GapMind for catabolism of small carbon sources


propionate catabolism in Cupriavidus basilensis 4G11

Best path

lctP, prpE, prpC, acnD, prpF, acn, prpB

Also see fitness data for the top candidates


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

24 steps (19 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lctP propionate permease RR42_RS21280 RR42_RS14610
prpE propionyl-CoA synthetase RR42_RS13880 RR42_RS13560
prpC 2-methylcitrate synthase RR42_RS11265 RR42_RS14475
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) RR42_RS11270 RR42_RS14490
prpF methylaconitate isomerase RR42_RS11275 RR42_RS23050
acn (2R,3S)-2-methylcitrate dehydratase RR42_RS11270 RR42_RS23515
prpB 2-methylisocitrate lyase RR42_RS12200 RR42_RS11260
Alternative steps:
dddA 3-hydroxypropionate dehydrogenase RR42_RS20290 RR42_RS29710
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase RR42_RS23710 RR42_RS18250
iolA malonate semialdehyde dehydrogenase (CoA-acylating) RR42_RS01580 RR42_RS34225
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit RR42_RS01600
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components RR42_RS01600
mctC propionate:H+ symporter RR42_RS06400
mctP propionate permease
pccA propionyl-CoA carboxylase, alpha subunit RR42_RS26895 RR42_RS32735
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit RR42_RS17700 RR42_RS29420
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit RR42_RS26895
pccB propionyl-CoA carboxylase, beta subunit RR42_RS26905 RR42_RS29410
pco propanyl-CoA oxidase RR42_RS08770 RR42_RS15400
prpD 2-methylcitrate dehydratase RR42_RS14485
putP propionate transporter; proline:Na+ symporter
SLC5A8 sodium-coupled monocarboxylate transporter

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.



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 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