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= 0021.0024.p (364 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... 551 e-158 gi|300310178|ref|YP_003774270.1| TRAP-type C4-dicarboxylate tran... 90 2e-19 gi|300312105|ref|YP_003776197.1| TRAP-type C4-dicarboxylate-bind... 72 6e-14 gi|300313112|ref|YP_003777204.1| TRAP-type C4-dicarboxylate tran... 66 4e-12 gi|300309847|ref|YP_003773939.1| TRAP-type C4-dicarboxylate tran... 62 5e-11 >gi|300311998|ref|YP_003776090.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 288 Score = 551 bits (1420), Expect = e-158, Method: Compositional matrix adjust. Identities = 265/278 (95%), Positives = 277/278 (99%) Query: 53 VRMFAQQVNEKTKGALKFEIYPGSSLMKTNAQFSALRKGALDMSLVPLNYAGGEVPETNI 112 +RMFAQQV+E+TKGALKFEIYPGSSLMKTNAQFSA+RKGALDMSLVPLNYAGGEVPETNI Sbjct: 1 MRMFAQQVSERTKGALKFEIYPGSSLMKTNAQFSAMRKGALDMSLVPLNYAGGEVPETNI 60 Query: 113 GLMPGLVTSYQQGAAWKNAEVGKELARILGEKGVVIVSWIWQAGGVASRGKPIVDPADAK 172 GLMPGLVTSYQQGAAWKNAEVGKELAR+L EKGV+IVSWIWQAGGVASRGKPIVDP+DAK Sbjct: 61 GLMPGLVTSYQQGAAWKNAEVGKELARVLAEKGVIIVSWIWQAGGVASRGKPIVDPSDAK 120 Query: 173 GMKVRGGSREMDLILKEAGAAVVTLPSNEIYAAMQTGAMDAAMTSSTSFMSFRLEEVAKS 232 GMKVRGGSREMDLILKEAGAAVVTLPSNEIYAAMQTGAMDAAMTSSTSFMSFRLEEVAK+ Sbjct: 121 GMKVRGGSREMDLILKEAGAAVVTLPSNEIYAAMQTGAMDAAMTSSTSFMSFRLEEVAKA 180 Query: 233 LTTGRDKAYWYMFEPLMMSKAVFERLPKDQQAVIMSVGADMEQFATKAAQADDIAVAQVY 292 LTTGRDKAYWYMFEPLM+SKAVFERLPKDQQ+VIM+VGA+MEQFATKAAQADDIAVAQVY Sbjct: 181 LTTGRDKAYWYMFEPLMISKAVFERLPKDQQSVIMAVGAEMEQFATKAAQADDIAVAQVY 240 Query: 293 QKAGAKVVDLNAEVVKKWQDIARNTAWKDFAARNANCA 330 QKAGAKVVDLNAEVVKKWQDIARNTAWKDFAARNANCA Sbjct: 241 QKAGAKVVDLNAEVVKKWQDIARNTAWKDFAARNANCA 278 >gi|300310178|ref|YP_003774270.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 334 Score = 90.1 bits (222), Expect = 2e-19, Method: Compositional matrix adjust. Identities = 76/278 (27%), Positives = 132/278 (47%), Gaps = 16/278 (5%) Query: 28 QTASLKISHQFPGGTLTEGDFRDRLVRMFAQQVNEKTKGALKFEIYPGSSLMKTNAQFSA 87 Q +K SH T +G +R F + + TKG +K E+YP S+L K + A Sbjct: 24 QPIVIKFSHVVANDT-PKGKAAER----FKELAEKATKGRVKIEVYPNSTLYKDKEELEA 78 Query: 88 LRKGALDM---SLVPLNYAGGEVPETNIGLMPGLVTSYQQGAAWKNAEVGKELARILGEK 144 L+ GA+ M SL G V E + +P + + + +GK+L + L K Sbjct: 79 