Align The dicarboxylate (succinate, fumarate, malate and oxaloacetate):H+ symporter, DctA (probably 3H+ are transported per succinate taken up (characterized)
to candidate 6938665 Sama_2768 proton/glutamate symporter (RefSeq)
Query= TCDB::P96603 (421 letters) >FitnessBrowser__SB2B:6938665 Length = 430 Score = 276 bits (707), Expect = 7e-79 Identities = 145/416 (34%), Positives = 246/416 (59%), Gaps = 9/416 (2%) Query: 7 LTVQVITAVIIGVIVGLVWPDVGKEMKPLGDTFINAVKMVIAPIIFFTIVLGIAKMGDMK 66 L +Q++T +++G+ VGLV +KP+G F+N +KM+I P++F ++++G+ M D Sbjct: 18 LWLQILTGMLLGIGVGLVLGPDASALKPIGTLFVNTIKMLIVPLVFCSLIVGVTSMQDTA 77 Query: 67 KVGKVGGKAFIYFEVVTTLALIIGLFVVNIMKPGAGLDYSKLEKGDVSQYTQNGGQGIDW 126 ++G++G K+F ++ T +A+ +GL V +++PGAGL LE D+S + +D Sbjct: 78 RMGRIGFKSFAFYLATTAIAISVGLMVGWLLEPGAGLS---LEGHDLSAEVKTAPSVMDT 134 Query: 127 IEFITHIVPSNMVDAFAKGDILQVLFFSILFGVGLAALGEKGKSVIDFFDKVSHVFFKII 186 + +IVP+N V A A G ILQV+ F++ GV L +G+ GK I F+ ++ +K+ Sbjct: 135 L---INIVPTNPVAALASGQILQVIVFAVALGVALVLIGDHGKPAIKVFESLAEAMYKLT 191 Query: 187 GYIMRAAPIGAFGAMAYTIGHFGLDSIKPLASLMMSVYITMFLFVFVALNIICKLY-GFS 245 +M+ AP G FG MA+ G +G+D + PL ++++VY+ L + +++ KL G S Sbjct: 192 DMVMKLAPYGVFGLMAWVAGEYGIDMLLPLIKVIIAVYLGCALHILGFYSLVLKLVAGLS 251 Query: 246 LWNYLRFIKDELLIVLGTSSSESVLPRMMDKMERY-GCSKSVVGLVIPTGYSFNLDGTSI 304 + + I + + + TSSS LP M Y G +K + V+P G + N+DGT++ Sbjct: 252 PIQFFKGISNAMAVAFTTSSSAGTLPASMKCASEYLGVNKKISSFVLPLGTTINMDGTAL 311 Query: 305 YLSMATVFLAQVFGVDLSIGQQITIILVLMLTSKGAAGVTGSGFIVLASTLSALQVIPLE 364 Y + +F+AQ FGVDL+ +TI+L L S G AGV G+G ++L L+ + +PLE Sbjct: 312 YQGVTALFVAQAFGVDLTWVDYLTIVLTATLASIGTAGVPGAGLVMLTLVLTTVG-LPLE 370 Query: 365 GLALLLGVDRFMSEGRAIVNLIGNGIATIIVAKSENEFDEAKSIEAVEGMKKMKTA 420 G+A++ G+DR + R +VN+ G+ +AT ++A+SE E D A +E +M A Sbjct: 371 GVAIIAGIDRILDMARTVVNVSGDLVATTVIARSEGEIDIAHYNADMETSSEMAQA 426 Lambda K H 0.326 0.143 0.408 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 451 Number of extensions: 28 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 421 Length of database: 430 Length adjustment: 32 Effective length of query: 389 Effective length of database: 398 Effective search space: 154822 Effective search space used: 154822 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory