GapMind for catabolism of small carbon sources


D-lactate catabolism in Jannaschia aquimarina GSW-M26

Best path

PGA1_c12640, PGA1_c12650, PGA1_c12660, PGA1_c12670, glcD, glcE, glcF


Overview: D-lactate catabolism in GapMind is based on D-lactate dehydrogenases, which form pyruvate.

14 steps (11 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
PGA1_c12640 D-lactate ABC transporter, ATP-binding component jaqu_RS18390 jaqu_RS07830
PGA1_c12650 D-lactate ABC transporter, permease component 1 jaqu_RS18385 jaqu_RS07825
PGA1_c12660 D-lactate ABC transporter, permease component 2 jaqu_RS18380
PGA1_c12670 D-lactate ABC transporter, substrate-binding component jaqu_RS18375
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) jaqu_RS01930 jaqu_RS14480
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) jaqu_RS01935
glcF D-lactate dehydrogenase, FeS subunit GlcF jaqu_RS01940
Alternative steps:
D-LDH D-lactate dehydrogenase jaqu_RS14480 jaqu_RS04515
larD D,L-lactic acid transporter
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit jaqu_RS01075
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component jaqu_RS01930 jaqu_RS03510
lctP D-lactate:H+ symporter LctP or LidP jaqu_RS04510
mctP D,L-lactic acid transporter

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.



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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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