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= 0004.0034.p (334 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... 683 0.0 gi|300312105|ref|YP_003776197.1| TRAP-type C4-dicarboxylate-bind... 523 e-150 gi|300313112|ref|YP_003777204.1| TRAP-type C4-dicarboxylate tran... 132 5e-32 gi|300309847|ref|YP_003773939.1| TRAP-type C4-dicarboxylate tran... 129 3e-31 gi|300310441|ref|YP_003774533.1| TRAP-type C4-dicarboxylate tran... 128 7e-31 >gi|300310178|ref|YP_003774270.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 334 Score = 683 bits (1762), Expect = 0.0, Method: Compositional matrix adjust. Identities = 333/334 (99%), Positives = 334/334 (100%) Query: 1 MKLKSILLAMTAAAIVSTNAFAQQPIVIKFSHVVANDTPKGKAAERFKELAEKATQGRVK 60 MKLKSILLAMTAAAIVSTNAFAQQPIVIKFSHVVANDTPKGKAAERFKELAEKAT+GRVK Sbjct: 1 MKLKSILLAMTAAAIVSTNAFAQQPIVIKFSHVVANDTPKGKAAERFKELAEKATKGRVK 60 Query: 61 IEVYPNSTLYKDKEELEALQLGAVQMLAPSLAKFGPLGVKEFEVFDLPYIFPTKEVLYRV 120 IEVYPNSTLYKDKEELEALQLGAVQMLAPSLAKFGPLGVKEFEVFDLPYIFPTKEVLYRV Sbjct: 61 IEVYPNSTLYKDKEELEALQLGAVQMLAPSLAKFGPLGVKEFEVFDLPYIFPTKEVLYRV 120 Query: 121 TEGPIGKDLFKKLEPKGITGLAYWDNGFKVMSANKPLHHPADFRGLKMRIQSSKVLDAQM 180 TEGPIGKDLFKKLEPKGITGLAYWDNGFKVMSANKPLHHPADFRGLKMRIQSSKVLDAQM Sbjct: 121 TEGPIGKDLFKKLEPKGITGLAYWDNGFKVMSANKPLHHPADFRGLKMRIQSSKVLDAQM 180 Query: 181 RALGANPQVLAFSEVYQALQTGVVDGTENPPSNLYTQKMHEVQKHVTVSNHGYLGYAVIV 240 RALGANPQVLAFSEVYQALQTGVVDGTENPPSNLYTQKMHEVQKHVTVSNHGYLGYAVIV Sbjct: 181 RALGANPQVLAFSEVYQALQTGVVDGTENPPSNLYTQKMHEVQKHVTVSNHGYLGYAVIV 240 Query: 241 NKKFWDGLPSDIRTQLEGAMKDATKYANAIAQQENDAALAAVEKTGKTTVYRLTDAEKAE 300 NKKFWDGLPSDIRTQLEGAMKDATKYANAIAQQENDAALAAVEKTGKTTVYRLTDAEKAE Sbjct: 241 NKKFWDGLPSDIRTQLEGAMKDATKYANAIAQQENDAALAAVEKTGKTTVYRLTDAEKAE 300 Query: 301 WRKALLPVQQQMASRIGKDLIDAVNKESAALGQK 334 WRKALLPVQQQMASRIGKDLIDAVNKESAALGQK Sbjct: 301 WRKALLPVQQQMASRIGKDLIDAVNKESAALGQK 334 >gi|300312105|ref|YP_003776197.1| TRAP-type C4-dicarboxylate-binding periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 344 Score = 523 bits (1346), Expect = e-150, Method: Compositional matrix adjust. Identities = 248/312 (79%), Positives = 278/312 (89%) Query: 23 QQPIVIKFSHVVANDTPKGKAAERFKELAEKATQGRVKIEVYPNSTLYKDKEELEALQLG 82 QQPI+IKFSHVVANDTPKGK AERFKELAEKATQGRVK+EVYPNSTLYKDKEELEALQLG Sbjct: 31 QQPIIIKFSHVVANDTPKGKGAERFKELAEKATQGRVKVEVYPNSTLYKDKEELEALQLG 90 Query: 83 AVQMLAPSLAKFGPLGVKEFEVFDLPYIFPTKEVLYRVTEGPIGKDLFKKLEPKGITGLA 142 +VQMLAPSLAKFGPLG +EFEVFDLPYIFP K VL RVTEGPIG+ LF+KLE KGI GLA Sbjct: 91 SVQMLAPSLAKFGPLGAREFEVFDLPYIFPDKAVLKRVTEGPIGQGLFQKLEGKGIKGLA 150 Query: 143 YWDNGFKVMSANKPLHHPADFRGLKMRIQSSKVLDAQMRALGANPQVLAFSEVYQALQTG 202 YWDNG KVM+AN+PLH ADFR LKMRIQSSKVLD Q RAL ANPQVLAFSEVYQA+QTG Sbjct: 151 YWDNGMKVMTANRPLHKVADFRALKMRIQSSKVLDEQFRALKANPQVLAFSEVYQAMQTG 210 Query: 203 VVDGTENPPSNLYTQKMHEVQKHVTVSNHGYLGYAVIVNKKFWDGLPSDIRTQLEGAMKD 262 VVDG+EN PSN+YTQKMHEVQ ++TVS+HGY+GYAVIVNKKFW+ LP+DIR+QLE AMK Sbjct: 211 VVDGSENTPSNVYTQKMHEVQSNLTVSDHGYIGYAVIVNKKFWEALPADIRSQLEAAMKQ 270 Query: 263 ATKYANAIAQQENDAALAAVEKTGKTTVYRLTDAEKAEWRKALLPVQQQMASRIGKDLID 322 AT YAN IAQ+END ALAA++ +GKT VY L++ EKAEWR+ALLPV + MA+R+G DLI+ Sbjct: 271 ATLYANTIAQKENDDALAAIKASGKTRVYTLSEQEKAEWRRALLPVHKSMAARVGADLIE 330 Query: 323 AVNKESAALGQK 334 A+ KES A G K Sbjct: 331 AIYKESEAAGVK 342 >gi|300313112|ref|YP_003777204.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 344 Score = 132 bits (331), Expect = 5e-32, Method: Compositional matrix adjust. Identities = 89/310 (28%), Positives = 164/310 (52%), Gaps = 30/310 (9%) Query: 14 AIVSTNAFAQQPIVIKFSHVVANDTP-----KGKAAERFKELAEKATQGRVKIEVYPNST 68 +VST+A A + F+ AN+ P +A E +AE+ ++GR+++++YPN+ Sbjct: 27 GLVSTSAHAAE-----FTFKYANNLPVTHPMNARAKEMAAAIAEQ-SKGRIELQLYPNNQ 80 Query: 69 LYKDKEELEALQLGAVQMLAPSLAKFGPLGVKEFEVFDLPYIFPTKEVLYRVTEGPIGKD 128 L D + L ++ GA+ S G L V ++ + + F ++ +G +G Sbjct: 81 LGTDTDMLSQVRAGAIDFFTLSPLILGTL-VPAAQISGIGFAFKDYSQVWPAMDGELGAH 139 Query: 129 LFKKLEPKGITGLAY---WDNGFK-VMSANKPLHHPADFRGLKMRIQSSKVLDAQMRALG 184 + K++E + T A+ WDNG++ + ++ KP+ D +G+K+R+ S + + +A Sbjct: 140 VRKQIEARS-TLFAFEKIWDNGYRQITNSTKPIKVAEDLKGMKLRVPPSPLWTSMFKAFD 198 Query: 185 ANPQVLAFSEVYQALQTGVVDGTENPPSNLYTQKMHEVQKHVTVSNHGYLGYAVIVNKKF 244 A P + F+EVY ALQT +V+G ENP + + T K++EVQK+ +++NH + G+ + NKK Sbjct: 199 AAPTSINFAEVYSALQTKIVEGQENPMAIISTAKLYEVQKYCSITNHMWDGFWFLGNKKS 258 Query: 245 WDGLPSDIRTQLEGAMKDATKYANAIAQQENDAALAAVEKTGKTTVYRLTDAEK------ 298 ++ LP D++ + + +A A ++ ND+ + E GK + DA+ Sbjct: 259 FERLPKDLQELMTRIINEAGVNQRADVRKLNDSLVD--EMKGKGLAFNNADADSFRAKLR 316 Query: 299 -----AEWRK 303 AEW+K Sbjct: 317 AAGFYAEWKK 326 >gi|300309847|ref|YP_003773939.