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= 0035.0059.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|300312105|ref|YP_003776197.1| TRAP-type C4-dicarboxylate-bind... 704 0.0 gi|300310178|ref|YP_003774270.1| TRAP-type C4-dicarboxylate tran... 521 e-149 gi|300309847|ref|YP_003773939.1| TRAP-type C4-dicarboxylate tran... 113 2e-26 gi|300313112|ref|YP_003777204.1| TRAP-type C4-dicarboxylate tran... 112 3e-26 gi|300310441|ref|YP_003774533.1| TRAP-type C4-dicarboxylate tran... 110 1e-25 >gi|300312105|ref|YP_003776197.1| TRAP-type C4-dicarboxylate-binding periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 344 Score = 704 bits (1817), Expect = 0.0, Method: Compositional matrix adjust. Identities = 342/344 (99%), Positives = 342/344 (99%) Query: 1 MTILPLRTALAACALVTLGLPQPAALAQQPQQPIIIKFSHVVANDTPKGKGAERFKELAE 60 MTILPLRTALAACA VTLGLPQPAALAQQPQQPIIIKFSHVVANDTPKGKGAERFKELAE Sbjct: 1 MTILPLRTALAACAFVTLGLPQPAALAQQPQQPIIIKFSHVVANDTPKGKGAERFKELAE 60 Query: 61 KATQGRVKVEVYPNSTLYKDKEELEALQLGSVQMLAPSLAKFGPLGAREFEVFDLPYIFP 120 KATQGRVKVEVYPNSTLYKDKEELEALQLGSVQMLAPSLAKFGPLGAREFEVFDLPYIFP Sbjct: 61 KATQGRVKVEVYPNSTLYKDKEELEALQLGSVQMLAPSLAKFGPLGAREFEVFDLPYIFP 120 Query: 121 DKAVLKRVTEGPIGQGLFQKLEGKGIKGLAYWDNGMKVMTANRPLHKVADFRALKMRIQS 180 DKAVLKRVTEGPIGQGLFQKLEGKGIKGLAYWDNGMKVMTANRPLHKVADFRALKMRIQS Sbjct: 121 DKAVLKRVTEGPIGQGLFQKLEGKGIKGLAYWDNGMKVMTANRPLHKVADFRALKMRIQS 180 Query: 181 SKVLDEQFRALKANPQVLAFSEVYQAMQTGVVDGSENTPSNVYTQKMHEVQSNLTVSDHG 240 SKVLDEQFRALKANPQVLAFSEVYQAMQTGVVDGSENTPSNVYTQKMHEVQSNLTVSDHG Sbjct: 181 SKVLDEQFRALKANPQVLAFSEVYQAMQTGVVDGSENTPSNVYTQKMHEVQSNLTVSDHG 240 Query: 241 YIGYAVIVNKKFWEALPGDIRSQLEAAMKQATLYANTIAQKENDDALAAIKASGKTRVYT 300 YIGYAVIVNKKFWEALP DIRSQLEAAMKQATLYANTIAQKENDDALAAIKASGKTRVYT Sbjct: 241 YIGYAVIVNKKFWEALPADIRSQLEAAMKQATLYANTIAQKENDDALAAIKASGKTRVYT 300 Query: 301 LSEQEKAEWRRALLPVHKSMAARVGADLIEAIYKESEAAGVKMN 344 LSEQEKAEWRRALLPVHKSMAARVGADLIEAIYKESEAAGVKMN Sbjct: 301 LSEQEKAEWRRALLPVHKSMAARVGADLIEAIYKESEAAGVKMN 344 >gi|300310178|ref|YP_003774270.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 334 Score = 521 bits (1341), Expect = e-149, Method: Compositional matrix adjust. Identities = 254/342 (74%), Positives = 289/342 (84%), Gaps = 8/342 (2%) Query: 1 MTILPLRTALAACALVTLGLPQPAALAQQPQQPIIIKFSHVVANDTPKGKGAERFKELAE 60 M + + A+ A A+V+ A AQQP I+IKFSHVVANDTPKGK AERFKELAE Sbjct: 1 MKLKSILLAMTAAAIVSTN-----AFAQQP---IVIKFSHVVANDTPKGKAAERFKELAE 