GapMind for catabolism of small carbon sources

 

L-lactate catabolism in Desulfovibrio vulgaris Hildenborough

Best path

lctP, lutA, lutB, lutC

Rules

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

19 steps (15 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lctP L-lactate:H+ symporter LctP or LidP DVU3284 DVU2110
lutA L-lactate dehydrogenase, LutA subunit DVU1783 DVU3033
lutB L-lactate dehydrogenase, LutB subunit DVU1782 DVU3033
lutC L-lactate dehydrogenase, LutC subunit DVU1781 DVU3032
Alternative steps:
ackA acetate kinase DVU0723 DVU3030
acs acetyl-CoA synthetase, AMP-forming DVU2969 DVU0748
DVU3032 L-lactate dehydrogenase, LutC-like component DVU3032 DVU1781
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components DVU3033 DVU1782
L-LDH L-lactate dehydrogenase DVU0600
larD D,L-lactic acid transporter LarD DVU3133
lctO L-lactate oxidase or 2-monooxygenase
lldE L-lactate dehydrogenase, LldE subunit DVU1783 DVU3033
lldF L-lactate dehydrogenase, LldF subunit DVU1782 DVU3033
lldG L-lactate dehydrogenase, LldG subunit DVU3032
mctP D,L-lactic acid transporter MctP
pta phosphate acetyltransferase DVU3029 DVU0627
SfMCT L-lactate transporter SfMCT DVU1163
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 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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