GapMind for catabolism of small carbon sources

 

propionate catabolism in Pseudomonas fluorescens FW300-N2E2

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 (16 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
putP propionate transporter; proline:Na+ symporter Pf6N2E2_3684
prpE propionyl-CoA synthetase Pf6N2E2_5659 Pf6N2E2_5149
prpC 2-methylcitrate synthase Pf6N2E2_6062 Pf6N2E2_5850
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) Pf6N2E2_6063 Pf6N2E2_2301
prpF methylaconitate isomerase Pf6N2E2_6064
acn (2R,3S)-2-methylcitrate dehydratase Pf6N2E2_6063 Pf6N2E2_564
prpB 2-methylisocitrate lyase Pf6N2E2_6061 Pf6N2E2_279
Alternative steps:
dddA 3-hydroxypropionate dehydrogenase Pf6N2E2_2094 Pf6N2E2_4677
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase Pf6N2E2_1147 Pf6N2E2_1934
iolA malonate semialdehyde dehydrogenase (CoA-acylating) Pf6N2E2_515 Pf6N2E2_3462
lctP propionate permease Pf6N2E2_3380 Pf6N2E2_329
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 Pf6N2E2_5849
mctP propionate permease
pccA propionyl-CoA carboxylase, alpha subunit Pf6N2E2_2194 Pf6N2E2_2411
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit Pf6N2E2_4278 Pf6N2E2_3512
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit Pf6N2E2_2192 Pf6N2E2_2409
pco propanyl-CoA oxidase Pf6N2E2_4036 Pf6N2E2_1146
prpD 2-methylcitrate dehydratase
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