GapMind for catabolism of small carbon sources


propionate catabolism in Photobacterium jeanii R-40508

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 (16 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lctP propionate permease A3K86_RS04430 A3K86_RS18465
prpE propionyl-CoA synthetase A3K86_RS09595
prpC 2-methylcitrate synthase A3K86_RS02435 A3K86_RS06340
prpD 2-methylcitrate dehydratase A3K86_RS02440
acn (2R,3S)-2-methylcitrate dehydratase A3K86_RS10550
prpB 2-methylisocitrate lyase A3K86_RS11865 A3K86_RS02430
Alternative steps:
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)
dddA 3-hydroxypropionate dehydrogenase A3K86_RS04400
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase A3K86_RS15920 A3K86_RS06710
iolA malonate semialdehyde dehydrogenase (CoA-acylating) A3K86_RS15930 A3K86_RS14375
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit A3K86_RS10020
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
mctC propionate:H+ symporter A3K86_RS09840
mctP propionate permease
pccA propionyl-CoA carboxylase, alpha subunit A3K86_RS09575
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit A3K86_RS09575
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit A3K86_RS07920
pccB propionyl-CoA carboxylase, beta subunit A3K86_RS15950
pco propanyl-CoA oxidase
prpF methylaconitate isomerase
putP propionate transporter; proline:Na+ symporter A3K86_RS18275
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