GapMind for catabolism of small carbon sources

 

L-lactate catabolism in Magnetospirillum magneticum AMB-1

Best path

lctP, lutA, lutB, lutC

Rules

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

19 steps (14 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lctP L-lactate:H+ symporter LctP or LidP AMB_RS20875
lutA L-lactate dehydrogenase, LutA subunit AMB_RS20885
lutB L-lactate dehydrogenase, LutB subunit AMB_RS20890
lutC L-lactate dehydrogenase, LutC subunit AMB_RS20895
Alternative steps:
ackA acetate kinase AMB_RS12860
acs acetyl-CoA synthetase, AMP-forming AMB_RS21140 AMB_RS11645
DVU3032 L-lactate dehydrogenase, LutC-like component AMB_RS20895
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components AMB_RS20890
L-LDH L-lactate dehydrogenase AMB_RS20025 AMB_RS22540
larD D,L-lactic acid transporter LarD
lctO L-lactate oxidase or 2-monooxygenase AMB_RS22540
lldE L-lactate dehydrogenase, LldE subunit AMB_RS20885
lldF L-lactate dehydrogenase, LldF subunit AMB_RS20890
lldG L-lactate dehydrogenase, LldG subunit
mctP D,L-lactic acid transporter MctP
pta phosphate acetyltransferase AMB_RS12865 AMB_RS01465
SfMCT L-lactate transporter SfMCT
Shew_2731 L-lactate:Na+ symporter, large component AMB_RS21920 AMB_RS13215
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 (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 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