GapMind for catabolism of small carbon sources

 

Definition of D-lactate catabolism

As rules and steps, or see full text

Rules

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

Steps

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

larD: D,L-lactic acid transporter

mctP: D,L-lactic acid transporter

PGA1_c12640: D-lactate ABC transporter, ATP-binding component

PGA1_c12650: D-lactate ABC transporter, permease component 1

PGA1_c12660: D-lactate ABC transporter, permease component 2

PGA1_c12670: D-lactate ABC transporter, substrate-binding component

D-LDH: D-lactate dehydrogenase

lctB: electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit

lctC: electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit

lctD: D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component

glcD: D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD)

glcE: D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE)

glcF: D-lactate dehydrogenase, FeS subunit GlcF

Links

Downloads

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