GapMind for catabolism of small carbon sources

 

propionate catabolism in Shewanella loihica PV-4

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 (16 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lctP propionate permease Shew_3135
prpE propionyl-CoA synthetase Shew_1533 Shew_2568
prpC 2-methylcitrate synthase Shew_1821 Shew_1650
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) Shew_1822
prpF methylaconitate isomerase Shew_1823
acn (2R,3S)-2-methylcitrate dehydratase Shew_1822 Shew_3424
prpB 2-methylisocitrate lyase Shew_1276 Shew_1820
Alternative steps:
dddA 3-hydroxypropionate dehydrogenase
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase Shew_2425 Shew_1670
iolA malonate semialdehyde dehydrogenase (CoA-acylating) Shew_0965 Shew_1668
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 Shew_2371
mctP propionate permease
pccA propionyl-CoA carboxylase, alpha subunit Shew_2573 Shew_3365
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit Shew_2573 Shew_3365
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit Shew_1220
pccB propionyl-CoA carboxylase, beta subunit Shew_2571 Shew_2867
pco propanyl-CoA oxidase Shew_0900
prpD 2-methylcitrate dehydratase
putP propionate transporter; proline:Na+ symporter Shew_2435 Shew_3013
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