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= 0034.0107.p (340 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... 495 e-141 gi|300312105|ref|YP_003776197.1| TRAP-type C4-dicarboxylate-bind... 453 e-129 gi|300313112|ref|YP_003777204.1| TRAP-type C4-dicarboxylate tran... 127 1e-30 gi|300309847|ref|YP_003773939.1| TRAP-type C4-dicarboxylate tran... 118 6e-28 gi|300310441|ref|YP_003774533.1| TRAP-type C4-dicarboxylate tran... 116 2e-27 >gi|300310178|ref|YP_003774270.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 334 Score = 495 bits (1274), Expect = e-141, Method: Compositional matrix adjust. Identities = 231/309 (74%), Positives = 271/309 (87%) Query: 26 LAQAPIVIKFSHVVAINTPKGKAAERFKELAEKATHGRVKVEVYPNSILYKDKEEMEALQ 85 AQ PIVIKFSHVVA +TPKGKAAERFKELAEKAT GRVK+EVYPNS LYKDKEE+EALQ Sbjct: 21 FAQQPIVIKFSHVVANDTPKGKAAERFKELAEKATKGRVKIEVYPNSTLYKDKEELEALQ 80 Query: 86 IGAVQILAPSLAKFGPLGVKEFEVFDLPYIFPTVTALHSVTQGAVGQQMFKKLEPKGITG 145 +GAVQ+LAPSLAKFGPLGVKEFEVFDLPYIFPT L+ VT+G +G+ +FKKLEPKGITG Sbjct: 81 LGAVQMLAPSLAKFGPLGVKEFEVFDLPYIFPTKEVLYRVTEGPIGKDLFKKLEPKGITG 140 Query: 146 LAYWDNGFKVMSANKILKSAADFKGLKLRIQSSKVLDAQMRTLGANPQMLAFSEVYQALQ 205 LAYWDNGFKVMSANK L ADF+GLK+RIQSSKVLDAQMR LGANPQ+LAFSEVYQALQ Sbjct: 141 LAYWDNGFKVMSANKPLHHPADFRGLKMRIQSSKVLDAQMRALGANPQVLAFSEVYQALQ 200 Query: 206 TGVVDGAENPPSNIYSQKMHEVQKYISVTNHGVIEYAVITNTKFWNSLPADIRGTLEIAL 265 TGVVDG ENPPSN+Y+QKMHEVQK+++V+NHG + YAVI N KFW+ LP+DIR LE A+ Sbjct: 201 TGVVDGTENPPSNLYTQKMHEVQKHVTVSNHGYLGYAVIVNKKFWDGLPSDIRTQLEGAM 260 Query: 266 KEATAYGNSIAQKENDDAIEAMRQSSKTSIYVLTDAERAALRKTLLPVQKEVAGRIGKEL 325 K+AT Y N+IAQ+END A+ A+ ++ KT++Y LTDAE+A RK LLPVQ+++A RIGK+L Sbjct: 261 KDATKYANAIAQQENDAALAAVEKTGKTTVYRLTDAEKAEWRKALLPVQQQMASRIGKDL 320 Query: 326 IDSINQTVA 334 ID++N+ A Sbjct: 321 IDAVNKESA 329 >gi|300312105|ref|YP_003776197.1| TRAP-type C4-dicarboxylate-binding periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 344 Score = 453 bits (1166), Expect = e-129, Method: Compositional matrix adjust. Identities = 217/332 (65%), Positives = 261/332 (78%), Gaps = 3/332 (0%) Query: 1 MHINKIVATLASLGTVGMLTSAPGVLAQAP---IVIKFSHVVAINTPKGKAAERFKELAE 57 M I + LA+ V + P LAQ P I+IKFSHVVA +TPKGK AERFKELAE Sbjct: 1 MTILPLRTALAACAFVTLGLPQPAALAQQPQQPIIIKFSHVVANDTPKGKGAERFKELAE 60 Query: 58 KATHGRVKVEVYPNSILYKDKEEMEALQIGAVQILAPSLAKFGPLGVKEFEVFDLPYIFP 117 KAT GRVKVEVYPNS