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= 0001.0024.p (340 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... 583 e-168 gi|300310178|ref|YP_003774270.1| TRAP-type C4-dicarboxylate tran... 89 7e-19 gi|300313112|ref|YP_003777204.1| TRAP-type C4-dicarboxylate tran... 69 8e-13 gi|300312105|ref|YP_003776197.1| TRAP-type C4-dicarboxylate-bind... 68 9e-13 gi|300309847|ref|YP_003773939.1| TRAP-type C4-dicarboxylate tran... 65 5e-12 >gi|300311998|ref|YP_003776090.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 288 Score = 583 bits (1504), Expect = e-168, Method: Compositional matrix adjust. Identities = 287/288 (99%), Positives = 288/288 (100%) Query: 53 VRMFAQQVSERTKGALKFEIYPGSSLMKTNAQFSAMRKGALDMSLVPLNYAGGEVPETNI 112 +RMFAQQVSERTKGALKFEIYPGSSLMKTNAQFSAMRKGALDMSLVPLNYAGGEVPETNI Sbjct: 1 MRMFAQQVSERTKGALKFEIYPGSSLMKTNAQFSAMRKGALDMSLVPLNYAGGEVPETNI 60 Query: 113 GLMPGLVTSYQQGAAWKNAEVGKELARVLAEKGVIIVSWIWQAGGVASRGKPIVDPSDAK 172 GLMPGLVTSYQQGAAWKNAEVGKELARVLAEKGVIIVSWIWQAGGVASRGKPIVDPSDAK Sbjct: 61 GLMPGLVTSYQQGAAWKNAEVGKELARVLAEKGVIIVSWIWQAGGVASRGKPIVDPSDAK 120 Query: 173 GMKVRGGSREMDLILKEAGAAVVTLPSNEIYAAMQTGAMDAAMTSSTSFMSFRLEEVAKA 232 GMKVRGGSREMDLILKEAGAAVVTLPSNEIYAAMQTGAMDAAMTSSTSFMSFRLEEVAKA Sbjct: 121 GMKVRGGSREMDLILKEAGAAVVTLPSNEIYAAMQTGAMDAAMTSSTSFMSFRLEEVAKA 180 Query: 233 LTTGRDKAYWYMFEPLMISKAVFERLPKDQQSVIMAVGAEMEQFATKAAQADDIAVAQVY 292 LTTGRDKAYWYMFEPLMISKAVFERLPKDQQSVIMAVGAEMEQFATKAAQADDIAVAQVY Sbjct: 181 LTTGRDKAYWYMFEPLMISKAVFERLPKDQQSVIMAVGAEMEQFATKAAQADDIAVAQVY 240 Query: 293 QKAGAKVVDLNAEVVKKWQDIARNTAWKDFAARNANCAKLLALAEKTL 340 QKAGAKVVDLNAEVVKKWQDIARNTAWKDFAARNANCAKLLALAEKTL Sbjct: 241 QKAGAKVVDLNAEVVKKWQDIARNTAWKDFAARNANCAKLLALAEKTL 288 >gi|300310178|ref|YP_003774270.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 334 Score = 88.6 bits (218), Expect = 7e-19, Method: Compositional matrix adjust. Identities = 73/278 (26%), Positives = 133/278 (47%), Gaps = 16/278 (5%) Query: 28 QTASLKISHQFPGGTLTEGDFRDRLVRMFAQQVSERTKGALKFEIYPGSSLMKTNAQFSA 87 Q +K SH T +G +R F + + TKG +K E+YP S+L K + A Sbjct: 24 QPIVIKFSHVVANDT-PKGKAAER----FKELAEKATKGRVKIEVYPNSTLYKDKEELEA 78 Query: 88 MRKGALDM---SLVPLNYAGGEVPETNIGLMPGLVTSYQQGAAWKNAEVGKELARVLAEK 144 ++ GA+ M SL G V E + +P + + + +GK+L + L K Sbjct: 79 LQLGAVQMLAPSLAKFGPLG--VKEFEVFDLPYIFPTKEVLYRVTEGPIGKDLFKKLEPK 136 Query: 