GapMind for catabolism of small carbon sources


Definition of propionate catabolism

As rules and steps, or see full text


Overview: Propionate degradation in GapMind is based on MetaCyc pathways for the 2-methylcitrate cycle (link, link) and for propanoyl-CoA degradation (link, link).


putP: propionate transporter; proline:Na+ symporter

SLC5A8: sodium-coupled monocarboxylate transporter

lctP: propionate permease

mctC: propionate:H+ symporter

mctP: propionate permease

pccA: propionyl-CoA carboxylase, alpha subunit

pccB: propionyl-CoA carboxylase, beta subunit

pccA1: propionyl-CoA carboxylase, biotin carboxyl carrier subunit

pccA2: propionyl-CoA carboxylase, biotin carboxylase subunit

prpE: propionyl-CoA synthetase

prpC: 2-methylcitrate synthase

prpD: 2-methylcitrate dehydratase

acn: (2R,3S)-2-methylcitrate dehydratase

prpB: 2-methylisocitrate lyase

acnD: 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)

prpF: methylaconitate isomerase

epi: methylmalonyl-CoA epimerase

mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components

mcm-large: methylmalonyl-CoA mutase, large (catalytic) subunit

mcm-small: methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit

pco: propanyl-CoA oxidase

hpcD: 3-hydroxypropionyl-CoA dehydratase

dddA: 3-hydroxypropionate dehydrogenase

iolA: malonate semialdehyde dehydrogenase (CoA-acylating)



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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