Align The dicarboxylate (succinate, fumarate, malate and oxaloacetate):H+ symporter, DctA (probably 3H+ are transported per succinate taken up (characterized)
to candidate 200106 SO0922 proton/glutamate symporter (NCBI ptt file)
Query= TCDB::P96603 (421 letters) >FitnessBrowser__MR1:200106 Length = 424 Score = 273 bits (698), Expect = 7e-78 Identities = 136/399 (34%), Positives = 240/399 (60%), Gaps = 9/399 (2%) Query: 7 LTVQVITAVIIGVIVGLVWPDVGKEMKPLGDTFINAVKMVIAPIIFFTIVLGIAKMGDMK 66 L +Q+ +++G++VG+ + +KP+G F+N +KM+I P++F ++++G+ M D Sbjct: 5 LWLQIFVGMVLGILVGVTLGEQASYLKPIGTLFVNTIKMLIVPLVFCSLIVGVTSMEDTA 64 Query: 67 KVGKVGGKAFIYFEVVTTLALIIGLFVVNIMKPGAGLDYSKLEKGDVSQYTQNGGQGIDW 126 K+G++G K+F ++ T +A+ +GL V +++PGAG+ + E + ++ + Sbjct: 65 KMGRIGFKSFSFYLCTTAIAISLGLVVGYVIQPGAGVPLLQHEAVNTAKEVPSV------ 118 Query: 127 IEFITHIVPSNMVDAFAKGDILQVLFFSILFGVGLAALGEKGKSVIDFFDKVSHVFFKII 186 ++ + IVP+N V A A G ILQV+ F++ G+ L +G+ GK I F+ ++ +K+ Sbjct: 119 MQTLIDIVPTNPVAALASGQILQVIVFAVALGIALVLIGDHGKPAIKVFESLAEAMYKLT 178 Query: 187 GYIMRAAPIGAFGAMAYTIGHFGLDSIKPLASLMMSVYITMFLFVFVALNIICKLYG-FS 245 +M+ AP G FG MA+ G +G+D + PL ++++VYI + V +I+ +L+ + Sbjct: 179 DMVMKLAPYGVFGLMAWVAGEYGIDMLWPLIKVIIAVYIGCIIHVLGFYSIVLRLFAKLN 238 Query: 246 LWNYLRFIKDELLIVLGTSSSESVLPRMMDKMERY-GCSKSVVGLVIPTGYSFNLDGTSI 304 ++ + I + + + TSSS LP M Y G +K + V+P G + N+DGT++ Sbjct: 239 PLHFFKGISNAMAVAFTTSSSAGTLPASMKCASEYLGVNKKISSFVLPLGTTINMDGTAL 298 Query: 305 YLSMATVFLAQVFGVDLSIGQQITIILVLMLTSKGAAGVTGSGFIVLASTLSALQVIPLE 364 Y + +F+AQ FG+DL+ +TIIL L S G AGV G+G ++L LS + +PLE Sbjct: 299 YQGVTALFVAQAFGIDLTWVDYLTIILTATLASIGTAGVPGAGLVMLTLVLSTVG-LPLE 357 Query: 365 GLALLLGVDRFMSEGRAIVNLIGNGIATIIVAKSENEFD 403 G+AL+ G+DR + R +VN+ G+ +AT ++AKSENE D Sbjct: 358 GVALIAGIDRILDMARTVVNVSGDLVATTVIAKSENELD 396 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: 444 Number of extensions: 30 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: 424 Length adjustment: 32 Effective length of query: 389 Effective length of database: 392 Effective search space: 152488 Effective search space used: 152488 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: 50 (23.9 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