LQLGAVQMLAPSLAKFGPLG--VKEFEVFDLPYIFPTKEVLYRVTEGPIGKDLFKKLEPK 136 Query: 145 GVVIVSWIWQAG-GVASRGKPIVDPADAKGMKVR-GGSREMDLILKEAGAAVVTLPSNEI 202 G+ +++ W G V S KP+ PAD +G+K+R S+ +D ++ GA L +E+ Sbjct: 137 GITGLAY-WDNGFKVMSANKPLHHPADFRGLKMRIQSSKVLDAQMRALGANPQVLAFSEV 195 Query: 203 YAAMQTGAMDAAMTSSTSFMSFRLEEVAKSLTTGRDKAYWYMFEPLMMSKAVFERLPKDQ 262 Y A+QTG +D ++ + ++ EV K +T + Y+ ++++K ++ LP D Sbjct: 196 YQALQTGVVDGTENPPSNLYTQKMHEVQKHVTVSN---HGYLGYAVIVNKKFWDGLPSDI 252 Query: 263 QAVIMSVGADMEQFATKAAQADDIAVAQVYQKAGAKVV 300 + + D ++A AQ ++ A +K G V Sbjct: 253 RTQLEGAMKDATKYANAIAQQENDAALAAVEKTGKTTV 290 >gi|300312105|ref|YP_003776197.1| TRAP-type C4-dicarboxylate-binding periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 344 Score = 72.4 bits (176), Expect = 6e-14, Method: Compositional matrix adjust. Identities = 80/321 (24%), Positives = 143/321 (44%), Gaps = 21/321 (6%) Query: 1 MTAFTRRHFLGTLAAAPLAAAMPAAWAQTAS----LKISHQFPGGTLTEGDFRDRLVRMF 56 MT R L A L PAA AQ +K SH T +G +R F Sbjct: 1 MTILPLRTALAACAFVTLGLPQPAALAQQPQQPIIIKFSHVVANDT-PKGKGAER----F 55 Query: 57 AQQVNEKTKGALKFEIYPGSSLMKTNAQFSALRKGALDM---SLVPLNYAGGEVPETNIG 113 + + T+G +K E+YP S+L K + AL+ G++ M SL G E + Sbjct: 56 KELAEKATQGRVKVEVYPNSTLYKDKEELEALQLGSVQMLAPSLAKFGPLGAR--EFEVF 113 Query: 114 LMPGLVTSYQQGAAWKNAEVGKELARILGEKGVVIVSWIWQAG-GVASRGKPIVDPADAK 172 +P + +G+ L + L KG+ +++ W G V + +P+ AD + Sbjct: 114 DLPYIFPDKAVLKRVTEGPIGQGLFQKLEGKGIKGLAY-WDNGMKVMTANRPLHKVADFR 172 Query: 173 GMKVR-GGSREMDLILKEAGAAVVTLPSNEIYAAMQTGAMDAAMTSSTSFMSFRLEEVAK 231 +K+R S+ +D + A L +E+Y AMQTG +D + + ++ + ++ EV Sbjct: 173 ALKMRIQSSKVLDEQFRALKANPQVLAFSEVYQAMQTGVVDGSENTPSNVYTQKMHEVQS 232 Query: 232 SLTTGRDKAYWYMFEPLMMSKAVFERLPKDQQAVIMSVGADMEQFATKAAQAD-DIAVAQ 290 +LT + Y+ ++++K +E LP D ++ + + +A AQ + D A+A Sbjct: 233 NLTVSD---HGYIGYAVIVNKKFWEALPADIRSQLEAAMKQATLYANTIAQKENDDALAA 289 Query: 291 VYQKAGAKVVDLNAEVVKKWQ 311 + +V L+ + +W+ Sbjct: 290 IKASGKTRVYTLSEQEKAEWR 310 >gi|300313112|ref|YP_003777204.