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= 0001.2729.p (337 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311998|ref|YP_003776090.1| TRAP-type C4-dicarboxylate tran... 567 e-163 gi|300310178|ref|YP_003774270.1| TRAP-type C4-dicarboxylate tran... 92 8e-20 gi|300312105|ref|YP_003776197.1| TRAP-type C4-dicarboxylate-bind... 69 5e-13 gi|300313112|ref|YP_003777204.1| TRAP-type C4-dicarboxylate tran... 68 1e-12 gi|300309847|ref|YP_003773939.1| TRAP-type C4-dicarboxylate tran... 66 3e-12 >gi|300311998|ref|YP_003776090.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 288 Score = 567 bits (1461), Expect = e-163, Method: Compositional matrix adjust. Identities = 276/288 (95%), Positives = 284/288 (98%) Query: 50 VRTFAQQVSERTKGALKFEIYPGSSLMKTNAQFSALRKGALDMSLVPLNYAGGEVPETNI 109 +R FAQQVSERTKGALKFEIYPGSSLMKTNAQFSA+RKGALDMSLVPLNYAGGEVPETNI Sbjct: 1 MRMFAQQVSERTKGALKFEIYPGSSLMKTNAQFSAMRKGALDMSLVPLNYAGGEVPETNI 60 Query: 110 GLMPGLVTSYQQGASWKNAEVGKELARVLGEKGVVIVSWIWQAGGVASRGKPIVDPADVK 169 GLMPGLVTSYQQGA+WKNAEVGKELARVL EKGV+IVSWIWQAGGVASRGKPIVDP+D K Sbjct: 61 GLMPGLVTSYQQGAAWKNAEVGKELARVLAEKGVIIVSWIWQAGGVASRGKPIVDPSDAK 120 Query: 170 GMKVRGGSREMDLILKEAGAAVVTLPSNEIYAAMQTGAMDAAMTSSTSFMSFRLEEVAKA 229 GMKVRGGSREMDLILKEAGAAVVTLPSNEIYAAMQTGAMDAAMTSSTSFMSFRLEEVAKA Sbjct: 121 GMKVRGGSREMDLILKEAGAAVVTLPSNEIYAAMQTGAMDAAMTSSTSFMSFRLEEVAKA 180 Query: 230 LTTGRDKAYWYMFEPLMMSKAVFERLPKDQQAVIMAVGAEMEQFATKAAQADDIAVAQVY 289 LTTGRDKAYWYMFEPLM+SKAVFERLPKDQQ+VIMAVGAEMEQFATKAAQADDIAVAQVY Sbjct: 181 LTTGRDKAYWYMFEPLMISKAVFERLPKDQQSVIMAVGAEMEQFATKAAQADDIAVAQVY 240 Query: 290 QKAGAKVVDLNAEVVKKWQDIARNTAWKDFAGRNASCAKLLALAEKTL 337 QKAGAKVVDLNAEVVKKWQDIARNTAWKDFA RNA+CAKLLALAEKTL Sbjct: 241 QKAGAKVVDLNAEVVKKWQDIARNTAWKDFAARNANCAKLLALAEKTL 288 >gi|300310178|ref|YP_003774270.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 334 Score = 91.7 bits (226), Expect = 8e-20, Method: Compositional matrix adjust. Identities = 81/302 (26%), Positives = 142/302 (47%), Gaps = 17/302 (5%) Query: 1 MTRRHFLGALAAAPLASAVPSVWAQSATLKISHQFPGGTITEGDFRDRLVRTFAQQVSER 60 M + L A+ AA + S + Q +K SH T +G +R F + + Sbjct: 1 MKLKSILLAMTAAAIVS-TNAFAQQPIVIKFSHVVANDT-PKGKAAER----FKELAEKA 54 Query: 61 TKGALKFEIYPGSSLMKTNAQFSALRKGALDM---SLVPLNYAGGEVPETNIGLMPGLVT 117 TKG +K E+YP S+L K + AL+ GA+ M SL G V E + +P + Sbjct: 55 TKGRVKIEVYPNSTLYKDKEELEALQLGAVQMLAPSLAKFGPLG--VKEFEVFDLPYIFP 112 Query: 118 