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= 0001.2800.p (343 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... 634 0.0 gi|300310178|ref|YP_003774270.1| TRAP-type C4-dicarboxylate tran... 520 e-149 gi|300309847|ref|YP_003773939.1| TRAP-type C4-dicarboxylate tran... 115 7e-27 gi|300313112|ref|YP_003777204.1| TRAP-type C4-dicarboxylate tran... 114 9e-27 gi|300310441|ref|YP_003774533.1| TRAP-type C4-dicarboxylate tran... 111 7e-26 >gi|300312105|ref|YP_003776197.1| TRAP-type C4-dicarboxylate-binding periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 344 Score = 634 bits (1636), Expect = 0.0, Method: Compositional matrix adjust. Identities = 305/344 (88%), Positives = 324/344 (94%), Gaps = 1/344 (0%) Query: 1 MTIIPRRAALAACVFATLTLPLAAKVAL-AQSTIVIKFSHVVANDTPKGKGAERFKELAE 59 MTI+P R ALAAC F TL LP A +A Q I+IKFSHVVANDTPKGKGAERFKELAE Sbjct: 1 MTILPLRTALAACAFVTLGLPQPAALAQQPQQPIIIKFSHVVANDTPKGKGAERFKELAE 60 Query: 60 KATNGRVKVEVYPNSTLYKDKEELEALQLGSVQMLAPSLAKFGPLGAKEFEVFDLPYIFP 119 KAT GRVKVEVYPNSTLYKDKEELEALQLGSVQMLAPSLAKFGPLGA+EFEVFDLPYIFP Sbjct: 61 KATQGRVKVEVYPNSTLYKDKEELEALQLGSVQMLAPSLAKFGPLGAREFEVFDLPYIFP 120 Query: 120 NKAVLKRVTEGPIGQGLFQRLESRGIKGLAYWDNGMKVMTANRPLHQVADFRALKMRIQS 179 +KAVLKRVTEGPIGQGLFQ+LE +GIKGLAYWDNGMKVMTANRPLH+VADFRALKMRIQS Sbjct: 121 DKAVLKRVTEGPIGQGLFQKLEGKGIKGLAYWDNGMKVMTANRPLHKVADFRALKMRIQS 180 Query: 180 SKVLDEQFRALKANPQVLAFSEVYQAMQTGVVDGSENTPSNIYTQKMYEVQSNLTVSDHG 239 SKVLDEQFRALKANPQVLAFSEVYQAMQTGVVDGSENTPSN+YTQKM+EVQSNLTVSDHG Sbjct: 181 SKVLDEQFRALKANPQVLAFSEVYQAMQTGVVDGSENTPSNVYTQKMHEVQSNLTVSDHG 240 Query: 240 YIGYAVIVNKKFWDALPADVRTQLEGAMKEATIYANNIAQKENDDALAAIKASGKTKVYT 299 YIGYAVIVNKKFW+ALPAD+R+QLE AMK+AT+YAN IAQKENDDALAAIKASGKT+VYT Sbjct: 241 YIGYAVIVNKKFWEALPADIRSQLEAAMKQATLYANTIAQKENDDALAAIKASGKTRVYT 300 Query: 300 LSEEEKTQWRRALLPVHKSMATRVGPELIEAIYKESEAAGVKMN 343 LSE+EK +WRRALLPVHKSMA RVG +LIEAIYKESEAAGVKMN Sbjct: 301 LSEQEKAEWRRALLPVHKSMAARVGADLIEAIYKESEAAGVKMN 344 >gi|300310178|ref|YP_003774270.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 334 Score = 520 bits (1340), Expect = e-149, Method: Compositional matrix adjust. Identities = 247/332 (74%), Positives = 284/332 (85%) Query: 10 LAACVFATLTLPLAAKVALAQSTIVIKFSHVVANDTPKGKGAERFKELAEKATNGRVKVE 69 L + + A + + A AQ IVIKFSHVVANDTPKGK AERFKELAEKAT GRVK+E Sbjct: 3 LKSILLAMTAAAIVSTNAFAQQPIVIKFSHVVANDTPKGKAAERFKELAEKATKGRVKIE 62 Query: 70 VYPNSTLYKDKEELEALQLGSVQMLAPSLAKFGPLGAKEFEVFDLPYIFPNKAVLKRVTE 129 