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 344 Score = 66.2 bits (160), Expect = 4e-12, Method: Compositional matrix adjust. Identities = 58/217 (26%), Positives = 99/217 (45%), Gaps = 13/217 (5%) Query: 60 VNEKTKGALKFEIYPGSSLMKTNAQFSALRKGALD-MSLVPLNYAGGEVPETNIGLMPGL 118 + E++KG ++ ++YP + L S +R GA+D +L PL G VP I + Sbjct: 63 IAEQSKGRIELQLYPNNQLGTDTDMLSQVRAGAIDFFTLSPL-ILGTLVPAAQISGIGFA 121 Query: 119 VTSYQQGAAWKNAEVGKELARILGEKGVVI-VSWIWQAG--GVASRGKPIVDPADAKGMK 175 Y Q + E+G + + + + + IW G + + KPI D KGMK Sbjct: 122 FKDYSQVWPAMDGELGAHVRKQIEARSTLFAFEKIWDNGYRQITNSTKPIKVAEDLKGMK 181 Query: 176 VRGGSREM-DLILKEAGAAVVTLPSNEIYAAMQTGAMDAAMTSSTSFMSFRLEEVAK--S 232 +R + + K AA ++ E+Y+A+QT ++ + +L EV K S Sbjct: 182 LRVPPSPLWTSMFKAFDAAPTSINFAEVYSALQTKIVEGQENPMAIISTAKLYEVQKYCS 241 Query: 233 LTTGRDKAYWYMFEPLMMSKAVFERLPKDQQAVIMSV 269 +T +W+ + +K FERLPKD Q ++ + Sbjct: 242 ITNHMWDGFWF-----LGNKKSFERLPKDLQELMTRI 273 >gi|300309847|ref|YP_003773939.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 345 Score = 62.4 bits (150), Expect = 5e-11, Method: Compositional matrix adjust. Identities = 69/274 (25%), Positives = 121/274 (44%), Gaps = 25/274 (9%) Query: 5 TRRHFL--GTLAAA-PLAAAM--PAAWAQTASLKISHQFPGGTLTEGDFRDRLVRMFAQQ 59 TRR+ L G + AA PL + + PA+ A+ S++F G R + Sbjct: 11 TRRNMLKAGAVGAALPLFSILSRPASAAE-----FSYKFATGQDPSHPVNKRAQEAI-DR 64 Query: 60 VNEKTKGALKFEIYPGSSLMKTNAQFSALRKGALDMSLVPLNYAGGEVPETNIGLMPGLV 119 + T G L+ +++P + L S +R G ++ VP G++ Sbjct: 65 IRNATNGRLEIKLFPANQLGSDTDLMSQVRNGGVEFFNQANTVLSTLVPAA--GIVNTGF 122 Query: 120 TSYQQGAAWK--NAEVGKELARILGEKGVVIVSWIWQAG--GVASRGKPIVDPADAKGMK 175 + GA WK + +G + + + G++ +S W G + + KP+ + D KG+K Sbjct: 123 AFHDYGAVWKAMDGPLGAHVRAQIEKVGLLTMSKPWDNGFRQITTSTKPVRNAGDVKGLK 182 Query: 176 VRGGSREMDLILKEA-GAAVVTLPSNEIYAAMQTGAMDAAMTSSTSFMSFRLEEVAKSLT 234 +R + M L A GA+ + NE+Y+++QT ++ + RL EV K T Sbjct: 183 LRVPAAPMLTSLFSALGASPTPINFNEVYSSLQTKLVEGQENPLAIISTARLYEVQKFCT 242 Query: 235 TGRD--KAYWYMFEPLMMSKAVFERLPKDQQAVI 266 AYW ++ ++ FE+LPKD Q ++ Sbjct: 243 ISNHVWDAYW-----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 0.318 0.131 0.385 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: 919,623 Number of extensions: 35149 Number of successful extensions: 121 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 107 Number of HSP's successfully gapped: 6 Length of query: 364 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 278 Effective length of database: 1,212,660 Effective search space: 337119480 Effective search space used: 337119480 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)