D-lactate catabolism in Bradyrhizobium diazoefficiens USDA110

GapMind for catabolism of small carbon sources

D-lactate catabolism in Bradyrhizobium diazoefficiens USDA110

Best path

lctP, glcD, glcE, glcF

Rules

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

all: D-lactate-transport and D-lactate-dehydrogenase
D-lactate-dehydrogenase:

D-LDH
or lctB, lctC and lctD
or glcD, glcE and glcF
Comment: Acetobacterium woodii uses an electron-bifurcating dehydrogenase (lctBCD) for growth on lactate. The Km for D-lactate is far below that for L-lactate (Km of 3.6 mM vs. 112 mM; PMID:24762045), so we consider it to be a D-lactate dehydrogenase. GlcDEF from E. coli (EC 1.1.99.14) is usually described as glycolate dehydrogenase or glycolate oxidase, but it has similar activity on D-lactate (PMID:4557653), and homologs from various Proteobacteria are important for D-lactate utilization. The physiological electron acceptor is not known, so terming GlcDEF an oxidase is questionable.

D-lactate-transport:

lctP
or larD
or mctP
or PGA1_c12640, PGA1_c12650, PGA1_c12660 and PGA1_c12670
Comment: Transporters were identified using query: transporter:D-lactate:(R)-lactate:D,L-lactic

14 steps (12 with candidates)

Or see definitions of steps

Step	Description	Best candidate	2nd candidate
lctP	D-lactate:H+ symporter LctP or LidP	BJA_RS38220
glcD	D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD)	BJA_RS38255	BJA_RS13255
glcE	D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE)	BJA_RS38245	BJA_RS40465
glcF	D-lactate dehydrogenase, FeS subunit GlcF	BJA_RS38240
Alternative steps:
D-LDH	D-lactate dehydrogenase	BJA_RS13255	BJA_RS33220
larD	D,L-lactic acid transporter
lctB	electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit	BJA_RS10005
lctC	electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit	BJA_RS08930	BJA_RS07015
lctD	D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component	BJA_RS38255	BJA_RS12655
mctP	D,L-lactic acid transporter	BJA_RS29815
PGA1_c12640	D-lactate ABC transporter, ATP-binding component	BJA_RS15815	BJA_RS05340
PGA1_c12650	D-lactate ABC transporter, permease component 1	BJA_RS20035	BJA_RS15810
PGA1_c12660	D-lactate ABC transporter, permease component 2	BJA_RS04485	BJA_RS07415
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 24 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