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= 0002.0185.p (345 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300309847|ref|YP_003773939.1| TRAP-type C4-dicarboxylate tran... 649 0.0 gi|300310441|ref|YP_003774533.1| TRAP-type C4-dicarboxylate tran... 633 0.0 gi|300313112|ref|YP_003777204.1| TRAP-type C4-dicarboxylate tran... 369 e-103 gi|300310178|ref|YP_003774270.1| TRAP-type C4-dicarboxylate tran... 128 7e-31 gi|300312105|ref|YP_003776197.1| TRAP-type C4-dicarboxylate-bind... 108 7e-25 >gi|300309847|ref|YP_003773939.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 345 Score = 649 bits (1673), Expect = 0.0, Method: Compositional matrix adjust. Identities = 308/345 (89%), Positives = 332/345 (96%) Query: 1 MKDEIASKKLSRRQILKAGAVGAALPLFSILTRPANAAEFTYKFATGQDPSHPVNKRAQE 60 M DE A K+++RR +LKAGAVGAALPLFSIL+RPA+AAEF+YKFATGQDPSHPVNKRAQE Sbjct: 1 MNDERAKKQVTRRNMLKAGAVGAALPLFSILSRPASAAEFSYKFATGQDPSHPVNKRAQE 60 Query: 61 AIDRIRNATNGRMEIKLFPANQLGSDTDLMSQIRNGGVEFFNQANTVLSTLVPAAGIVNT 120 AIDRIRNATNGR+EIKLFPANQLGSDTDLMSQ+RNGGVEFFNQANTVLSTLVPAAGIVNT Sbjct: 61 AIDRIRNATNGRLEIKLFPANQLGSDTDLMSQVRNGGVEFFNQANTVLSTLVPAAGIVNT 120 Query: 121 GFAFHDYKEVWQAMDGPLGAYVRAQIEKVGLLTMSKPWDNGFRQITTSTKAIRSAADVKG 180 GFAFHDY VW+AMDGPLGA+VRAQIEKVGLLTMSKPWDNGFRQITTSTK +R+A DVKG Sbjct: 121 GFAFHDYGAVWKAMDGPLGAHVRAQIEKVGLLTMSKPWDNGFRQITTSTKPVRNAGDVKG 180 Query: 181 LKLRVPAAPMLTSLFSALGASPTPINFNEVYSSLQTKLVEGQENPLAIISTARLYEVQKF 240 LKLRVPAAPMLTSLFSALGASPTPINFNEVYSSLQTKLVEGQENPLAIISTARLYEVQKF Sbjct: 181 LKLRVPAAPMLTSLFSALGASPTPINFNEVYSSLQTKLVEGQENPLAIISTARLYEVQKF 240 Query: 241 CTLSNHVWDAYWILGNRRAFDKLPKDIQEIVRRELDQAATDERADIASFSGMARNDLAGK 300 CT+SNHVWDAYWILGNRRAF+KLPKDIQEIVRRELD+AA+DERADIA+FSG ARNDLA K Sbjct: 241 CTISNHVWDAYWILGNRRAFEKLPKDIQEIVRRELDKAASDERADIAAFSGFARNDLASK 300 Query: 301 GLQIIDADKDSFKQALAQANFYKDMRARFGEEAWKLLESSVGTRG 345 GLQI++ADKDSFK+ALA+ANFYKDMRA+FGE+AWKLLE SVG G Sbjct: 301 GLQIVEADKDSFKEALARANFYKDMRAKFGEDAWKLLEGSVGALG 345 >gi|300310441|ref|YP_003774533.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 348 Score = 633 bits (1632), Expect = 0.0, Method: Compositional matrix adjust. Identities = 299/336 (88%), Positives = 326/336 (97%) Query: 10 LSRRQILKAGAVGAALPLFSILTRPANAAEFTYKFATGQDPSHPVNKRAQEAIDRIRNAT 69 +SRRQ+LKAGAVGAALPLFSI++RPANAAEF YKFATGQDPSHPVNKRAQ+AIDRIR AT Sbjct: 13 VSRRQLLKAGAVGAALPLFSIMSRPANAAEFNYKFATGQDPSHPVNKRAQQAIDRIREAT 72 Query: 70 NGRMEIKLFPANQLGSDTDLMSQIRNGGVEFFNQANTVLSTLVPAAGIVNTGFAFHDYKE 129 GR++IKLFPANQLGSDTDLMSQIRNGGVEFFNQA+ VLSTLVPAAGIVNTGFAFHDYKE Sbjct: 