52 Query: 61 KATQGRVKVEVYPNSTLYKDKEELEALQLGSVQMLAPSLAKFGPLGAREFEVFDLPYIFP 120 KAT+GRVK+EVYPNSTLYKDKEELEALQLG+VQMLAPSLAKFGPLG +EFEVFDLPYIFP Sbjct: 53 KATKGRVKIEVYPNSTLYKDKEELEALQLGAVQMLAPSLAKFGPLGVKEFEVFDLPYIFP 112 Query: 121 DKAVLKRVTEGPIGQGLFQKLEGKGIKGLAYWDNGMKVMTANRPLHKVADFRALKMRIQS 180 K VL RVTEGPIG+ LF+KLE KGI GLAYWDNG KVM+AN+PLH ADFR LKMRIQS Sbjct: 113 TKEVLYRVTEGPIGKDLFKKLEPKGITGLAYWDNGFKVMSANKPLHHPADFRGLKMRIQS 172 Query: 181 SKVLDEQFRALKANPQVLAFSEVYQAMQTGVVDGSENTPSNVYTQKMHEVQSNLTVSDHG 240 SKVLD Q RAL ANPQVLAFSEVYQA+QTGVVDG+EN PSN+YTQKMHEVQ ++TVS+HG Sbjct: 173 SKVLDAQMRALGANPQVLAFSEVYQALQTGVVDGTENPPSNLYTQKMHEVQKHVTVSNHG 232 Query: 241 YIGYAVIVNKKFWEALPGDIRSQLEAAMKQATLYANTIAQKENDDALAAIKASGKTRVYT 300 Y+GYAVIVNKKFW+ LP DIR+QLE AMK AT YAN IAQ+END ALAA++ +GKT VY Sbjct: 233 YLGYAVIVNKKFWDGLPSDIRTQLEGAMKDATKYANAIAQQENDAALAAVEKTGKTTVYR 292 Query: 301 LSEQEKAEWRRALLPVHKSMAARVGADLIEAIYKESEAAGVK 342 L++ EKAEWR+ALLPV + MA+R+G DLI+A+ KES A G K Sbjct: 293 LTDAEKAEWRKALLPVQQQMASRIGKDLIDAVNKESAALGQK 334 >gi|300309847|ref|YP_003773939.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 345 Score = 113 bits (283), Expect = 2e-26, Method: Compositional matrix adjust. Identities = 85/328 (25%), Positives = 165/328 (50%), Gaps = 29/328 (8%) Query: 11 AACALVTLGLPQPAALAQQPQQPIIIKFSHVVANDTPKGKGAERFKELAEKATQGRVKVE 70 AA L ++ L +PA+ A+ KF+ P K A+ + AT GR++++ Sbjct: 23 AALPLFSI-LSRPASAAE-----FSYKFATGQDPSHPVNKRAQEAIDRIRNATNGRLEIK 76 Query: 71 VYPNSTLYKDKEELEALQLGSVQMLAPS---LAKFGPLGAREFEVFDLPYIFPDKAVLKR 127 ++P + L D + + ++ G V+ + L+ P + + + F D + + Sbjct: 77 LFPANQLGSDTDLMSQVRNGGVEFFNQANTVLSTLVPAAG----IVNTGFAFHDYGAVWK 132 Query: 128 VTEGPIGQGLFQKLEGKGIKGLAY-WDNGMK-VMTANRPLHKVADFRALKMRIQSSKVLD 185 +GP+G + ++E G+ ++ WDNG + + T+ +P+ D + LK+R+ ++ +L Sbjct: 133 AMDGPLGAHVRAQIEKVGLLTMSKPWDNGFRQITTSTKPVRNAGDVKGLKLRVPAAPMLT 192 Query: 186 EQFRALKANPQVLAFSEVYQAMQTGVVDGSENTPSNVYTQKMHEVQSNLTVSDHGYIGYA 245 F AL A+P + F+EVY ++QT +V+G EN + + T +++EVQ T+S+H + Y Sbjct: 193 SLFSALGASPTPINFNEVYSSLQTKLVEGQENPLAIISTARLYEVQKFCTISNHVWDAYW 252 Query: 246 VIVNKKFWEALPGDIRSQLEAAMKQATLYANTIAQKENDDALAAIKASGKTRVYT----L 301 ++ N++ +E LP DI+ + + +A A E D +AA + + + + Sbjct: 253 ILGNRRAFEKLPKDIQEIVRRELDKA-------ASDERAD-IAAFSGFARNDLASKGLQI 304 Query: 302 SEQEKAEWRRAL--LPVHKSMAARVGAD 327 E +K ++ AL +K M A+ G D Sbjct: 305 VEADKDSFKEALARANFYKDMRAKFGED 332 >gi|300313112|ref|YP_003777204.