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= 0257.0013.p (354 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310441|ref|YP_003774533.1| TRAP-type C4-dicarboxylate tran... 396 e-111 gi|300309847|ref|YP_003773939.1| TRAP-type C4-dicarboxylate tran... 383 e-107 gi|300313112|ref|YP_003777204.1| TRAP-type C4-dicarboxylate tran... 333 1e-92 gi|300310178|ref|YP_003774270.1| TRAP-type C4-dicarboxylate tran... 111 1e-25 gi|300312105|ref|YP_003776197.1| TRAP-type C4-dicarboxylate-bind... 89 6e-19 >gi|300310441|ref|YP_003774533.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 348 Score = 396 bits (1017), Expect = e-111, Method: Compositional matrix adjust. Identities = 185/343 (53%), Positives = 251/343 (73%), Gaps = 3/343 (0%) Query: 14 NSSSDLPSAKRRSLLTAAAT---LPLFTVWSGPARAAEFNYKLATGQSLDQPINARLKQA 70 NS S RR LL A A LPLF++ S PA AAEFNYK ATGQ P+N R +QA Sbjct: 5 NSKPGKTSVSRRQLLKAGAVGAALPLFSIMSRPANAAEFNYKFATGQDPSHPVNKRAQQA 64 Query: 71 TDRIREASAGRLDIRFFPASQLGSDTDLLTQVRSGGVEFLNIAGSVISTVVPLAAITNVG 130 DRIREA+ GRLDI+ FPA+QLGSDTDL++Q+R+GGVEF N A V+ST+VP A I N G Sbjct: 65 IDRIREATGGRLDIKLFPANQLGSDTDLMSQIRNGGVEFFNQASVVLSTLVPAAGIVNTG 124 Query: 131 FTYSDYQQVWSSVDGDLGKLIRAQIDKSGFVSVAKAGDNSFRQISSASKPIKTPADLQGY 190 F + DY++VW ++DG LG +RAQI+K G ++++K DN FRQI++++KPIKT ADL+G Sbjct: 125 FAFHDYKEVWQAMDGPLGAYVRAQIEKVGLLTMSKPWDNGFRQITTSTKPIKTAADLKGL 184 Query: 191 RIRVPVSPMFTSLFKSLGANPTSINFNELYTALQTKLVDGQENGLVAIDSGKLYEVQKYI 250 ++RVP +PM TSLF +LGA+PT INFNE+Y++LQTKLV+GQEN L I + +LYEVQK+ Sbjct: 185 KLRVPAAPMLTSLFSALGASPTPINFNEVYSSLQTKLVEGQENPLAIISTARLYEVQKFC 244 Query: 251 TQTNHIWDPFWMLGNRRAFANLPDDLKKIVQREFDRAYMEQRGDVEQLNTTLKDQLTKKG 310 T +NH+WD +W+LGNRRAF LP D+++IV+RE D+A ++R D+ L+ ++ L KG Sbjct: 245 TISNHVWDAYWILGNRRAFEKLPKDIQEIVRRELDKAATDERADIASLSGFARNDLQGKG 304 Query: 311 IVFETANRDSFRKALSDAGFYKEWRDKFGAAPWAALEAVVGKM 353 + A+++SF++AL+ FYK+ R KFG W L+ VG + Sbjct: 305 VQIIEADKNSFKEALARGSFYKDLRAKFGDDAWKLLQNSVGSL 347 >gi|300309847|ref|YP_003773939.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 345 Score = 383 bits (983), Expect = e-107, Method: Compositional matrix adjust. Identities = 175/333 (52%), Positives = 245/333 (73%), Gaps = 3/333 (0%) Query: 24 RRSLLTAAAT---LPLFTVWSGPARAAEFNYKLATGQSLDQPINARLKQATDRIREASAG 80 RR++L A A LPLF++ S PA AAEF+YK ATGQ P+N R ++A DRIR A+ G Sbjct: 12 RRNMLKAGAVGAALPLFSILSRPASAAEFSYKFATGQDPSHPVNKRAQEAIDRIRNATNG 71 Query: 81 RLDIRFFPASQLGSDTDLLTQVRSGGVEFLNIAGSVISTVVPLAAITNVGFTYSDYQQVW 140 RL+I+ FPA+QLGSDTDL++QVR+GGVEF N A +V+ST+VP A I N GF + DY VW Sbjct: 72 RLEIKLFPANQLGSDTDLMSQVRNGGVEFFNQANTVLSTLVPAAGIVNTGFAFHDYGAVW 131 Query: 141 SSVDGDLGKLIRAQIDKSGFVSVAKAGDNSFRQISSASKPIKTPADLQGYRIRVPVSPMF 200 ++DG LG +RAQI+K G ++++K DN FRQI++++KP++ D++G ++RVP +PM Sbjct: 132 KAMDGPLGAHVRAQIEKVGLLTMSKPWDNGFRQITTSTKPVRNAGDVKGLKLRVPAAPML 191 Query: 201 TSLFKSLGANPTSINFNELYTALQTKLVDGQENGLVAIDSGKLYEVQKYITQTNHIWDPF 260 TSLF +LGA+PT INFNE+Y++LQTKLV+GQEN L I + +LYEVQK+ T +NH+WD + Sbjct: 192 TSLFSALGASPTPINFNEVYSSLQTKLVEGQENPLAIISTARLYEVQKFCTISNHVWDAY 251 Query: 261 WMLGNRRAFANLPDDLKKIVQREFDRAYMEQRGDVEQLNTTLKDQLTKKGIVFETANRDS 320 W+LGNRRAF LP D+++IV+RE D+A ++R D+ + ++ L KG+ A++DS Sbjct: 252 WILGNRRAFEKLPKDIQEIVRRELDKAASDERADIAAFSGFARNDLASKGLQIVEADKDS 311 Query: 321 FRKALSDAGFYKEWRDKFGAAPWAALEAVVGKM 353 F++AL+ A FYK+ R KFG W LE VG + Sbjct: 312 FKEALARANFYKDMRAKFGEDAWKLLEGSVGAL 344 >gi|300313112|ref|YP_003777204.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 344 Score = 333 bits (854), Expect = 1e-92, Method: Compositional matrix adjust. Identities = 151/315 (47%), Positives = 220/315 (69%), Gaps = 1/315 (0%) Query: 41 SGPARAAEFNYKLATGQSLDQPINARLKQATDRIREASAGRLDIRFFPASQLGSDTDLLT 100 S A AAEF +K A + P+NAR K+ I E S GR++++ +P +QLG+DTD+L+ Sbjct: 30 STSAHAAEFTFKYANNLPVTHPMNARAKEMAAAIAEQSKGRIELQLYPNNQLGTDTDMLS 89 Query: 101 QVRSGGVEFLNIAGSVISTVVPLAAITNVGFTYSDYQQVWSSVDGDLGKLIRAQID-KSG 159 QVR+G ++F ++ ++ T+VP A I+ +GF + DY QVW ++DG+LG +R QI+ +S Sbjct: 90 QVRAGAIDFFTLSPLILGTLVPAAQISGIGFAFKDYSQVWPAMDGELGAHVRKQIEARST 149 Query: 160 FVSVAKAGDNSFRQISSASKPIKTPADLQGYRIRVPVSPMFTSLFKSLGANPTSINFNEL 219 + K DN +RQI++++KPIK DL+G ++RVP SP++TS+FK+ A PTSINF E+ Sbjct: 150 LFAFEKIWDNGYRQITNSTKPIKVAEDLKGMKLRVPPSPLWTSMFKAFDAAPTSINFAEV 209 Query: 220 YTALQTKLVDGQENGLVAIDSGKLYEVQKYITQTNHIWDPFWMLGNRRAFANLPDDLKKI 279 Y+ALQTK+V+GQEN + I + KLYEVQKY + TNH+WD FW LGN+++F LP DL+++ Sbjct: 210 YSALQTKIVEGQENPMAIISTAKLYEVQKYCSITNHMWDGFWFLGNKKSFERLPKDLQEL 269 Query: 280 VQREFDRAYMEQRGDVEQLNTTLKDQLTKKGIVFETANRDSFRKALSDAGFYKEWRDKFG 339 + R + A + QR DV +LN +L D++ KG+ F A+ DSFR L AGFY EW+ KFG Sbjct: 270 MTRIINEAGVNQRADVRKLNDSLVDEMKGKGLAFNNADADSFRAKLRAAGFYAEWKKKFG 329 Query: 340 AAPWAALEAVVGKMS 354 PWA LE GK++ Sbjct: 330 DEPWALLEKYTGKLA 344 >gi|300310178|ref|YP_003774270.