VYPNSTLYKDKEELEALQLG+VQMLAPSLAKFGPLG KEFEVFDLPYIFP K VL RVTE Sbjct: 63 VYPNSTLYKDKEELEALQLGAVQMLAPSLAKFGPLGVKEFEVFDLPYIFPTKEVLYRVTE 122 Query: 130 GPIGQGLFQRLESRGIKGLAYWDNGMKVMTANRPLHQVADFRALKMRIQSSKVLDEQFRA 189 GPIG+ LF++LE +GI GLAYWDNG KVM+AN+PLH ADFR LKMRIQSSKVLD Q RA Sbjct: 123 GPIGKDLFKKLEPKGITGLAYWDNGFKVMSANKPLHHPADFRGLKMRIQSSKVLDAQMRA 182 Query: 190 LKANPQVLAFSEVYQAMQTGVVDGSENTPSNIYTQKMYEVQSNLTVSDHGYIGYAVIVNK 249 L ANPQVLAFSEVYQA+QTGVVDG+EN PSN+YTQKM+EVQ ++TVS+HGY+GYAVIVNK Sbjct: 183 LGANPQVLAFSEVYQALQTGVVDGTENPPSNLYTQKMHEVQKHVTVSNHGYLGYAVIVNK 242 Query: 250 KFWDALPADVRTQLEGAMKEATIYANNIAQKENDDALAAIKASGKTKVYTLSEEEKTQWR 309 KFWD LP+D+RTQLEGAMK+AT YAN IAQ+END ALAA++ +GKT VY L++ EK +WR Sbjct: 243 KFWDGLPSDIRTQLEGAMKDATKYANAIAQQENDAALAAVEKTGKTTVYRLTDAEKAEWR 302 Query: 310 RALLPVHKSMATRVGPELIEAIYKESEAAGVK 341 +ALLPV + MA+R+G +LI+A+ KES A G K Sbjct: 303 KALLPVQQQMASRIGKDLIDAVNKESAALGQK 334 >gi|300309847|ref|YP_003773939.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 345 Score = 115 bits (287), Expect = 7e-27, Method: Compositional matrix adjust. Identities = 74/277 (26%), Positives = 142/277 (51%), Gaps = 16/277 (5%) Query: 4 IPRRAALAACVFATLTLPLAAKVALAQSTIVIKFSHVVANDT--PKGKGAERFKELAEKA 61 + RR L A LPL + ++ S + D P K A+ + A Sbjct: 10 VTRRNMLKAGAVGA-ALPLFSILSRPASAAEFSYKFATGQDPSHPVNKRAQEAIDRIRNA 68 Query: 62 TNGRVKVEVYPNSTLYKDKEELEALQLGSVQMLAPS---LAKFGPLGAKEFEVFDLPYIF 118 TNGR++++++P + L D + + ++ G V+ + L+ P + + + F Sbjct: 69 TNGRLEIKLFPANQLGSDTDLMSQVRNGGVEFFNQANTVLSTLVPAAG----IVNTGFAF 124 Query: 119 PNKAVLKRVTEGPIGQGLFQRLESRGIKGLAY-WDNGMK-VMTANRPLHQVADFRALKMR 176 + + + +GP+G + ++E G+ ++ WDNG + + T+ +P+ D + LK+R Sbjct: 125 HDYGAVWKAMDGPLGAHVRAQIEKVGLLTMSKPWDNGFRQITTSTKPVRNAGDVKGLKLR 184 Query: 177 IQSSKVLDEQFRALKANPQVLAFSEVYQAMQTGVVDGSENTPSNIYTQKMYEVQSNLTVS 236 + ++ +L F AL A+P + F+EVY ++QT +V+G EN + I T ++YEVQ T+S Sbjct: 185 VPAAPMLTSLFSALGASPTPINFNEVYSSLQTKLVEGQENPLAIISTARLYEVQKFCTIS 244 Query: 237 DHGYIGYAVIVNKKFWDALPAD----VRTQLEGAMKE 269 +H + Y ++ N++ ++ LP D VR +L+ A + Sbjct: 245 NHVWDAYWILGNRRAFEKLPKDIQEIVRRELDKAASD 281 >gi|300313112|ref|YP_003777204.