LYKDKEE+EALQ+G+VQ+LAPSLAKFGPLG +EFEVFDLPYIFP Sbjct: 61 KATQGRVKVEVYPNSTLYKDKEELEALQLGSVQMLAPSLAKFGPLGAREFEVFDLPYIFP 120 Query: 118 TVTALHSVTQGAVGQQMFKKLEPKGITGLAYWDNGFKVMSANKILKSAADFKGLKLRIQS 177 L VT+G +GQ +F+KLE KGI GLAYWDNG KVM+AN+ L ADF+ LK+RIQS Sbjct: 121 DKAVLKRVTEGPIGQGLFQKLEGKGIKGLAYWDNGMKVMTANRPLHKVADFRALKMRIQS 180 Query: 178 SKVLDAQMRTLGANPQMLAFSEVYQALQTGVVDGAENPPSNIYSQKMHEVQKYISVTNHG 237 SKVLD Q R L ANPQ+LAFSEVYQA+QTGVVDG+EN PSN+Y+QKMHEVQ ++V++HG Sbjct: 181 SKVLDEQFRALKANPQVLAFSEVYQAMQTGVVDGSENTPSNVYTQKMHEVQSNLTVSDHG 240 Query: 238 VIEYAVITNTKFWNSLPADIRGTLEIALKEATAYGNSIAQKENDDAIEAMRQSSKTSIYV 297 I YAVI N KFW +LPADIR LE A+K+AT Y N+IAQKENDDA+ A++ S KT +Y Sbjct: 241 YIGYAVIVNKKFWEALPADIRSQLEAAMKQATLYANTIAQKENDDALAAIKASGKTRVYT 300 Query: 298 LTDAERAALRKTLLPVQKEVAGRIGKELIDSI 329 L++ E+A R+ LLPV K +A R+G +LI++I Sbjct: 301 LSEQEKAEWRRALLPVHKSMAARVGADLIEAI 332 >gi|300313112|ref|YP_003777204.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 344 Score = 127 bits (320), Expect = 1e-30, Method: Compositional matrix adjust. Identities = 80/283 (28%), Positives = 144/283 (50%), Gaps = 6/283 (2%) Query: 29 APIVIKFSHVVAINTPKGKAAERFKELAEKATHGRVKVEVYPNSILYKDKEEMEALQIGA 88 A K+++ + + P A+ + + GR+++++YPN+ L D + + ++ GA Sbjct: 36 AEFTFKYANNLPVTHPMNARAKEMAAAIAEQSKGRIELQLYPNNQLGTDTDMLSQVRAGA 95 Query: 89 VQILAPSLAKFGPLGVKEFEVFDLPYIFPTVTALHSVTQGAVGQQMFKKLEPKGITGLAY 148 + S G L V ++ + + F + + G +G + K++E + T A+ Sbjct: 96 IDFFTLSPLILGTL-VPAAQISGIGFAFKDYSQVWPAMDGELGAHVRKQIEARS-TLFAF 153 Query: 149 ---WDNGFK-VMSANKILKSAADFKGLKLRIQSSKVLDAQMRTLGANPQMLAFSEVYQAL 204 WDNG++ + ++ K +K A D KG+KLR+ S + + + A P + F+EVY AL Sbjct: 154 EKIWDNGYRQITNSTKPIKVAEDLKGMKLRVPPSPLWTSMFKAFDAAPTSINFAEVYSAL 213 Query: 205 QTGVVDGAENPPSNIYSQKMHEVQKYISVTNHGVIEYAVITNTKFWNSLPADIRGTLEIA 264 QT +V+G ENP + I + K++EVQKY S+TNH + + N K + LP D++ + Sbjct: 214 QTKIVEGQENPMAIISTAKLYEVQKYCSITNHMWDGFWFLGNKKSFERLPKDLQELMTRI 273 Query: 265 LKEATAYGNSIAQKENDDAIEAMRQSSKTSIYVLTDAERAALR 307 + EA + +K ND ++ M+ D+ RA LR Sbjct: 274 INEAGVNQRADVRKLNDSLVDEMKGKGLAFNNADADSFRAKLR 316 >gi|300309847|ref|YP_003773939.