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 334 Score = 111 bits (277), Expect = 1e-25, Method: Compositional matrix adjust. Identities = 64/217 (29%), Positives = 123/217 (56%), Gaps = 13/217 (5%) Query: 69 QATDRIRE----ASAGRLDIRFFPASQLGSDTDLLTQVRSGGVEFLNIAGSVISTVVPLA 124 +A +R +E A+ GR+ I +P S L D + L ++ G V+ L ++ PL Sbjct: 42 KAAERFKELAEKATKGRVKIEVYPNSTLYKDKEELEALQLGAVQML---APSLAKFGPLG 98 Query: 125 A----ITNVGFTYSDYQQVWSSVDGDLGKLIRAQIDKSGFVSVAKAGDNSFRQISSASKP 180 + ++ + + + ++ +G +GK + +++ G +A DN F+ + SA+KP Sbjct: 99 VKEFEVFDLPYIFPTKEVLYRVTEGPIGKDLFKKLEPKGITGLA-YWDNGFK-VMSANKP 156 Query: 181 IKTPADLQGYRIRVPVSPMFTSLFKSLGANPTSINFNELYTALQTKLVDGQENGLVAIDS 240 + PAD +G ++R+ S + + ++LGANP + F+E+Y ALQT +VDG EN + + Sbjct: 157 LHHPADFRGLKMRIQSSKVLDAQMRALGANPQVLAFSEVYQALQTGVVDGTENPPSNLYT 216 Query: 241 GKLYEVQKYITQTNHIWDPFWMLGNRRAFANLPDDLK 277 K++EVQK++T +NH + + ++ N++ + LP D++ Sbjct: 217 QKMHEVQKHVTVSNHGYLGYAVIVNKKFWDGLPSDIR 253 >gi|300312105|ref|YP_003776197.1| TRAP-type C4-dicarboxylate-binding periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 344 Score = 89.0 bits (219), Expect = 6e-19, Method: Compositional matrix adjust. Identities = 56/228 (24%), Positives = 121/228 (53%), Gaps = 12/228 (5%) Query: 66 RLKQATDRIREASAGRLDIRFFPASQLGSDTDLLTQVRSGGVEFLNIAGSVISTVVPLAA 125 R K+ ++ A+ GR+ + +P S L D + L ++ G V+ L ++ PL A Sbjct: 54 RFKELAEK---ATQGRVKVEVYPNSTLYKDKEELEALQLGSVQML---APSLAKFGPLGA 107 Query: 126 ----ITNVGFTYSDYQQVWSSVDGDLGKLIRAQIDKSGFVSVAKAGDNSFRQISSASKPI 181 + ++ + + D + +G +G+ + +++ G +A DN + + +A++P+ Sbjct: 108 REFEVFDLPYIFPDKAVLKRVTEGPIGQGLFQKLEGKGIKGLA-YWDNGMK-VMTANRPL 165 Query: 182 KTPADLQGYRIRVPVSPMFTSLFKSLGANPTSINFNELYTALQTKLVDGQENGLVAIDSG 241 AD + ++R+ S + F++L ANP + F+E+Y A+QT +VDG EN + + Sbjct: 166 HKVADFRALKMRIQSSKVLDEQFRALKANPQVLAFSEVYQAMQTGVVDGSENTPSNVYTQ 225 Query: 242 KLYEVQKYITQTNHIWDPFWMLGNRRAFANLPDDLKKIVQREFDRAYM 289 K++EVQ +T ++H + + ++ N++ + LP D++ ++ +A + Sbjct: 226 KMHEVQSNLTVSDHGYIGYAVIVNKKFWEALPADIRSQLEAAMKQATL 273 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 0.317 0.132 0.380 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: 1,033,677 Number of extensions: 41135 Number of successful extensions: 131 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 126 Number of HSP's successfully gapped: 6 Length of query: 354 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 268 Effective length of database: 1,212,660 Effective search space: 324992880 Effective search space used: 324992880 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)