L-lactate catabolism in Burkholderia phytofirmans PsJN

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

Rules

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

all: L-lactate-transport and L-lactate-degradation
L-lactate-degradation:

L-LDH
or lldE, lldF and lldG
or lutA, lutB and lutC
or DVU3033 and DVU3032
or lctO and acs
or lctO, ackA and pta
Comment: Various L-lactate dehydrogenases are known, with different numbers of subunits; these all form pyruvate. Or, after L-lactate oxidase (lctO) forms acetate, the acetate is activated to acetyl-CoA.

L-lactate-transport:

lctP
or SfMCT
or larD
or mctP
or Shew_2731 and Shew_2732
Comment: Transporters were identified using query: transporter:L-lactate:(S)-lactate:D,L-lactic and prokaryotic lactate transporters were examined as well. Exchangers for lactate/citrate or lactate/malate were ignored.

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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources