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= 0131.0008.p (342 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... 526 e-151 gi|300310178|ref|YP_003774270.1| TRAP-type C4-dicarboxylate tran... 90 3e-19 gi|300312105|ref|YP_003776197.1| TRAP-type C4-dicarboxylate-bind... 69 5e-13 gi|300309847|ref|YP_003773939.1| TRAP-type C4-dicarboxylate tran... 65 6e-12 gi|300313112|ref|YP_003777204.1| TRAP-type C4-dicarboxylate tran... 64 2e-11 >gi|300311998|ref|YP_003776090.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 288 Score = 526 bits (1356), Expect = e-151, Method: Compositional matrix adjust. Identities = 255/287 (88%), Positives = 269/287 (93%) Query: 56 RMFAEGVTKRTNGSLKFEIYPGSSLMKVNAQFSAMRKGALDLSLVPLNYAGGEVPETNIG 115 RMFA+ V++RT G+LKFEIYPGSSLMK NAQFSAMRKGALD+SLVPLNYAGGEVPETNIG Sbjct: 2 RMFAQQVSERTKGALKFEIYPGSSLMKTNAQFSAMRKGALDMSLVPLNYAGGEVPETNIG 61 Query: 116 LMPGLVTSYAQGSAWKNAEVGKELARILAEKGILIVSWIWQAGGVASRTKPIINPEDAKG 175 LMPGLVTSY QG+AWKNAEVGKELAR+LAEKG++IVSWIWQAGGVASR KPI++P DAKG Sbjct: 62 LMPGLVTSYQQGAAWKNAEVGKELARVLAEKGVIIVSWIWQAGGVASRGKPIVDPSDAKG 121 Query: 176 MKVRGGSREMDLILKEAGAAVVTLPSNEIYAAMQTGAMDAAMTSSTSFISFRLEEVAKAL 235 MKVRGGSREMDLILKEAGAAVVTLPSNEIYAAMQTGAMDAAMTSSTSF+SFRLEEVAKAL Sbjct: 122 MKVRGGSREMDLILKEAGAAVVTLPSNEIYAAMQTGAMDAAMTSSTSFMSFRLEEVAKAL 181 Query: 236 TTGRDKAYWYMFEPLMISKAVFERLTKDQQAAIMAVGAEMEQFALKAAQTDDVAVAAVYQ 295 TTGRDKAYWYMFEPLMISKAVFERL KDQQ+ IMAVGAEMEQFA KAAQ DD+AVA VYQ Sbjct: 182 TTGRDKAYWYMFEPLMISKAVFERLPKDQQSVIMAVGAEMEQFATKAAQADDIAVAQVYQ 241 Query: 296 KAGAKVVDLNAATVKKWQDIARATAWKDFGARNANCANLLKLAEKLL 342 KAGAKVVDLNA VKKWQDIAR TAWKDF ARNANCA LL LAEK L Sbjct: 242 KAGAKVVDLNAEVVKKWQDIARNTAWKDFAARNANCAKLLALAEKTL 288 >gi|300310178|ref|YP_003774270.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 334 Score = 89.7 bits (221), Expect = 3e-19, Method: Compositional matrix adjust. Identities = 84/315 (26%), Positives = 149/315 (47%), Gaps = 20/315 (6%) Query: 5 KRRSIIGALATAPLWTAGSSAWAQGAPTSLKISHQFPGGTINEGDFRDRLTRMFAEGVTK 64 K +SI+ A+ A + ++A+AQ P +K SH T + + F E K Sbjct: 2 KLKSILLAMTAAAI--VSTNAFAQ-QPIVIKFSHVVANDTP-----KGKAAERFKELAEK 53 Query: 65 RTNGSLKFEIYPGSSLMKVNAQFSAMRKGALDL---SLVPLNYAGGEVPETNIGLMPGLV 121 T G +K E+YP S+L K + A++ GA+ + SL G V E + +P + Sbjct: 