GapMind for catabolism of small carbon sources

 

propionate catabolism in Shewanella sp. ANA-3

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 (14 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lctP propionate permease Shewana3_2904
prpE propionyl-CoA synthetase Shewana3_2523 Shewana3_1675
prpC 2-methylcitrate synthase Shewana3_3826 Shewana3_1705
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) Shewana3_3827
prpF methylaconitate isomerase Shewana3_3828
acn (2R,3S)-2-methylcitrate dehydratase Shewana3_3827 Shewana3_0433
prpB 2-methylisocitrate lyase Shewana3_3825 Shewana3_2942
Alternative steps:
dddA 3-hydroxypropionate dehydrogenase
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase Shewana3_2768 Shewana3_1461
iolA malonate semialdehyde dehydrogenase (CoA-acylating) Shewana3_3107 Shewana3_2770
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 Shewana3_1575
mctP propionate permease
pccA propionyl-CoA carboxylase, alpha subunit Shewana3_1669 Shewana3_3438
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit Shewana3_1669 Shewana3_3438
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit Shewana3_1671
pco propanyl-CoA oxidase
prpD 2-methylcitrate dehydratase
putP propionate transporter; proline:Na+ symporter Shewana3_1451 Shewana3_4055
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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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