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:

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