54 ATKGRVKIEVYPNSTLYKDKEELEALQLGAVQMLAPSLAKFGPLG--VKEFEVFDLPYIF 111 Query: 122 TSYAQGSAWKNAEVGKELARILAEKGILIVSWIWQAG-GVASRTKPIINPEDAKGMKVR- 179 + +GK+L + L KGI +++ W G V S KP+ +P D +G+K+R Sbjct: 112 PTKEVLYRVTEGPIGKDLFKKLEPKGITGLAY-WDNGFKVMSANKPLHHPADFRGLKMRI 170 Query: 180 GGSREMDLILKEAGAAVVTLPSNEIYAAMQTGAMDAAMTSSTSFISFRLEEVAKALTTGR 239 S+ +D ++ GA L +E+Y A+QTG +D ++ + ++ EV K +T Sbjct: 171 QSSKVLDAQMRALGANPQVLAFSEVYQALQTGVVDGTENPPSNLYTQKMHEVQKHVTVSN 230 Query: 240 DKAYWYMFEPLMISKAVFERLTKDQQAAIMAVGAEMEQFALK-AAQTDDVAVAAVYQKAG 298 + Y+ ++++K ++ L D + + + ++A A Q +D A+AAV + Sbjct: 231 ---HGYLGYAVIVNKKFWDGLPSDIRTQLEGAMKDATKYANAIAQQENDAALAAVEKTGK 287 Query: 299 AKVVDLNAATVKKWQ 313 V L A +W+ Sbjct: 288 TTVYRLTDAEKAEWR 302 >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 = 81/321 (25%), Positives = 143/321 (44%), Gaps = 19/321 (5%) Query: 1 MTSQKRRSIIGALATAPLWTAGSSAWAQGA--PTSLKISHQFPGGTINEGDFRDRLTRMF 58 MT R+ + A A L +A AQ P +K SH T +G +R F Sbjct: 1 MTILPLRTALAACAFVTLGLPQPAALAQQPQQPIIIKFSHVVANDT-PKGKGAER----F 55 Query: 59 AEGVTKRTNGSLKFEIYPGSSLMKVNAQFSAMRKGALDL---SLVPLNYAGGEVPETNIG 115 E K T G +K E+YP S+L K + A++ G++ + SL G E + Sbjct: 56 KELAEKATQGRVKVEVYPNSTLYKDKEELEALQLGSVQMLAPSLAKFGPLGAR--EFEVF 113 Query: 116 LMPGLVTSYAQGSAWKNAEVGKELARILAEKGILIVSWIWQAG-GVASRTKPIINPEDAK 174 +P + A +G+ L + L KGI +++ W G V + +P+ D + Sbjct: 114 DLPYIFPDKAVLKRVTEGPIGQGLFQKLEGKGIKGLAY-WDNGMKVMTANRPLHKVADFR 172 Query: 175 GMKVR-GGSREMDLILKEAGAAVVTLPSNEIYAAMQTGAMDAAMTSSTSFISFRLEEVAK 233 +K+R S+ +D + A L +E+Y AMQTG +D + + ++ + ++ EV Sbjct: 173 ALKMRIQSSKVLDEQFRALKANPQVLAFSEVYQAMQTGVVDGSENTPSNVYTQKMHEVQS 232 Query: 234 ALTTGRDKAYWYMFEPLMISKAVFERLTKDQQAAIMAVGAEMEQFALKAAQTD-DVAVAA 292 LT + Y+ ++++K +E L D ++ + A + +A AQ + D A+AA Sbjct: 233 NLTVSD---HGYIGYAVIVNKKFWEALPADIRSQLEAAMKQATLYANTIAQKENDDALAA 289 Query: 293 VYQKAGAKVVDLNAATVKKWQ 313 + +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 = 6e-12, Method: Compositional matrix adjust. Identities = 75/286 (26%), Positives = 127/286 (44%), Gaps = 50/286 (17%) Query: 66 TNGSLKFEIYPGSSLMKVNAQFSAMRKGALDL---------SLVPLNYAGGEVPETNIGL 116 TNG L+ +++P + L S +R G ++ +LVP A G V N G Sbjct: 69 TNGRLEIKLFPANQLGSDTDLMSQVRNGGVEFFNQANTVLSTLVP---AAGIV---NTGF 122 Query: 117 