GapMind for catabolism of small carbon sources


propionate catabolism in Marinomonas arctica 328

Best path

putP, 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 (17 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
putP propionate transporter; proline:Na+ symporter DK187_RS13450
prpE propionyl-CoA synthetase DK187_RS06350
prpC 2-methylcitrate synthase DK187_RS09225 DK187_RS04785
prpD 2-methylcitrate dehydratase DK187_RS09230
acn (2R,3S)-2-methylcitrate dehydratase DK187_RS10545 DK187_RS13240
prpB 2-methylisocitrate lyase DK187_RS09220 DK187_RS06645
Alternative steps:
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) DK187_RS10545
dddA 3-hydroxypropionate dehydrogenase DK187_RS17925
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase DK187_RS04965 DK187_RS04960
iolA malonate semialdehyde dehydrogenase (CoA-acylating) DK187_RS07670 DK187_RS08870
lctP propionate permease
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit DK187_RS07855
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit DK187_RS07855 DK187_RS12875
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components DK187_RS07855
mctC propionate:H+ symporter DK187_RS05405
mctP propionate permease
pccA propionyl-CoA carboxylase, alpha subunit DK187_RS06470 DK187_RS09690
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit DK187_RS09690 DK187_RS06470
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit
pco propanyl-CoA oxidase
prpF methylaconitate isomerase DK187_RS04090 DK187_RS09720
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