GapMind for catabolism of small carbon sources


propionate catabolism in Ruegeria conchae TW15

Best path

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


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
prpE propionyl-CoA synthetase G7G_RS0104455 G7G_RS0105955
pccA propionyl-CoA carboxylase, alpha subunit G7G_RS0113355 G7G_RS0117665
pccB propionyl-CoA carboxylase, beta subunit G7G_RS0113330 G7G_RS0117675
epi methylmalonyl-CoA epimerase G7G_RS0112770
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit G7G_RS0113370 G7G_RS0117980
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit G7G_RS0113370 G7G_RS0117980
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase G7G_RS0113975 G7G_RS0120980
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) G7G_RS0113975
dddA 3-hydroxypropionate dehydrogenase G7G_RS0101190 G7G_RS0113310
hpcD 3-hydroxypropionyl-CoA dehydratase G7G_RS0116465 G7G_RS0122460
iolA malonate semialdehyde dehydrogenase (CoA-acylating) G7G_RS0106675 G7G_RS0111640
lctP propionate permease
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components G7G_RS0113370 G7G_RS0117980
mctC propionate:H+ symporter G7G_RS0105940
mctP propionate permease
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit G7G_RS0113355 G7G_RS0120085
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit G7G_RS0120080
pco propanyl-CoA oxidase G7G_RS0107335 G7G_RS0117695
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase G7G_RS0107985
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 24 2021. The underlying query database was built on Sep 17 2021.



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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