GapMind for catabolism of small carbon sources


propionate catabolism in Oceanisphaera arctica V1-41

Best path

lctP, prpE, prpC, prpD, acn, prpB


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 (15 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lctP propionate permease UN63_RS04455
prpE propionyl-CoA synthetase UN63_RS07990 UN63_RS15435
prpC 2-methylcitrate synthase UN63_RS01195 UN63_RS07100
prpD 2-methylcitrate dehydratase
acn (2R,3S)-2-methylcitrate dehydratase UN63_RS13445 UN63_RS09715
prpB 2-methylisocitrate lyase UN63_RS01190
Alternative steps:
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) UN63_RS09715
dddA 3-hydroxypropionate dehydrogenase UN63_RS03420
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase UN63_RS10750 UN63_RS10745
iolA malonate semialdehyde dehydrogenase (CoA-acylating) UN63_RS16535 UN63_RS08995
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit UN63_RS11590
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
mctC propionate:H+ symporter
mctP propionate permease
pccA propionyl-CoA carboxylase, alpha subunit UN63_RS13355 UN63_RS08005
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit UN63_RS08005 UN63_RS13355
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit UN63_RS08790
pccB propionyl-CoA carboxylase, beta subunit UN63_RS13345
pco propanyl-CoA oxidase
prpF methylaconitate isomerase
putP propionate transporter; proline:Na+ symporter UN63_RS01690 UN63_RS07560
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 24 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:

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