GapMind for catabolism of small carbon sources

 

L-lactate catabolism in Dinoroseobacter shibae DFL-12

Best path

Shew_2731, Shew_2732, L-LDH

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 (7 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
Shew_2731 L-lactate:Na+ symporter, large component Dshi_3556
Shew_2732 L-lactate:Na+ symporter, small component Dshi_3555
L-LDH L-lactate dehydrogenase Dshi_0948 Dshi_2876
Alternative steps:
ackA acetate kinase Dshi_0632 Dshi_5006
acs acetyl-CoA synthetase, AMP-forming Dshi_3553 Dshi_1399
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components
larD D,L-lactic acid transporter LarD
lctO L-lactate oxidase or 2-monooxygenase Dshi_0948 Dshi_2484
lctP L-lactate:H+ symporter LctP or LidP
lldE L-lactate dehydrogenase, LldE subunit
lldF L-lactate dehydrogenase, LldF subunit
lldG L-lactate dehydrogenase, LldG subunit
lutA L-lactate dehydrogenase, LutA subunit
lutB L-lactate dehydrogenase, LutB subunit
lutC L-lactate dehydrogenase, LutC subunit
mctP D,L-lactic acid transporter MctP
pta phosphate acetyltransferase Dshi_1825 Dshi_0633
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 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, the preprint 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