GapMind for catabolism of small carbon sources


propionate catabolism in Pseudomonas fluorescens FW300-N1B4

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 Pf1N1B4_1487
prpE propionyl-CoA synthetase Pf1N1B4_3430 Pf1N1B4_2849
prpC 2-methylcitrate synthase Pf1N1B4_3820 Pf1N1B4_3676
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) Pf1N1B4_3821 Pf1N1B4_3888
prpF methylaconitate isomerase Pf1N1B4_3822 Pf1N1B4_4463
acn (2R,3S)-2-methylcitrate dehydratase Pf1N1B4_3821 Pf1N1B4_4564
prpB 2-methylisocitrate lyase Pf1N1B4_3819 Pf1N1B4_4042
Alternative steps:
dddA 3-hydroxypropionate dehydrogenase Pf1N1B4_4450 Pf1N1B4_2416
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase Pf1N1B4_4788 Pf1N1B4_5593
iolA malonate semialdehyde dehydrogenase (CoA-acylating) Pf1N1B4_4277 Pf1N1B4_1238
lctP propionate permease Pf1N1B4_1186 Pf1N1B4_4246
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 Pf1N1B4_3673
mctP propionate permease
pccA propionyl-CoA carboxylase, alpha subunit Pf1N1B4_225 Pf1N1B4_3984
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit Pf1N1B4_2010 Pf1N1B4_1309
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit Pf1N1B4_3986 Pf1N1B4_222
pco propanyl-CoA oxidase Pf1N1B4_1816
prpD 2-methylcitrate dehydratase Pf1N1B4_3823
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