GapMind for catabolism of small carbon sources

 

L-lactate catabolism in Cupriavidus basilensis 4G11

Best path

lctP, lutA, lutB, lutC

Also see fitness data for the top candidates

Rules

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

19 steps (13 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lctP L-lactate:H+ symporter LctP or LidP RR42_RS21280 RR42_RS14610
lutA L-lactate dehydrogenase, LutA subunit RR42_RS21295 RR42_RS07430
lutB L-lactate dehydrogenase, LutB subunit RR42_RS21285 RR42_RS07435
lutC L-lactate dehydrogenase, LutC subunit RR42_RS21290 RR42_RS14200
Alternative steps:
ackA acetate kinase RR42_RS03800 RR42_RS22745
acs acetyl-CoA synthetase, AMP-forming RR42_RS13880 RR42_RS10650
DVU3032 L-lactate dehydrogenase, LutC-like component RR42_RS14200
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components RR42_RS07435 RR42_RS21285
L-LDH L-lactate dehydrogenase RR42_RS03780 RR42_RS29130
larD D,L-lactic acid transporter LarD
lctO L-lactate oxidase or 2-monooxygenase
lldE L-lactate dehydrogenase, LldE subunit RR42_RS07430 RR42_RS21295
lldF L-lactate dehydrogenase, LldF subunit RR42_RS21285 RR42_RS07435
lldG L-lactate dehydrogenase, LldG subunit
mctP D,L-lactic acid transporter MctP
pta phosphate acetyltransferase RR42_RS33690 RR42_RS03805
SfMCT L-lactate transporter SfMCT
Shew_2731 L-lactate:Na+ symporter, large component RR42_RS13875
Shew_2732 L-lactate:Na+ symporter, small 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.

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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