GapMind for catabolism of small carbon sources

 

propionate catabolism in Dyella japonica UNC79MFTsu3.2

Best path

putP, 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 (17 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
putP propionate transporter; proline:Na+ symporter
prpE propionyl-CoA synthetase N515DRAFT_0016 N515DRAFT_3075
prpC 2-methylcitrate synthase N515DRAFT_0021 N515DRAFT_2064
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) N515DRAFT_0029 N515DRAFT_1419
prpF methylaconitate isomerase N515DRAFT_0030
acn (2R,3S)-2-methylcitrate dehydratase N515DRAFT_0029 N515DRAFT_1420
prpB 2-methylisocitrate lyase N515DRAFT_4123 N515DRAFT_0020
Alternative steps:
dddA 3-hydroxypropionate dehydrogenase N515DRAFT_4337
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase N515DRAFT_1164 N515DRAFT_0416
iolA malonate semialdehyde dehydrogenase (CoA-acylating) N515DRAFT_3729 N515DRAFT_2488
lctP propionate permease
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit N515DRAFT_0973
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit N515DRAFT_0973
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components N515DRAFT_0973
mctC propionate:H+ symporter
mctP propionate permease
pccA propionyl-CoA carboxylase, alpha subunit N515DRAFT_0927 N515DRAFT_3374
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit N515DRAFT_3374 N515DRAFT_0927
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit N515DRAFT_0936
pco propanyl-CoA oxidase N515DRAFT_0484 N515DRAFT_0492
prpD 2-methylcitrate dehydratase N515DRAFT_0031
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, 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