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 345 Score = 129 bits (325), Expect = 3e-31, Method: Compositional matrix adjust. Identities = 84/303 (27%), Positives = 160/303 (52%), Gaps = 19/303 (6%) Query: 39 PKGKAAERFKELAEKATQGRVKIEVYPNSTLYKDKEELEALQLGAVQMLAPSLAKFGPLG 98 P K A+ + AT GR++I+++P + L D + + ++ G V+ + L Sbjct: 53 PVNKRAQEAIDRIRNATNGRLEIKLFPANQLGSDTDLMSQVRNGGVEFFNQANTVLSTL- 111 Query: 99 VKEFEVFDLPYIFPTKEVLYRVTEGPIGKDLFKKLEPKGITGLAY-WDNGFK-VMSANKP 156 V + + + F +++ +GP+G + ++E G+ ++ WDNGF+ + ++ KP Sbjct: 112 VPAAGIVNTGFAFHDYGAVWKAMDGPLGAHVRAQIEKVGLLTMSKPWDNGFRQITTSTKP 171 Query: 157 LHHPADFRGLKMRIQSSKVLDAQMRALGANPQVLAFSEVYQALQTGVVDGTENPPSNLYT 216 + + D +GLK+R+ ++ +L + ALGA+P + F+EVY +LQT +V+G ENP + + T Sbjct: 172 VRNAGDVKGLKLRVPAAPMLTSLFSALGASPTPINFNEVYSSLQTKLVEGQENPLAIIST 231 Query: 217 QKMHEVQKHVTVSNHGYLGYAVIVNKKFWDGLPSDI----RTQLEGAMKDATKYANAIAQ 272 +++EVQK T+SNH + Y ++ N++ ++ LP DI R +L+ A D A + Sbjct: 232 ARLYEVQKFCTISNHVWDAYWILGNRRAFEKLPKDIQEIVRRELDKAASDERADIAAFSG 291 Query: 273 -QENDAALAAVEKTGKTTVYRLTDAEKAEWRKALLPVQ--QQMASRIGKDLIDAVNKESA 329 ND A ++ + +A+K +++AL + M ++ G+D + Sbjct: 292 FARNDLASKGLQ---------IVEADKDSFKEALARANFYKDMRAKFGEDAWKLLEGSVG 342 Query: 330 ALG 332 ALG Sbjct: 343 ALG 345 >gi|300310441|ref|YP_003774533.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 348 Score = 128 bits (321), Expect = 7e-31, Method: Compositional matrix adjust. Identities = 71/230 (30%), Positives = 134/230 (58%), Gaps = 7/230 (3%) Query: 39 PKGKAAERFKELAEKATQGRVKIEVYPNSTLYKDKEELEALQLGAVQMLAPSLAKFGPLG 98 P K A++ + +AT GR+ I+++P + L D + + ++ G V+ + L Sbjct: 56 PVNKRAQQAIDRIREATGGRLDIKLFPANQLGSDTDLMSQIRNGGVEFFNQASVVLSTL- 114 Query: 99 VKEFEVFDLPYIFPTKEVLYRVTEGPIGKDLFKKLEPKGITGLAY-WDNGFK-VMSANKP 156 V + + + F + +++ +GP+G + ++E G+ ++ WDNGF+ + ++ KP Sbjct: 115 VPAAGIVNTGFAFHDYKEVWQAMDGPLGAYVRAQIEKVGLLTMSKPWDNGFRQITTSTKP 174 Query: 157 LHHPADFRGLKMRIQSSKVLDAQMRALGANPQVLAFSEVYQALQTGVVDGTENPPSNLYT 216 + AD +GLK+R+ ++ +L + ALGA+P + F+EVY +LQT +V+G ENP + + T Sbjct: 175 IKTAADLKGLKLRVPAAPMLTSLFSALGASPTPINFNEVYSSLQTKLVEGQENPLAIIST 234 Query: 217 QKMHEVQKHVTVSNHGYLGYAVIVNKKFWDGLPSDI----RTQLEGAMKD 262 +++EVQK T+SNH + Y ++ N++ ++ LP DI R +L+ 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 0.368 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: 948,773 Number of extensions: 37654 Number of successful extensions: 156 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 150 Number of HSP's successfully gapped: 6 Length of query: 334 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 248 Effective length of database: 1,212,660 Effective search space: 300739680 Effective search space used: 300739680 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)