145 GVIIVSWIWQAG-GVASRGKPIVDPSDAKGMKVR-GGSREMDLILKEAGAAVVTLPSNEI 202 G+ +++ W G V S KP+ P+D +G+K+R S+ +D ++ GA L +E+ Sbjct: 137 GITGLAY-WDNGFKVMSANKPLHHPADFRGLKMRIQSSKVLDAQMRALGANPQVLAFSEV 195 Query: 203 YAAMQTGAMDAAMTSSTSFMSFRLEEVAKALTTGRDKAYWYMFEPLMISKAVFERLPKDQ 262 Y A+QTG +D ++ + ++ EV K +T + Y+ ++++K ++ LP D Sbjct: 196 YQALQTGVVDGTENPPSNLYTQKMHEVQKHVTVSN---HGYLGYAVIVNKKFWDGLPSDI 252 Query: 263 QSVIMAVGAEMEQFATKAAQADDIAVAQVYQKAGAKVV 300 ++ + + ++A AQ ++ A +K G V Sbjct: 253 RTQLEGAMKDATKYANAIAQQENDAALAAVEKTGKTTV 290 >gi|300313112|ref|YP_003777204.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 344 Score = 68.6 bits (166), Expect = 8e-13, Method: Compositional matrix adjust. Identities = 71/275 (25%), Positives = 121/275 (44%), Gaps = 14/275 (5%) Query: 5 TRRQFLGTLAAAPLASAVPSVWAQTASLKISHQFPGGTLTEGDFRDRLVRMFAQQVSERT 64 TRR FL T + A A+A V + + + ++ R M A ++E++ Sbjct: 9 TRRNFLKTASVASAAAATGLVSTSAHAAEFTFKYANNLPVTHPMNARAKEM-AAAIAEQS 67 Query: 65 KGALKFEIYPGSSLMKTNAQFSAMRKGALD-MSLVPLNYAGGEVPETNIGLMPGLVTSYQ 123 KG ++ ++YP + L S +R GA+D +L PL G VP I + Y Sbjct: 68 KGRIELQLYPNNQLGTDTDMLSQVRAGAIDFFTLSPL-ILGTLVPAAQISGIGFAFKDYS 126 Query: 124 QGAAWKNAEVGKELARVLAEKGVII-VSWIWQAG--GVASRGKPIVDPSDAKGMKVRGGS 180 Q + E+G + + + + + IW G + + KPI D KGMK+R Sbjct: 127 QVWPAMDGELGAHVRKQIEARSTLFAFEKIWDNGYRQITNSTKPIKVAEDLKGMKLRVPP 186 Query: 181 REM-DLILKEAGAAVVTLPSNEIYAAMQTGAMDAAMTSSTSFMSFRLEEVAK--ALTTGR 237 + + K AA ++ E+Y+A+QT ++ + +L EV K ++T Sbjct: 187 SPLWTSMFKAFDAAPTSINFAEVYSALQTKIVEGQENPMAIISTAKLYEVQKYCSITNHM 246 Query: 238 DKAYWYMFEPLMISKAVFERLPKDQQSVIMAVGAE 272 +W++ +K FERLPKD Q ++ + E Sbjct: 247 WDGFWFLG-----NKKSFERLPKDLQELMTRIINE 276 >gi|300312105|ref|YP_003776197.1| TRAP-type C4-dicarboxylate-binding periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 344 Score = 68.2 bits (165), Expect = 9e-13, Method: Compositional matrix adjust. Identities = 77/321 (23%), Positives = 142/321 (44%), Gaps = 21/321 (6%) Query: 1 MSAFTRRQFLGTLAAAPLASAVPSVWAQTAS----LKISHQFPGGTLTEGDFRDRLVRMF 56 M+ R L A L P+ AQ +K SH T +G +R F Sbjct: 1 MTILPLRTALAACAFVTLGLPQPAALAQQPQQPIIIKFSHVVANDT-PKGKGAER----F 55 Query: 57 AQQVSERTKGALKFEIYPGSSLMKTNAQFSAMRKGALDM---SLVPLNYAGGEVPETNIG 113 + + T+G +K E+YP S+L K + A++ G++ M SL G E + Sbjct: 56 KELAEKATQGRVKVEVYPNSTLYKDKEELEALQLGSVQMLAPSLAKFGPLGAR--EFEVF 113 Query: 114 