73 GGRLDIKLFPANQLGSDTDLMSQIRNGGVEFFNQASVVLSTLVPAAGIVNTGFAFHDYKE 132 Query: 130 VWQAMDGPLGAYVRAQIEKVGLLTMSKPWDNGFRQITTSTKAIRSAADVKGLKLRVPAAP 189 VWQAMDGPLGAYVRAQIEKVGLLTMSKPWDNGFRQITTSTK I++AAD+KGLKLRVPAAP Sbjct: 133 VWQAMDGPLGAYVRAQIEKVGLLTMSKPWDNGFRQITTSTKPIKTAADLKGLKLRVPAAP 192 Query: 190 MLTSLFSALGASPTPINFNEVYSSLQTKLVEGQENPLAIISTARLYEVQKFCTLSNHVWD 249 MLTSLFSALGASPTPINFNEVYSSLQTKLVEGQENPLAIISTARLYEVQKFCT+SNHVWD Sbjct: 193 MLTSLFSALGASPTPINFNEVYSSLQTKLVEGQENPLAIISTARLYEVQKFCTISNHVWD 252 Query: 250 AYWILGNRRAFDKLPKDIQEIVRRELDQAATDERADIASFSGMARNDLAGKGLQIIDADK 309 AYWILGNRRAF+KLPKDIQEIVRRELD+AATDERADIAS SG ARNDL GKG+QII+ADK Sbjct: 253 AYWILGNRRAFEKLPKDIQEIVRRELDKAATDERADIASLSGFARNDLQGKGVQIIEADK 312 Query: 310 DSFKQALAQANFYKDMRARFGEEAWKLLESSVGTRG 345 +SFK+ALA+ +FYKD+RA+FG++AWKLL++SVG+ G Sbjct: 313 NSFKEALARGSFYKDLRAKFGDDAWKLLQNSVGSLG 348 >gi|300313112|ref|YP_003777204.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 344 Score = 369 bits (948), Expect = e-103, Method: Compositional matrix adjust. Identities = 171/338 (50%), Positives = 244/338 (72%), Gaps = 1/338 (0%) Query: 6 ASKKLSRRQILKAGAVGAALPLFSILTRPANAAEFTYKFATGQDPSHPVNKRAQEAIDRI 65 ++ K++RR LK +V +A +++ A+AAEFT+K+A +HP+N RA+E I Sbjct: 4 STGKITRRNFLKTASVASAAAATGLVSTSAHAAEFTFKYANNLPVTHPMNARAKEMAAAI 63 Query: 66 RNATNGRMEIKLFPANQLGSDTDLMSQIRNGGVEFFNQANTVLSTLVPAAGIVNTGFAFH 125 + GR+E++L+P NQLG+DTD++SQ+R G ++FF + +L TLVPAA I GFAF Sbjct: 64 AEQSKGRIELQLYPNNQLGTDTDMLSQVRAGAIDFFTLSPLILGTLVPAAQISGIGFAFK 123 Query: 126 DYKEVWQAMDGPLGAYVRAQIE-KVGLLTMSKPWDNGFRQITTSTKAIRSAADVKGLKLR 184 DY +VW AMDG LGA+VR QIE + L K WDNG+RQIT STK I+ A D+KG+KLR Sbjct: 124 DYSQVWPAMDGELGAHVRKQIEARSTLFAFEKIWDNGYRQITNSTKPIKVAEDLKGMKLR 183 Query: 185 VPAAPMLTSLFSALGASPTPINFNEVYSSLQTKLVEGQENPLAIISTARLYEVQKFCTLS 244 VP +P+ TS+F A A+PT INF EVYS+LQTK+VEGQENP+AIISTA+LYEVQK+C+++ Sbjct: 184 VPPSPLWTSMFKAFDAAPTSINFAEVYSALQTKIVEGQENPMAIISTAKLYEVQKYCSIT 243 Query: 245 NHVWDAYWILGNRRAFDKLPKDIQEIVRRELDQAATDERADIASFSGMARNDLAGKGLQI 304 NH+WD +W LGN+++F++LPKD+QE++ R +++A ++RAD+ + +++ GKGL Sbjct: 244 NHMWDGFWFLGNKKSFERLPKDLQELMTRIINEAGVNQRADVRKLNDSLVDEMKGKGLAF 303 Query: 305 IDADKDSFKQALAQANFYKDMRARFGEEAWKLLESSVG 342 +AD DSF+ L A FY + + +FG+E W LLE G Sbjct: 304 NNADADSFRAKLRAAGFYAEWKKKFGDEPWALLEKYTG 341 >gi|300310178|ref|YP_003774270.