GapMind for catabolism of small carbon sources

 

propionate catabolism in Pseudomonas stutzeri RCH2

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 (17 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lctP propionate permease Psest_3836 Psest_0955
prpE propionyl-CoA synthetase Psest_2657 Psest_2220
prpC 2-methylcitrate synthase Psest_2320 Psest_2499
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) Psest_2319 Psest_2521
prpF methylaconitate isomerase Psest_2318
acn (2R,3S)-2-methylcitrate dehydratase Psest_2319 Psest_2309
prpB 2-methylisocitrate lyase Psest_2321 Psest_2567
Alternative steps:
dddA 3-hydroxypropionate dehydrogenase Psest_2633
epi methylmalonyl-CoA epimerase Psest_4071
hpcD 3-hydroxypropionyl-CoA dehydratase Psest_2437 Psest_3109
iolA malonate semialdehyde dehydrogenase (CoA-acylating) Psest_2436 Psest_3781
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 Psest_2938 Psest_0347
mctP propionate permease
pccA propionyl-CoA carboxylase, alpha subunit Psest_1080 Psest_1019
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit Psest_4085 Psest_1019
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit Psest_1083
pco propanyl-CoA oxidase Psest_3830
prpD 2-methylcitrate dehydratase
putP propionate transporter; proline:Na+ symporter Psest_3075 Psest_3078
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.

Links

Downloads

Related tools

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