LMPGLVTSYQQGAAWKNAEVGKELARVLAEKGVIIVSWIWQAG-GVASRGKPIVDPSDAK 172 +P + +G+ L + L KG+ +++ W G V + +P+ +D + 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 ALTTGRDKAYWYMFEPLMISKAVFERLPKDQQSVIMAVGAEMEQFATKAAQA-DDIAVAQ 290 LT + Y+ ++++K +E LP D +S + A + +A AQ +D A+A Sbjct: 233 NLTVSD---HGYIGYAVIVNKKFWEALPADIRSQLEAAMKQATLYANTIAQKENDDALAA 289 Query: 291 VYQKAGAKVVDLNAEVVKKWQ 311 + +V L+ + +W+ Sbjct: 290 IKASGKTRVYTLSEQEKAEWR 310 >gi|300309847|ref|YP_003773939.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 345 Score = 65.5 bits (158), Expect = 5e-12, Method: Compositional matrix adjust. Identities = 88/349 (25%), Positives = 156/349 (44%), Gaps = 59/349 (16%) Query: 5 TRRQFLGTLAAAPLASAVP--SVWAQTASL-KISHQFPGGTLTEGDFRDRLVRMFAQQVS 61 TRR L A + +A+P S+ ++ AS + S++F G R AQ+ Sbjct: 11 TRRNML---KAGAVGAALPLFSILSRPASAAEFSYKFATGQDPSHPVNKR-----AQEAI 62 Query: 62 ER----TKGALKFEIYPGSSLMKTNAQFSAMRKGALDM---------SLVPLNYAGGEVP 108 +R T G L+ +++P + L S +R G ++ +LVP A G V Sbjct: 63 DRIRNATNGRLEIKLFPANQLGSDTDLMSQVRNGGVEFFNQANTVLSTLVP---AAGIV- 118 Query: 109 ETNIGLMPGLVTSYQQGAAWK--NAEVGKELARVLAEKGVIIVSWIWQAG--GVASRGKP 164 N G + GA WK + +G + + + G++ +S W G + + KP Sbjct: 119 --NTGF-----AFHDYGAVWKAMDGPLGAHVRAQIEKVGLLTMSKPWDNGFRQITTSTKP 171 Query: 165 IVDPSDAKGMKVRGGSREMDLILKEA-GAAVVTLPSNEIYAAMQTGAMDAAMTSSTSFMS 223 + + D KG+K+R + M L A GA+ + NE+Y+++QT ++ + Sbjct: 172 VRNAGDVKGLKLRVPAAPMLTSLFSALGASPTPINFNEVYSSLQTKLVEGQENPLAIIST 231 Query: 224 FRLEEVAKALTTGRD--KAYWYMFEPLMISKAVFERLPKDQQSVIMAVGAEMEQFATKAA 281 RL EV K T AYW ++ ++ FE+LPKD Q ++ E+++ A+ Sbjct: 232 ARLYEVQKFCTISNHVWDAYW-----ILGNRRAFEKLPKDIQEIVR---RELDKAASD-- 281 Query: 282 QADDIAVAQVYQK-----AGAKVVDLNAEVVKKWQDIARNTAWKDFAAR 325 + DIA + + G ++V+ + + K + +AR +KD A+ Sbjct: 282 ERADIAAFSGFARNDLASKGLQIVEADKDSFK--EALARANFYKDMRAK 328 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 0.128 0.367 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: 919,910 Number of extensions: 35211 Number of successful extensions: 124 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 111 Number of HSP's successfully gapped: 6 Length of query: 340 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 254 Effective length of database: 1,212,660 Effective search space: 308015640 Effective search space used: 308015640 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)