GapMind for catabolism of small carbon sources


propionate catabolism in Pseudomonas fluorescens GW456-L13

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 (18 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
putP propionate transporter; proline:Na+ symporter PfGW456L13_221
prpE propionyl-CoA synthetase PfGW456L13_1963 PfGW456L13_1517
prpC 2-methylcitrate synthase PfGW456L13_4117 PfGW456L13_4274
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) PfGW456L13_4116 PfGW456L13_4052
prpF methylaconitate isomerase PfGW456L13_4115
acn (2R,3S)-2-methylcitrate dehydratase PfGW456L13_4116 PfGW456L13_3378
prpB 2-methylisocitrate lyase PfGW456L13_4118 PfGW456L13_2633
Alternative steps:
dddA 3-hydroxypropionate dehydrogenase PfGW456L13_3561 PfGW456L13_1082
epi methylmalonyl-CoA epimerase PfGW456L13_3114 PfGW456L13_1425
hpcD 3-hydroxypropionyl-CoA dehydratase PfGW456L13_3427 PfGW456L13_2984
iolA malonate semialdehyde dehydrogenase (CoA-acylating) PfGW456L13_2 PfGW456L13_5146
lctP propionate permease PfGW456L13_5114
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 PfGW456L13_4275 PfGW456L13_2421
mctP propionate permease
pccA propionyl-CoA carboxylase, alpha subunit PfGW456L13_2284 PfGW456L13_2588
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit PfGW456L13_728 PfGW456L13_52
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit PfGW456L13_2590 PfGW456L13_2287
pco propanyl-CoA oxidase PfGW456L13_554 PfGW456L13_2983
prpD 2-methylcitrate dehydratase PfGW456L13_4114
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:

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