GapMind for catabolism of small carbon sources

 

propionate catabolism in Desulfovibrio vulgaris Miyazaki F

Best path

lctP, prpE, pco, hpcD, dddA, iolA

Also see fitness data for the top candidates

Rules

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 (8 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lctP propionate permease DvMF_2129 DvMF_1861
prpE propionyl-CoA synthetase DvMF_1775 DvMF_2783
pco propanyl-CoA oxidase DvMF_0766
hpcD 3-hydroxypropionyl-CoA dehydratase
dddA 3-hydroxypropionate dehydrogenase
iolA malonate semialdehyde dehydrogenase (CoA-acylating) DvMF_2146
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase DvMF_3021
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)
epi methylmalonyl-CoA epimerase
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
mctC propionate:H+ symporter DvMF_0315
mctP propionate permease
pccA propionyl-CoA carboxylase, alpha subunit DvMF_0417 DvMF_0817
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit DvMF_0417 DvMF_0817
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase
putP propionate transporter; proline:Na+ symporter
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.

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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 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