GapMind for catabolism of small carbon sources


propionate catabolism in Klebsiella michiganensis M5al

Best path

putP, prpE, prpC, acnD, prpF, acn, prpB

Also see fitness data for the top candidates


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 BWI76_RS10800
prpE propionyl-CoA synthetase BWI76_RS02095
prpC 2-methylcitrate synthase BWI76_RS08385 BWI76_RS19140
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) BWI76_RS11940
prpF methylaconitate isomerase BWI76_RS04370 BWI76_RS14180
acn (2R,3S)-2-methylcitrate dehydratase BWI76_RS04910 BWI76_RS11940
prpB 2-methylisocitrate lyase BWI76_RS01665
Alternative steps:
dddA 3-hydroxypropionate dehydrogenase BWI76_RS07610
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase BWI76_RS13115 BWI76_RS13120
iolA malonate semialdehyde dehydrogenase (CoA-acylating) BWI76_RS03070 BWI76_RS02840
lctP propionate permease BWI76_RS27185
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit BWI76_RS23935
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit BWI76_RS23935
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components BWI76_RS23935
mctC propionate:H+ symporter BWI76_RS02085
mctP propionate permease
pccA propionyl-CoA carboxylase, alpha subunit BWI76_RS25540 BWI76_RS13985
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit BWI76_RS25540 BWI76_RS13985
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit
pco propanyl-CoA oxidase
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.



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 (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 paper from 2022 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