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 344 Score = 112 bits (281), Expect = 3e-26, Method: Compositional matrix adjust. Identities = 70/267 (26%), Positives = 140/267 (52%), Gaps = 12/267 (4%) Query: 37 KFSHVVANDTP-----KGKGAERFKELAEKATQGRVKVEVYPNSTLYKDKEELEALQLGS 91 +F+ AN+ P + E +AE+ ++GR+++++YPN+ L D + L ++ G+ Sbjct: 37 EFTFKYANNLPVTHPMNARAKEMAAAIAEQ-SKGRIELQLYPNNQLGTDTDMLSQVRAGA 95 Query: 92 VQMLAPSLAKFGPLGAREFEVFDLPYIFPDKAVLKRVTEGPIGQGLFQKLEGKGIKGLAY 151 + S G L ++ + + F D + + +G +G + +++E + A+ Sbjct: 96 IDFFTLSPLILGTL-VPAAQISGIGFAFKDYSQVWPAMDGELGAHVRKQIEARSTL-FAF 153 Query: 152 ---WDNGMKVMT-ANRPLHKVADFRALKMRIQSSKVLDEQFRALKANPQVLAFSEVYQAM 207 WDNG + +T + +P+ D + +K+R+ S + F+A A P + F+EVY A+ Sbjct: 154 EKIWDNGYRQITNSTKPIKVAEDLKGMKLRVPPSPLWTSMFKAFDAAPTSINFAEVYSAL 213 Query: 208 QTGVVDGSENTPSNVYTQKMHEVQSNLTVSDHGYIGYAVIVNKKFWEALPGDIRSQLEAA 267 QT +V+G EN + + T K++EVQ ++++H + G+ + NKK +E LP D++ + Sbjct: 214 QTKIVEGQENPMAIISTAKLYEVQKYCSITNHMWDGFWFLGNKKSFERLPKDLQELMTRI 273 Query: 268 MKQATLYANTIAQKENDDALAAIKASG 294 + +A + +K ND + +K G Sbjct: 274 INEAGVNQRADVRKLNDSLVDEMKGKG 300 >gi|300310441|ref|YP_003774533.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 348 Score = 110 bits (276), Expect = 1e-25, Method: Compositional matrix adjust. Identities = 63/230 (27%), Positives = 128/230 (55%), Gaps = 9/230 (3%) Query: 47 PKGKGAERFKELAEKATQGRVKVEVYPNSTLYKDKEELEALQLGSVQMLAPS---LAKFG 103 P K A++ + +AT GR+ ++++P + L D + + ++ G V+ + L+ Sbjct: 56 PVNKRAQQAIDRIREATGGRLDIKLFPANQLGSDTDLMSQIRNGGVEFFNQASVVLSTLV 115 Query: 104 PLGAREFEVFDLPYIFPDKAVLKRVTEGPIGQGLFQKLEGKGIKGLAY-WDNGMK-VMTA 161 P + + + F D + + +GP+G + ++E G+ ++ WDNG + + T+ Sbjct: 116 PAAG----IVNTGFAFHDYKEVWQAMDGPLGAYVRAQIEKVGLLTMSKPWDNGFRQITTS 171 Query: 162 NRPLHKVADFRALKMRIQSSKVLDEQFRALKANPQVLAFSEVYQAMQTGVVDGSENTPSN 221 +P+ AD + LK+R+ ++ +L F AL A+P + F+EVY ++QT +V+G EN + Sbjct: 172 TKPIKTAADLKGLKLRVPAAPMLTSLFSALGASPTPINFNEVYSSLQTKLVEGQENPLAI 231 Query: 222 VYTQKMHEVQSNLTVSDHGYIGYAVIVNKKFWEALPGDIRSQLEAAMKQA 271 + T +++EVQ T+S+H + Y ++ N++ +E LP DI+ + + +A Sbjct: 232 ISTARLYEVQKFCTISNHVWDAYWILGNRRAFEKLPKDIQEIVRRELDKA 281 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 0.316 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: 920,303 Number of extensions: 34592 Number of successful extensions: 142 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 136 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 (21.6 bits) S2: 131 (55.1 bits)