GapMind for catabolism of small carbon sources

 

propionate catabolism in Sinorhizobium meliloti 1021

Best path

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

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 (18 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
putP propionate transporter; proline:Na+ symporter
prpE propionyl-CoA synthetase SMc04093 SMc04095
pccA propionyl-CoA carboxylase, alpha subunit SM_b20756 SM_b21124
pccB propionyl-CoA carboxylase, beta subunit SM_b20755 SM_b21122
epi methylmalonyl-CoA epimerase SMc01930
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit SM_b20757
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit SM_b20757
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase SMc03846
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) SMc03846
dddA 3-hydroxypropionate dehydrogenase SMc03116 SM_b20496
hpcD 3-hydroxypropionyl-CoA dehydratase SMc01153 SMc04398
iolA malonate semialdehyde dehydrogenase (CoA-acylating) SMc00781 SM_b20891
lctP propionate permease
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components SM_b20757
mctC propionate:H+ symporter
mctP propionate permease
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit SM_b20756 SMc01345
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit SMc03895
pco propanyl-CoA oxidase SM_b21181 SM_b21121
prpB 2-methylisocitrate lyase SMc00768
prpC 2-methylcitrate synthase SMc02087
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase SMc00497
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.

Links

Downloads

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 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