKKLEPKGITGLAYWDNGFKVMSANKPLHHPADFRGLKMRIQSSKVL 176 Query: 181 DAQMRALGANPQVLAFSEVYQALQTGVVDGTENPPSNLYTQKMHEVQKYVTVSNHGYLGY 240 DAQMRALGANPQVLAFSEVYQALQTGVVDGTENPPSNLYTQKMHEVQK+VTVSNHGYLGY Sbjct: 177 DAQMRALGANPQVLAFSEVYQALQTGVVDGTENPPSNLYTQKMHEVQKHVTVSNHGYLGY 236 Query: 241 AVIVNKKFWDGLPSDIRTELEGAMKDATKYANAIAQQENDAALAAVEKTGKTTVYRLTDA 300 AVIVNKKFWDGLPSDIRT+LEGAMKDATKYANAIAQQENDAALAAVEKTGKTTVYRLTDA Sbjct: 237 AVIVNKKFWDGLPSDIRTQLEGAMKDATKYANAIAQQENDAALAAVEKTGKTTVYRLTDA 296 Query: 301 EKAEWRKALLPVQQQMASRIGKDLIDAVNKEAAALGQK 338 EKAEWRKALLPVQQQMASRIGKDLIDAVNKE+AALGQK Sbjct: 297 EKAEWRKALLPVQQQMASRIGKDLIDAVNKESAALGQK 334 >gi|300312105|ref|YP_003776197.1| TRAP-type C4-dicarboxylate-binding periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 344 Score = 518 bits (1333), Expect = e-148, Method: Compositional matrix adjust. Identities = 255/342 (74%), Positives = 290/342 (84%), Gaps = 4/342 (1%) Query: 1 MKLKSIVFAMATAAVVNVGLA-ASALAQQP---IIIKFSHVVANDTPKGKAAERFKELAE 56 M + + A+A A V +GL +ALAQQP IIIKFSHVVANDTPKGK AERFKELAE Sbjct: 1 MTILPLRTALAACAFVTLGLPQPAALAQQPQQPIIIKFSHVVANDTPKGKGAERFKELAE 60 Query: 57 KATKGRVKVEVYPNSTLYKDKEELEALQLGAVQMLAPSLAKFGPLGVKEFEVFDLPYIFP 116 KAT+GRVKVEVYPNSTLYKDKEELEALQLG+VQMLAPSLAKFGPLG +EFEVFDLPYIFP Sbjct: 61 KATQGRVKVEVYPNSTLYKDKEELEALQLGSVQMLAPSLAKFGPLGAREFEVFDLPYIFP 120 Query: 117 SKEVLYRVTEGPIGRELFKKLEPKGITGLAYWDNGFKVMSANKPLRHPNDFRGLKMRIQS 176 K VL RVTEGPIG+ LF+KLE KGI GLAYWDNG KVM+AN+PL DFR LKMRIQS Sbjct: 121 DKAVLKRVTEGPIGQGLFQKLEGKGIKGLAYWDNGMKVMTANRPLHKVADFRALKMRIQS 180 Query: 177 SKVLDAQMRALGANPQVLAFSEVYQALQTGVVDGTENPPSNLYTQKMHEVQKYVTVSNHG 236 SKVLD Q RAL ANPQVLAFSEVYQA+QTGVVDG+EN PSN+YTQKMHEVQ +TVS+HG Sbjct: 181 SKVLDEQFRALKANPQVLAFSEVYQAMQTGVVDGSENTPSNVYTQKMHEVQSNLTVSDHG 240 Query: 237 YLGYAVIVNKKFWDGLPSDIRTELEGAMKDATKYANAIAQQENDAALAAVEKTGKTTVYR 296 Y+GYAVIVNKKFW+ LP+DIR++LE AMK AT YAN IAQ+END ALAA++ +GKT VY Sbjct: 241 YIGYAVIVNKKFWEALPADIRSQLEAAMKQATLYANTIAQKENDDALAAIKASGKTRVYT 300 Query: 297 LTDAEKAEWRKALLPVQQQMASRIGKDLIDAVNKEAAALGQK 338 L++ EKAEWR+ALLPV + MA+R+G DLI+A+ KE+ A G K Sbjct: 301 LSEQEKAEWRRALLPVHKSMAARVGADLIEAIYKESEAAGVK 342 >gi|300309847|ref|YP_003773939.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 345 Score = 134 bits (338), Expect = 8e-33, Method: Compositional matrix adjust. Identities = 85/303 (28%), Positives = 162/303 (53%), Gaps = 19/303 (6%) Query: 43 PKGKAAERFKELAEKATKGRVKVEVYPNSTLYKDKEELEALQLGAVQMLAPSLAKFGPLG 102 P K A+ + AT GR++++++P + L D + + ++ G V+ + L Sbjct: 53 PVNKRAQEAIDRIRNATNGRLEIKLFPANQLGSDTDLMSQVRNGGVEFFNQANTVLSTL- 111 Query: 103 VKEFEVFDLPYIFPSKEVLYRVTEGPIGRELFKKLEPKGITGLAY-WDNGFK-VMSANKP 160 V + + + F +++ +GP+G + ++E G+ ++ WDNGF+ + ++ KP Sbjct: 112 VPAAGIVNTGFAFHDYGAVWKAMDGPLGAHVRAQIEKVGLLTMSKPWDNGFRQITTSTKP 171 Query: 161 LRHPNDFRGLKMRIQSSKVLDAQMRALGANPQVLAFSEVYQALQTGVVDGTENPPSNLYT 220 +R+ D +GLK+R+ ++ +L + ALGA+P + F+EVY +LQT +V+G ENP + + T Sbjct: 172 VRNAGDVKGLKLRVPAAPMLTSLFSALGASPTPINFNEVYSSLQTKLVEGQENPLAIIST 231 Query: 