SYQQGASWKNAEVGKELARVLGEKGVVIVSWIWQAG-GVASRGKPIVDPADVKGMKVR-G 175 + + +GK+L + L KG+ +++ W G V S KP+ PAD +G+K+R Sbjct: 113 TKEVLYRVTEGPIGKDLFKKLEPKGITGLAY-WDNGFKVMSANKPLHHPADFRGLKMRIQ 171 Query: 176 GSREMDLILKEAGAAVVTLPSNEIYAAMQTGAMDAAMTSSTSFMSFRLEEVAKALTTGRD 235 S+ +D ++ GA L +E+Y A+QTG +D ++ + ++ EV K +T Sbjct: 172 SSKVLDAQMRALGANPQVLAFSEVYQALQTGVVDGTENPPSNLYTQKMHEVQKHVTVSN- 230 Query: 236 KAYWYMFEPLMMSKAVFERLPKDQQAVIMAVGAEMEQFATKAAQADDIAVAQVYQKAGAK 295 + Y+ ++++K ++ LP D + + + ++A AQ ++ A +K G Sbjct: 231 --HGYLGYAVIVNKKFWDGLPSDIRTQLEGAMKDATKYANAIAQQENDAALAAVEKTGKT 288 Query: 296 VV 297 V Sbjct: 289 TV 290 >gi|300312105|ref|YP_003776197.1| TRAP-type C4-dicarboxylate-binding periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 344 Score = 68.9 bits (167), Expect = 5e-13, Method: Compositional matrix adjust. Identities = 78/315 (24%), Positives = 141/315 (44%), Gaps = 21/315 (6%) Query: 4 RHFLGALAAAPLASAVPSVWAQSA----TLKISHQFPGGTITEGDFRDRLVRTFAQQVSE 59 R L A A L P+ AQ +K SH T +G +R F + + Sbjct: 7 RTALAACAFVTLGLPQPAALAQQPQQPIIIKFSHVVANDT-PKGKGAER----FKELAEK 61 Query: 60 RTKGALKFEIYPGSSLMKTNAQFSALRKGALDM---SLVPLNYAGGEVPETNIGLMPGLV 116 T+G +K E+YP S+L K + AL+ G++ M SL G E + +P + Sbjct: 62 ATQGRVKVEVYPNSTLYKDKEELEALQLGSVQMLAPSLAKFGPLGAR--EFEVFDLPYIF 119 Query: 117 TSYQQGASWKNAEVGKELARVLGEKGVVIVSWIWQAG-GVASRGKPIVDPADVKGMKVR- 174 +G+ L + L KG+ +++ W G V + +P+ AD + +K+R Sbjct: 120 PDKAVLKRVTEGPIGQGLFQKLEGKGIKGLAY-WDNGMKVMTANRPLHKVADFRALKMRI 178 Query: 175 GGSREMDLILKEAGAAVVTLPSNEIYAAMQTGAMDAAMTSSTSFMSFRLEEVAKALTTGR 234 S+ +D + A L +E+Y AMQTG +D + + ++ + ++ EV LT Sbjct: 179 QSSKVLDEQFRALKANPQVLAFSEVYQAMQTGVVDGSENTPSNVYTQKMHEVQSNLTVSD 238 Query: 235 DKAYWYMFEPLMMSKAVFERLPKDQQAVIMAVGAEMEQFATKAAQA-DDIAVAQVYQKAG 293 + Y+ ++++K +E LP D ++ + A + +A AQ +D A+A + Sbjct: 239 ---HGYIGYAVIVNKKFWEALPADIRSQLEAAMKQATLYANTIAQKENDDALAAIKASGK 295 Query: 294 AKVVDLNAEVVKKWQ 308 +V L+ + +W+ Sbjct: 296 TRVYTLSEQEKAEWR 310 >gi|300313112|ref|YP_003777204.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 344 Score = 67.8 bits (164), Expect = 1e-12, Method: Compositional matrix adjust. Identities = 73/280 (26%), Positives = 126/280 (45%), Gaps = 22/280 (7%) Query: 1 MTRRHFLGALAAAPLASAV----PSVWAQSATLKISHQFPGGTITEGDFRDRLVRTFAQQ 56 +TRR+FL + A A+A S A T K ++ P +T + + A Sbjct: 8 ITRRNFLKTASVASAAAATGLVSTSAHAAEFTFKYANNLP---VTHP--MNARAKEMAAA 62 Query: 57 