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 334 Score = 128 bits (321), Expect = 7e-31, Method: Compositional matrix adjust. Identities = 85/290 (29%), Positives = 157/290 (54%), Gaps = 19/290 (6%) Query: 53 PVNKRAQEAIDRIRNATNGRMEIKLFPANQLGSDTDLMSQIRNGGVEFFNQANTVLSTL- 111 P K A+ + AT GR++I+++P + L D + + ++ G V+ + L Sbjct: 39 PKGKAAERFKELAEKATKGRVKIEVYPNSTLYKDKEELEALQLGAVQMLAPSLAKFGPLG 98 Query: 112 VPAAGIVNTGFAFHDYKEVWQAMDGPLGAYVRAQIEKVGLLTMSKPWDNGFRQITTSTKA 171 V + + + F + +++ +GP+G + ++E G+ ++ WDNGF+ + ++ K Sbjct: 99 VKEFEVFDLPYIFPTKEVLYRVTEGPIGKDLFKKLEPKGITGLAY-WDNGFK-VMSANKP 156 Query: 172 IRSAADVKGLKLRVPAAPMLTSLFSALGASPTPINFNEVYSSLQTKLVEGQENPLAIIST 231 + AD +GLK+R+ ++ +L + ALGA+P + F+EVY +LQT +V+G ENP + + T Sbjct: 157 LHHPADFRGLKMRIQSSKVLDAQMRALGANPQVLAFSEVYQALQTGVVDGTENPPSNLYT 216 Query: 232 ARLYEVQKFCTLSNHVWDAYWILGNRRAFDKLPKDIQEIVRRELDQAATDERADIASFSG 291 +++EVQK T+SNH + Y ++ N++ +D LP DI R +L+ A D A+ Sbjct: 217 QKMHEVQKHVTVSNHGYLGYAVIVNKKFWDGLPSDI----RTQLEGAMKDA-TKYANAIA 271 Query: 292 MARNDLA-------GKG--LQIIDADKDSFKQALAQANFYKDMRARFGEE 332 ND A GK ++ DA+K +++AL + M +R G++ Sbjct: 272 QQENDAALAAVEKTGKTTVYRLTDAEKAEWRKALLPVQ--QQMASRIGKD 319 >gi|300312105|ref|YP_003776197.1| TRAP-type C4-dicarboxylate-binding periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 344 Score = 108 bits (270), Expect = 7e-25, Method: Compositional matrix adjust. Identities = 62/230 (26%), Positives = 126/230 (54%), Gaps = 9/230 (3%) Query: 53 PVNKRAQEAIDRIRNATNGRMEIKLFPANQLGSDTDLMSQIRNGGVEFFNQANTVLSTLV 112 P K A+ + AT GR++++++P + L D + + ++ G V+ + L+ Sbjct: 47 PKGKGAERFKELAEKATQGRVKVEVYPNSTLYKDKEELEALQLGSVQMLAPS---LAKFG 103 Query: 113 PAAG----IVNTGFAFHDYKEVWQAMDGPLGAYVRAQIEKVGLLTMSKPWDNGFRQITTS 168 P + + + F D + + +GP+G + ++E G+ ++ WDNG + + T+ Sbjct: 104 PLGAREFEVFDLPYIFPDKAVLKRVTEGPIGQGLFQKLEGKGIKGLAY-WDNGMK-VMTA 161 Query: 169 TKAIRSAADVKGLKLRVPAAPMLTSLFSALGASPTPINFNEVYSSLQTKLVEGQENPLAI 228 + + AD + LK+R+ ++ +L F AL A+P + F+EVY ++QT +V+G EN + Sbjct: 162 NRPLHKVADFRALKMRIQSSKVLDEQFRALKANPQVLAFSEVYQAMQTGVVDGSENTPSN 221 Query: 229 ISTARLYEVQKFCTLSNHVWDAYWILGNRRAFDKLPKDIQEIVRRELDQA 278 + T +++EVQ T+S+H + Y ++ N++ ++ LP DI+ + + QA Sbjct: 222 VYTQKMHEVQSNLTVSDHGYIGYAVIVNKKFWEALPADIRSQLEAAMKQA 271 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 0.318 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: 1,043,912 Number of extensions: 43082 Number of successful extensions: 118 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 115 Number of HSP's successfully gapped: 6 Length of query: 345 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 259 Effective length of database: 1,212,660 Effective search space: 314078940 Effective search space used: 314078940 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)