GapMind for catabolism of small carbon sources


propionate catabolism in Phaeobacter inhibens BS107

Best path

putP, prpE, pccA, pccB, epi, mcm-large, mcm-small

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 (15 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
putP propionate transporter; proline:Na+ symporter
prpE propionyl-CoA synthetase PGA1_c11900 PGA1_c12950
pccA propionyl-CoA carboxylase, alpha subunit PGA1_c21540 PGA1_c10330
pccB propionyl-CoA carboxylase, beta subunit PGA1_c21600 PGA1_c10320
epi methylmalonyl-CoA epimerase PGA1_c24490
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit PGA1_c21510 PGA1_c03840
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit PGA1_c21510 PGA1_c03840
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase PGA1_c18830
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) PGA1_c18830
dddA 3-hydroxypropionate dehydrogenase PGA1_c30400 PGA1_c21660
hpcD 3-hydroxypropionyl-CoA dehydratase PGA1_c36500 PGA1_262p01980
iolA malonate semialdehyde dehydrogenase (CoA-acylating) PGA1_c17300 PGA1_c21670
lctP propionate permease
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components PGA1_c21510 PGA1_c03840
mctC propionate:H+ symporter
mctP propionate permease
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit PGA1_c21540 PGA1_c12600
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase PGA1_c15710
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase PGA1_c28860 PGA1_c16970
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase
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