VSERTKGALKFEIYPGSSLMKTNAQFSALRKGALD-MSLVPLNYAGGEVPETNIGLMPGL 115 ++E++KG ++ ++YP + L S +R GA+D +L PL G VP I + Sbjct: 63 IAEQSKGRIELQLYPNNQLGTDTDMLSQVRAGAIDFFTLSPL-ILGTLVPAAQISGIGFA 121 Query: 116 VTSYQQGASWKNAEVGKELARVLGEKGVVI-VSWIWQAG--GVASRGKPIVDPADVKGMK 172 Y Q + E+G + + + + + IW G + + KPI D+KGMK Sbjct: 122 FKDYSQVWPAMDGELGAHVRKQIEARSTLFAFEKIWDNGYRQITNSTKPIKVAEDLKGMK 181 Query: 173 VRGGSREM-DLILKEAGAAVVTLPSNEIYAAMQTGAMDAAMTSSTSFMSFRLEEVAK--A 229 +R + + K AA ++ E+Y+A+QT ++ + +L EV K + Sbjct: 182 LRVPPSPLWTSMFKAFDAAPTSINFAEVYSALQTKIVEGQENPMAIISTAKLYEVQKYCS 241 Query: 230 LTTGRDKAYWYMFEPLMMSKAVFERLPKDQQAVIMAVGAE 269 +T +W+ + +K FERLPKD Q ++ + E Sbjct: 242 ITNHMWDGFWF-----LGNKKSFERLPKDLQELMTRIINE 276 >gi|300309847|ref|YP_003773939.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 345 Score = 66.2 bits (160), Expect = 3e-12, Method: Compositional matrix adjust. Identities = 77/286 (26%), Positives = 129/286 (45%), Gaps = 47/286 (16%) Query: 1 MTRRHFL--GALAAA-PLASAVPSVWAQSATLKISHQFPGGTITEGDFRDRLVRTFAQQV 57 +TRR+ L GA+ AA PL S + ++ + S++F G R AQ+ Sbjct: 10 VTRRNMLKAGAVGAALPLFSILSR---PASAAEFSYKFATGQDPSHPVNKR-----AQEA 61 Query: 58 SER----TKGALKFEIYPGSSLMKTNAQFSALRKGALDM---------SLVPLNYAGGEV 104 +R T G L+ +++P + L S +R G ++ +LVP A G V Sbjct: 62 IDRIRNATNGRLEIKLFPANQLGSDTDLMSQVRNGGVEFFNQANTVLSTLVP---AAGIV 118 Query: 105 PETNIGLMPGLVTSYQQGASWK--NAEVGKELARVLGEKGVVIVSWIWQAG--GVASRGK 160 N G + GA WK + +G + + + G++ +S W G + + K Sbjct: 119 ---NTGF-----AFHDYGAVWKAMDGPLGAHVRAQIEKVGLLTMSKPWDNGFRQITTSTK 170 Query: 161 PIVDPADVKGMKVRGGSREMDLILKEA-GAAVVTLPSNEIYAAMQTGAMDAAMTSSTSFM 219 P+ + DVKG+K+R + M L A GA+ + NE+Y+++QT ++ Sbjct: 171 PVRNAGDVKGLKLRVPAAPMLTSLFSALGASPTPINFNEVYSSLQTKLVEGQENPLAIIS 230 Query: 220 SFRLEEVAKALTTGRD--KAYWYMFEPLMMSKAVFERLPKDQQAVI 263 + RL EV K T AYW ++ ++ FE+LPKD Q ++ Sbjct: 231 TARLYEVQKFCTISNHVWDAYW-----ILGNRRAFEKLPKDIQEIV 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 0.317 0.129 0.370 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: 942,660 Number of extensions: 36881 Number of successful extensions: 116 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 101 Number of HSP's successfully gapped: 6 Length of query: 337 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 251 Effective length of database: 1,212,660 Effective search space: 304377660 Effective search space used: 304377660 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)