GapMind for catabolism of small carbon sources

 

L-lactate catabolism in Dechlorosoma suillum PS

Best path

lctP, lctO, acs

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
lctP L-lactate:H+ symporter LctP or LidP
lctO L-lactate oxidase or 2-monooxygenase Dsui_1668
acs acetyl-CoA synthetase, AMP-forming Dsui_2003 Dsui_2187
Alternative steps:
ackA acetate kinase Dsui_1003 Dsui_3033
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components Dsui_1583 Dsui_0126
L-LDH L-lactate dehydrogenase Dsui_1668
larD D,L-lactic acid transporter LarD
lldE L-lactate dehydrogenase, LldE subunit Dsui_1582
lldF L-lactate dehydrogenase, LldF subunit Dsui_0126 Dsui_1583
lldG L-lactate dehydrogenase, LldG subunit
lutA L-lactate dehydrogenase, LutA subunit Dsui_1582
lutB L-lactate dehydrogenase, LutB subunit Dsui_1583 Dsui_0126
lutC L-lactate dehydrogenase, LutC subunit Dsui_0123 Dsui_1584
mctP D,L-lactic acid transporter MctP
pta phosphate acetyltransferase Dsui_3032 Dsui_0130
SfMCT L-lactate transporter SfMCT
Shew_2731 L-lactate:Na+ symporter, large component Dsui_2006 Dsui_0290
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, 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