GapMind for catabolism of small carbon sources


propionate catabolism in Magnetospirillum magneticum AMB-1

Best path

lctP, prpE, pccA, pccB, epi, mcm-large, mcm-small


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 AMB_RS20875
prpE propionyl-CoA synthetase AMB_RS21140 AMB_RS11645
pccA propionyl-CoA carboxylase, alpha subunit AMB_RS21445 AMB_RS03465
pccB propionyl-CoA carboxylase, beta subunit AMB_RS21450 AMB_RS03475
epi methylmalonyl-CoA epimerase AMB_RS12960
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit AMB_RS01570
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit AMB_RS01570
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase AMB_RS22255 AMB_RS18485
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) AMB_RS18485
dddA 3-hydroxypropionate dehydrogenase
hpcD 3-hydroxypropionyl-CoA dehydratase AMB_RS03265 AMB_RS13040
iolA malonate semialdehyde dehydrogenase (CoA-acylating) AMB_RS04115 AMB_RS06710
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components AMB_RS01570
mctC propionate:H+ symporter AMB_RS13215 AMB_RS07815
mctP propionate permease
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit AMB_RS21445 AMB_RS13620
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase AMB_RS16315 AMB_RS03480
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase AMB_RS14105
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase AMB_RS01270
putP propionate transporter; proline:Na+ symporter
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:

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