GapMind for catabolism of small carbon sources

 

propionate catabolism in Pseudomonas simiae WCS417

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 PS417_02180
prpE propionyl-CoA synthetase PS417_21750 PS417_23925
prpC 2-methylcitrate synthase PS417_21075 PS417_08870
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) PS417_21070 PS417_07515
prpF methylaconitate isomerase PS417_21065 PS417_07225
acn (2R,3S)-2-methylcitrate dehydratase PS417_21070 PS417_14990
prpB 2-methylisocitrate lyase PS417_21080 PS417_16570
Alternative steps:
dddA 3-hydroxypropionate dehydrogenase PS417_10560 PS417_26345
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase PS417_13845 PS417_10680
iolA malonate semialdehyde dehydrogenase (CoA-acylating) PS417_10925 PS417_03250
lctP propionate permease PS417_24105
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 PS417_08865
mctP propionate permease
pccA propionyl-CoA carboxylase, alpha subunit PS417_19595 PS417_17030
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit PS417_28215 PS417_02965
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit PS417_17020 PS417_19580
pco propanyl-CoA oxidase PS417_00580 PS417_13850
prpD 2-methylcitrate dehydratase PS417_21060
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