GapMind for catabolism of small carbon sources

 

L-lactate catabolism in Dokdonella koreensis DS-123

Best path

lctP, lutA, lutB, lutC

Rules

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

19 steps (10 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lctP L-lactate:H+ symporter LctP or LidP
lutA L-lactate dehydrogenase, LutA subunit I596_RS04110
lutB L-lactate dehydrogenase, LutB subunit I596_RS04120
lutC L-lactate dehydrogenase, LutC subunit I596_RS04115
Alternative steps:
ackA acetate kinase I596_RS06530
acs acetyl-CoA synthetase, AMP-forming I596_RS00340 I596_RS03300
DVU3032 L-lactate dehydrogenase, LutC-like component I596_RS04115
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components I596_RS04120
L-LDH L-lactate dehydrogenase
larD D,L-lactic acid transporter LarD
lctO L-lactate oxidase or 2-monooxygenase
lldE L-lactate dehydrogenase, LldE subunit I596_RS04110
lldF L-lactate dehydrogenase, LldF subunit I596_RS04120
lldG L-lactate dehydrogenase, LldG subunit
mctP D,L-lactic acid transporter MctP
pta phosphate acetyltransferase I596_RS13815
SfMCT L-lactate transporter SfMCT
Shew_2731 L-lactate:Na+ symporter, large component
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 24 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 (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:

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