GapMind for catabolism of small carbon sources

 

propionate catabolism in Pseudomonas fluorescens FW300-N2E3

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 AO353_12815
prpE propionyl-CoA synthetase AO353_03060 AO353_14365
prpC 2-methylcitrate synthase AO353_00895 AO353_01860
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) AO353_00890 AO353_00565
prpF methylaconitate isomerase AO353_00885 AO353_26715
acn (2R,3S)-2-methylcitrate dehydratase AO353_00890 AO353_21605
prpB 2-methylisocitrate lyase AO353_00900 AO353_27735
Alternative steps:
dddA 3-hydroxypropionate dehydrogenase AO353_26740 AO353_07810
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase AO353_25675 AO353_24830
iolA malonate semialdehyde dehydrogenase (CoA-acylating) AO353_21350 AO353_06080
lctP propionate permease AO353_05700 AO353_23340
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 AO353_01865
mctP propionate permease
pccA propionyl-CoA carboxylase, alpha subunit AO353_20335 AO353_19305
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit AO353_10030 AO353_13675
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit AO353_20345 AO353_19320
pco propanyl-CoA oxidase AO353_11100
prpD 2-methylcitrate dehydratase AO353_00880
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