GapMind for catabolism of small carbon sources

 

propionate catabolism in Shewanella oneidensis MR-1

Best path

lctP, prpE, prpC, acnD, prpF, acn, prpB

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 (14 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lctP propionate permease SO0827 SO1522
prpE propionyl-CoA synthetase SO2743
prpC 2-methylcitrate synthase SO0344 SO1926
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) SO0343
prpF methylaconitate isomerase SO0342
acn (2R,3S)-2-methylcitrate dehydratase SO0343 SO0432
prpB 2-methylisocitrate lyase SO0345 SO1484
Alternative steps:
dddA 3-hydroxypropionate dehydrogenase
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase SO1680 SO3088
iolA malonate semialdehyde dehydrogenase (CoA-acylating) SO1678 SO3496
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 SO2857
mctP propionate permease
pccA propionyl-CoA carboxylase, alpha subunit SO1894 SO0840
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit SO1894 SO0840
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit SO1896
pco propanyl-CoA oxidase
prpD 2-methylcitrate dehydratase
putP propionate transporter; proline:Na+ symporter SO3097.4
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 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