GapMind for catabolism of small carbon sources


Definition of L-lactate catabolism

As rules and steps, or see full text


Overview: L-lactate degradation in GapMind is based on L-lactate dehydrogenases or oxidases.


lctP: L-lactate:H+ symporter LctP or LidP

SfMCT: L-lactate transporter SfMCT

larD: D,L-lactic acid transporter LarD

mctP: D,L-lactic acid transporter MctP

Shew_2731: L-lactate:Na+ symporter, large component

Shew_2732: L-lactate:Na+ symporter, small component

L-LDH: L-lactate dehydrogenase

lldE: L-lactate dehydrogenase, LldE subunit

lldF: L-lactate dehydrogenase, LldF subunit

lldG: L-lactate dehydrogenase, LldG subunit

lutA: L-lactate dehydrogenase, LutA subunit

lutB: L-lactate dehydrogenase, LutB subunit

lutC: L-lactate dehydrogenase, LutC subunit

DVU3033: L-lactate dehydrogenase, fused LutA/LutB components

DVU3032: L-lactate dehydrogenase, LutC-like component

lctO: L-lactate oxidase or 2-monooxygenase

acs: acetyl-CoA synthetase, AMP-forming

ackA: acetate kinase

pta: phosphate acetyltransferase



Related tools

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