GapMind for catabolism of small carbon sources

 

propionate catabolism in Escherichia coli BW25113

Best path

putP, prpE, prpC, prpD, 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 (18 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
putP propionate transporter; proline:Na+ symporter b1015
prpE propionyl-CoA synthetase b4069 b0335
prpC 2-methylcitrate synthase b0333 b0720
prpD 2-methylcitrate dehydratase b0334
acn (2R,3S)-2-methylcitrate dehydratase b0118 b1276
prpB 2-methylisocitrate lyase b0331 b4015
Alternative steps:
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) b1276
dddA 3-hydroxypropionate dehydrogenase b0311
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase b1393 b2341
iolA malonate semialdehyde dehydrogenase (CoA-acylating) b2661 b0312
lctP propionate permease b2975 b3603
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit b2917
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit b2917 b4019
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components b2917
mctC propionate:H+ symporter b4067
mctP propionate permease
pccA propionyl-CoA carboxylase, alpha subunit b3256
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit b3256
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit
pco propanyl-CoA oxidase
prpF methylaconitate isomerase b0769
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