GapMind for catabolism of small carbon sources


propionate catabolism in Dinoroseobacter shibae DFL-12

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 (16 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
putP propionate transporter; proline:Na+ symporter
prpE propionyl-CoA synthetase Dshi_0825 Dshi_1399
pccA propionyl-CoA carboxylase, alpha subunit Dshi_0723 Dshi_1301
pccB propionyl-CoA carboxylase, beta subunit Dshi_0718 Dshi_1300
epi methylmalonyl-CoA epimerase Dshi_2630
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit Dshi_0726 Dshi_2855
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit Dshi_0726 Dshi_2855
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase Dshi_1851 Dshi_2060
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) Dshi_1851
dddA 3-hydroxypropionate dehydrogenase Dshi_0804 Dshi_1428
hpcD 3-hydroxypropionyl-CoA dehydratase Dshi_3370 Dshi_1048
iolA malonate semialdehyde dehydrogenase (CoA-acylating) Dshi_1747 Dshi_0577
lctP propionate permease
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components Dshi_0726 Dshi_2855
mctC propionate:H+ symporter
mctP propionate permease
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit Dshi_0723 Dshi_1395
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase Dshi_2357 Dshi_1297
prpB 2-methylisocitrate lyase Dshi_0689 Dshi_1092
prpC 2-methylcitrate synthase Dshi_1806
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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