GapMind for catabolism of small carbon sources

 

L-lactate catabolism in Echinicola vietnamensis KMM 6221, DSM 17526

Best path

Shew_2731, Shew_2732, 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.

19 steps (12 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
Shew_2731 L-lactate:Na+ symporter, large component Echvi_1267
Shew_2732 L-lactate:Na+ symporter, small component Echvi_1266
lldE L-lactate dehydrogenase, LldE subunit Echvi_1569
lldF L-lactate dehydrogenase, LldF subunit Echvi_1568
lldG L-lactate dehydrogenase, LldG subunit Echvi_1567
Alternative steps:
ackA acetate kinase
acs acetyl-CoA synthetase, AMP-forming Echvi_1268
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components Echvi_1568
L-LDH L-lactate dehydrogenase Echvi_2076
larD D,L-lactic acid transporter LarD Echvi_1769
lctO L-lactate oxidase or 2-monooxygenase
lctP L-lactate:H+ symporter LctP or LidP
lutA L-lactate dehydrogenase, LutA subunit Echvi_1569
lutB L-lactate dehydrogenase, LutB subunit Echvi_1568
lutC L-lactate dehydrogenase, LutC subunit
mctP D,L-lactic acid transporter MctP
pta phosphate acetyltransferase Echvi_4081
SfMCT L-lactate transporter SfMCT

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 (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