221 QKMHEVQKYVTVSNHGYLGYAVIVNKKFWDGLPSDI----RTELEGAMKDATKYANAIAQ 276 +++EVQK+ T+SNH + Y ++ N++ ++ LP DI R EL+ A D A + Sbjct: 232 ARLYEVQKFCTISNHVWDAYWILGNRRAFEKLPKDIQEIVRRELDKAASDERADIAAFSG 291 Query: 277 -QENDAALAAVEKTGKTTVYRLTDAEKAEWRKALLPVQ--QQMASRIGKDLIDAVNKEAA 333 ND A ++ + +A+K +++AL + M ++ G+D + Sbjct: 292 FARNDLASKGLQ---------IVEADKDSFKEALARANFYKDMRAKFGEDAWKLLEGSVG 342 Query: 334 ALG 336 ALG Sbjct: 343 ALG 345 >gi|300313112|ref|YP_003777204.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 344 Score = 134 bits (336), Expect = 1e-32, Method: Compositional matrix adjust. Identities = 86/295 (29%), Positives = 158/295 (53%), Gaps = 25/295 (8%) Query: 33 KFSHVVANDTP-----KGKAAERFKELAEKATKGRVKVEVYPNSTLYKDKEELEALQLGA 87 +F+ AN+ P +A E +AE+ +KGR+++++YPN+ L D + L ++ GA Sbjct: 37 EFTFKYANNLPVTHPMNARAKEMAAAIAEQ-SKGRIELQLYPNNQLGTDTDMLSQVRAGA 95 Query: 88 VQMLAPSLAKFGPLGVKEFEVFDLPYIFPSKEVLYRVTEGPIGRELFKKLEPKGITGLAY 147 + S G L V ++ + + F ++ +G +G + K++E + T A+ Sbjct: 96 IDFFTLSPLILGTL-VPAAQISGIGFAFKDYSQVWPAMDGELGAHVRKQIEARS-TLFAF 153 Query: 148 ---WDNGFK-VMSANKPLRHPNDFRGLKMRIQSSKVLDAQMRALGANPQVLAFSEVYQAL 203 WDNG++ + ++ KP++ D +G+K+R+ S + + +A A P + F+EVY AL Sbjct: 154 EKIWDNGYRQITNSTKPIKVAEDLKGMKLRVPPSPLWTSMFKAFDAAPTSINFAEVYSAL 213 Query: 204 QTGVVDGTENPPSNLYTQKMHEVQKYVTVSNHGYLGYAVIVNKKFWDGLPSDIRTELEGA 263 QT +V+G ENP + + T K++EVQKY +++NH + G+ + NKK ++ LP D++ + Sbjct: 214 QTKIVEGQENPMAIISTAKLYEVQKYCSITNHMWDGFWFLGNKKSFERLPKDLQELMTRI 273 Query: 264 MKDATKYANAIAQQENDAALAAVEKTGKTTVYRLTDAEK-----------AEWRK 307 + +A A ++ ND+ + E GK + DA+ AEW+K Sbjct: 274 INEAGVNQRADVRKLNDSLVD--EMKGKGLAFNNADADSFRAKLRAAGFYAEWKK 326 >gi|300310441|ref|YP_003774533.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 348 Score = 129 bits (325), Expect = 3e-31, Method: Compositional matrix adjust. Identities = 70/230 (30%), Positives = 135/230 (58%), Gaps = 7/230 (3%) Query: 43 PKGKAAERFKELAEKATKGRVKVEVYPNSTLYKDKEELEALQLGAVQMLAPSLAKFGPLG 102 P K A++ + +AT GR+ ++++P + L D + + ++ G V+ + L Sbjct: 56 PVNKRAQQAIDRIREATGGRLDIKLFPANQLGSDTDLMSQIRNGGVEFFNQASVVLSTL- 114 Query: 103 VKEFEVFDLPYIFPSKEVLYRVTEGPIGRELFKKLEPKGITGLAY-WDNGFK-VMSANKP 160 V + + + F + +++ +GP+G + ++E G+ ++ WDNGF+ + ++ KP Sbjct: 115 VPAAGIVNTGFAFHDYKEVWQAMDGPLGAYVRAQIEKVGLLTMSKPWDNGFRQITTSTKP 174 Query: 161 LRHPNDFRGLKMRIQSSKVLDAQMRALGANPQVLAFSEVYQALQTGVVDGTENPPSNLYT 220 ++ D +GLK+R+ ++ +L + ALGA+P + F+EVY +LQT +V+G ENP + + T Sbjct: 175 IKTAADLKGLKLRVPAAPMLTSLFSALGASPTPINFNEVYSSLQTKLVEGQENPLAIIST 234 Query: 221 QKMHEVQKYVTVSNHGYLGYAVIVNKKFWDGLPSDI----RTELEGAMKD 266 +++EVQK+ T+SNH + Y ++ N++ ++ LP DI R EL+ A D Sbjct: 235 ARLYEVQKFCTISNHVWDAYWILGNRRAFEKLPKDIQEIVRRELDKAATD 284 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 0.131 0.367 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: 958,960 Number of extensions: 37798 Number of successful extensions: 162 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 156 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)