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 344 Score = 114 bits (286), Expect = 9e-27, Method: Compositional matrix adjust. Identities = 73/275 (26%), Positives = 143/275 (52%), Gaps = 12/275 (4%) Query: 28 LAQSTIVIKFSHVVANDTP-----KGKGAERFKELAEKATNGRVKVEVYPNSTLYKDKEE 82 ++ S +F+ AN+ P + E +AE+ + GR+++++YPN+ L D + Sbjct: 29 VSTSAHAAEFTFKYANNLPVTHPMNARAKEMAAAIAEQ-SKGRIELQLYPNNQLGTDTDM 87 Query: 83 LEALQLGSVQMLAPSLAKFGPLGAKEFEVFDLPYIFPNKAVLKRVTEGPIGQGLFQRLES 142 L ++ G++ S G L ++ + + F + + + +G +G + +++E+ Sbjct: 88 LSQVRAGAIDFFTLSPLILGTL-VPAAQISGIGFAFKDYSQVWPAMDGELGAHVRKQIEA 146 Query: 143 RGIKGLAY---WDNGMKVMT-ANRPLHQVADFRALKMRIQSSKVLDEQFRALKANPQVLA 198 R A+ WDNG + +T + +P+ D + +K+R+ S + F+A A P + Sbjct: 147 RSTL-FAFEKIWDNGYRQITNSTKPIKVAEDLKGMKLRVPPSPLWTSMFKAFDAAPTSIN 205 Query: 199 FSEVYQAMQTGVVDGSENTPSNIYTQKMYEVQSNLTVSDHGYIGYAVIVNKKFWDALPAD 258 F+EVY A+QT +V+G EN + I T K+YEVQ ++++H + G+ + NKK ++ LP D Sbjct: 206 FAEVYSALQTKIVEGQENPMAIISTAKLYEVQKYCSITNHMWDGFWFLGNKKSFERLPKD 265 Query: 259 VRTQLEGAMKEATIYANNIAQKENDDALAAIKASG 293 ++ + + EA + +K ND + +K G Sbjct: 266 LQELMTRIINEAGVNQRADVRKLNDSLVDEMKGKG 300 >gi|300310441|ref|YP_003774533.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 348 Score = 111 bits (278), Expect = 7e-26, Method: Compositional matrix adjust. Identities = 70/266 (26%), Positives = 139/266 (52%), Gaps = 12/266 (4%) Query: 2 TIIPRRAALAACVFATLTLPLAAKVALAQSTIVIKFSHVVANDT--PKGKGAERFKELAE 59 T + RR L A LPL + ++ + + D P K A++ + Sbjct: 11 TSVSRRQLLKAGAVGA-ALPLFSIMSRPANAAEFNYKFATGQDPSHPVNKRAQQAIDRIR 69 Query: 60 KATNGRVKVEVYPNSTLYKDKEELEALQLGSVQMLAPS---LAKFGPLGAKEFEVFDLPY 116 +AT GR+ ++++P + L D + + ++ G V+ + L+ P + + + Sbjct: 70 EATGGRLDIKLFPANQLGSDTDLMSQIRNGGVEFFNQASVVLSTLVPAAG----IVNTGF 125 Query: 117 IFPNKAVLKRVTEGPIGQGLFQRLESRGIKGLAY-WDNGMK-VMTANRPLHQVADFRALK 174 F + + + +GP+G + ++E G+ ++ WDNG + + T+ +P+ AD + LK Sbjct: 126 AFHDYKEVWQAMDGPLGAYVRAQIEKVGLLTMSKPWDNGFRQITTSTKPIKTAADLKGLK 185 Query: 175 MRIQSSKVLDEQFRALKANPQVLAFSEVYQAMQTGVVDGSENTPSNIYTQKMYEVQSNLT 234 +R+ ++ +L F AL A+P + F+EVY ++QT +V+G EN + I T ++YEVQ T Sbjct: 186 LRVPAAPMLTSLFSALGASPTPINFNEVYSSLQTKLVEGQENPLAIISTARLYEVQKFCT 245 Query: 235 VSDHGYIGYAVIVNKKFWDALPADVR 260 +S+H + Y ++ N++ ++ LP D++ Sbjct: 246 ISNHVWDAYWILGNRRAFEKLPKDIQ 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 0.316 0.130 0.364 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: 945,987 Number of extensions: 36090 Number of successful extensions: 128 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 122 Number of HSP's successfully gapped: 6 Length of query: 343 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 257 Effective length of database: 1,212,660 Effective search space: 311653620 Effective search space used: 311653620 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)