GapMind for catabolism of small carbon sources


L-lactate catabolism in Burkholderia phytofirmans PsJN

Best path

mctP, lldE, lldF, lldG

Also see fitness data for the top candidates


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

19 steps (18 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
mctP D,L-lactic acid transporter MctP BPHYT_RS22245 BPHYT_RS06030
lldE L-lactate dehydrogenase, LldE subunit BPHYT_RS26975 BPHYT_RS12810
lldF L-lactate dehydrogenase, LldF subunit BPHYT_RS26970 BPHYT_RS12805
lldG L-lactate dehydrogenase, LldG subunit BPHYT_RS26965
Alternative steps:
ackA acetate kinase BPHYT_RS06125 BPHYT_RS26200
acs acetyl-CoA synthetase, AMP-forming BPHYT_RS07000 BPHYT_RS27780
DVU3032 L-lactate dehydrogenase, LutC-like component BPHYT_RS14530
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components BPHYT_RS12805 BPHYT_RS26970
L-LDH L-lactate dehydrogenase BPHYT_RS31690 BPHYT_RS27110
larD D,L-lactic acid transporter LarD BPHYT_RS16500
lctO L-lactate oxidase or 2-monooxygenase BPHYT_RS31690
lctP L-lactate:H+ symporter LctP or LidP BPHYT_RS13235
lutA L-lactate dehydrogenase, LutA subunit BPHYT_RS12810 BPHYT_RS26975
lutB L-lactate dehydrogenase, LutB subunit BPHYT_RS12805 BPHYT_RS26970
lutC L-lactate dehydrogenase, LutC subunit BPHYT_RS14530
pta phosphate acetyltransferase BPHYT_RS21700 BPHYT_RS27695
SfMCT L-lactate transporter SfMCT
Shew_2731 L-lactate:Na+ symporter, large component BPHYT_RS07010 BPHYT_RS25605
Shew_2732 L-lactate:Na+ symporter, small component BPHYT_RS07005

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