GapMind for catabolism of small carbon sources


D-lactate catabolism in Burkholderia phytofirmans PsJN

Best path

mctP, glcD, glcE, glcF

Also see fitness data for the top candidates


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

14 steps (12 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
mctP D,L-lactic acid transporter BPHYT_RS22245 BPHYT_RS06030
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) BPHYT_RS31645 BPHYT_RS03510
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) BPHYT_RS31650 BPHYT_RS03505
glcF D-lactate dehydrogenase, FeS subunit GlcF BPHYT_RS31655 BPHYT_RS03500
Alternative steps:
D-LDH D-lactate dehydrogenase BPHYT_RS03515 BPHYT_RS03835
larD D,L-lactic acid transporter BPHYT_RS16500
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit BPHYT_RS20830 BPHYT_RS14800
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component BPHYT_RS31645 BPHYT_RS03515
lctP D-lactate:H+ symporter LctP or LidP BPHYT_RS13235
PGA1_c12640 D-lactate ABC transporter, ATP-binding component BPHYT_RS21495 BPHYT_RS15595
PGA1_c12650 D-lactate ABC transporter, permease component 1 BPHYT_RS19470 BPHYT_RS32505
PGA1_c12660 D-lactate ABC transporter, permease component 2 BPHYT_RS21490 BPHYT_RS00695
PGA1_c12670 D-lactate ABC transporter, substrate-binding component

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 17 2021. The underlying query database was built on Sep 17 2021.



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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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