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 345 Score = 118 bits (296), Expect = 6e-28, Method: Compositional matrix adjust. Identities = 74/263 (28%), Positives = 141/263 (53%), Gaps = 7/263 (2%) Query: 14 GTVGMLTSAPGVLAQAPIVIKFSHVVAI----NTPKGKAAERFKELAEKATHGRVKVEVY 69 G VG +L++ +FS+ A + P K A+ + AT+GR++++++ Sbjct: 19 GAVGAALPLFSILSRPASAAEFSYKFATGQDPSHPVNKRAQEAIDRIRNATNGRLEIKLF 78 Query: 70 PNSILYKDKEEMEALQIGAVQILAPSLAKFGPLGVKEFEVFDLPYIFPTVTALHSVTQGA 129 P + L D + M ++ G V+ + L V + + + F A+ G Sbjct: 79 PANQLGSDTDLMSQVRNGGVEFFNQANTVLSTL-VPAAGIVNTGFAFHDYGAVWKAMDGP 137 Query: 130 VGQQMFKKLEPKGITGLAY-WDNGFK-VMSANKILKSAADFKGLKLRIQSSKVLDAQMRT 187 +G + ++E G+ ++ WDNGF+ + ++ K +++A D KGLKLR+ ++ +L + Sbjct: 138 LGAHVRAQIEKVGLLTMSKPWDNGFRQITTSTKPVRNAGDVKGLKLRVPAAPMLTSLFSA 197 Query: 188 LGANPQMLAFSEVYQALQTGVVDGAENPPSNIYSQKMHEVQKYISVTNHGVIEYAVITNT 247 LGA+P + F+EVY +LQT +V+G ENP + I + +++EVQK+ +++NH Y ++ N Sbjct: 198 LGASPTPINFNEVYSSLQTKLVEGQENPLAIISTARLYEVQKFCTISNHVWDAYWILGNR 257 Query: 248 KFWNSLPADIRGTLEIALKEATA 270 + + LP DI+ + L +A + Sbjct: 258 RAFEKLPKDIQEIVRRELDKAAS 280 >gi|300310441|ref|YP_003774533.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 348 Score = 116 bits (291), Expect = 2e-27, Method: Compositional matrix adjust. Identities = 68/227 (29%), Positives = 127/227 (55%), Gaps = 3/227 (1%) Query: 44 PKGKAAERFKELAEKATHGRVKVEVYPNSILYKDKEEMEALQIGAVQILAPSLAKFGPLG 103 P K A++ + +AT GR+ ++++P + L D + M ++ G V+ + L Sbjct: 56 PVNKRAQQAIDRIREATGGRLDIKLFPANQLGSDTDLMSQIRNGGVEFFNQASVVLSTL- 114 Query: 104 VKEFEVFDLPYIFPTVTALHSVTQGAVGQQMFKKLEPKGITGLAY-WDNGFK-VMSANKI 161 V + + + F + G +G + ++E G+ ++ WDNGF+ + ++ K Sbjct: 115 VPAAGIVNTGFAFHDYKEVWQAMDGPLGAYVRAQIEKVGLLTMSKPWDNGFRQITTSTKP 174 Query: 162 LKSAADFKGLKLRIQSSKVLDAQMRTLGANPQMLAFSEVYQALQTGVVDGAENPPSNIYS 221 +K+AAD KGLKLR+ ++ +L + LGA+P + F+EVY +LQT +V+G ENP + I + Sbjct: 175 IKTAADLKGLKLRVPAAPMLTSLFSALGASPTPINFNEVYSSLQTKLVEGQENPLAIIST 234 Query: 222 QKMHEVQKYISVTNHGVIEYAVITNTKFWNSLPADIRGTLEIALKEA 268 +++EVQK+ +++NH Y ++ N + + LP DI+ + L +A Sbjct: 235 ARLYEVQKFCTISNHVWDAYWILGNRRAFEKLPKDIQEIVRRELDKA 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 0.315 0.130 0.357 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: 923,270 Number of extensions: 34723 Number of successful extensions: 117 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 112 Number of HSP's successfully gapped: 6 Length of query: 340 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 254 Effective length of database: 1,212,660 Effective search space: 308015640 Effective search space used: 308015640 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)