MPGLVTSYAQGSAWK--NAEVGKELARILAEKGILIVSWIWQAG--GVASRTKPIINPED 172 + G+ WK + +G + + + G+L +S W G + + TKP+ N D Sbjct: 123 -----AFHDYGAVWKAMDGPLGAHVRAQIEKVGLLTMSKPWDNGFRQITTSTKPVRNAGD 177 Query: 173 AKGMKVRGGSREMDLILKEA-GAAVVTLPSNEIYAAMQTGAMDAAMTSSTSFISFRLEEV 231 KG+K+R + M L A GA+ + NE+Y+++QT ++ + RL EV Sbjct: 178 VKGLKLRVPAAPMLTSLFSALGASPTPINFNEVYSSLQTKLVEGQENPLAIISTARLYEV 237 Query: 232 AKALTTGRD--KAYWYMFEPLMISKAVFERLTKDQQAAIMAVGAEMEQFALKAAQTDDVA 289 K T AYW ++ ++ FE+L KD Q E+ + L A +D+ A Sbjct: 238 QKFCTISNHVWDAYW-----ILGNRRAFEKLPKDIQ--------EIVRRELDKAASDERA 284 Query: 290 VAAVYQ--------KAGAKVVDLNAATVKKWQDIARATAWKDFGAR 327 A + G ++V+ + + K + +ARA +KD A+ Sbjct: 285 DIAAFSGFARNDLASKGLQIVEADKDSFK--EALARANFYKDMRAK 328 >gi|300313112|ref|YP_003777204.1| TRAP-type C4-dicarboxylate transport system periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 344 Score = 63.9 bits (154), Expect = 2e-11, Method: Compositional matrix adjust. Identities = 59/214 (27%), Positives = 98/214 (45%), Gaps = 13/214 (6%) Query: 59 AEGVTKRTNGSLKFEIYPGSSLMKVNAQFSAMRKGALD-LSLVPLNYAGGEVPETNIGLM 117 A + +++ G ++ ++YP + L S +R GA+D +L PL G VP I + Sbjct: 60 AAAIAEQSKGRIELQLYPNNQLGTDTDMLSQVRAGAIDFFTLSPL-ILGTLVPAAQISGI 118 Query: 118 PGLVTSYAQGSAWKNAEVGKELAR-ILAEKGILIVSWIWQAG--GVASRTKPIINPEDAK 174 Y+Q + E+G + + I A + IW G + + TKPI ED K Sbjct: 119 GFAFKDYSQVWPAMDGELGAHVRKQIEARSTLFAFEKIWDNGYRQITNSTKPIKVAEDLK 178 Query: 175 GMKVRGGSREM-DLILKEAGAAVVTLPSNEIYAAMQTGAMDAAMTSSTSFISFRLEEVAK 233 GMK+R + + K AA ++ E+Y+A+QT ++ + +L EV K Sbjct: 179 GMKLRVPPSPLWTSMFKAFDAAPTSINFAEVYSALQTKIVEGQENPMAIISTAKLYEVQK 238 Query: 234 --ALTTGRDKAYWYMFEPLMISKAVFERLTKDQQ 265 ++T +W+ + +K FERL KD Q Sbjct: 239 YCSITNHMWDGFWF-----LGNKKSFERLPKDLQ 267 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 0.129 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: 1,038,680 Number of extensions: 42566 Number of successful extensions: 150 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 143 Number of HSP's successfully gapped: 6 Length of query: 342 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 256 Effective length of database: 1,212,660 Effective search space: 310440960 Effective search space used: 310440960 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)