GapMind for catabolism of small carbon sources

 

propionate catabolism in Sedimenticola selenatireducens DSM 17993

Best path

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

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 (16 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
putP propionate transporter; proline:Na+ symporter
prpE propionyl-CoA synthetase A3GO_RS0103965 A3GO_RS0111360
pccA propionyl-CoA carboxylase, alpha subunit A3GO_RS0103980 A3GO_RS0114350
pccB propionyl-CoA carboxylase, beta subunit A3GO_RS0103975 A3GO_RS0114360
epi methylmalonyl-CoA epimerase A3GO_RS0103990 A3GO_RS0105820
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit A3GO_RS0103970 A3GO_RS0114395
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit A3GO_RS0103970
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase A3GO_RS0104620 A3GO_RS0104540
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) A3GO_RS0104540
dddA 3-hydroxypropionate dehydrogenase
hpcD 3-hydroxypropionyl-CoA dehydratase A3GO_RS0114405 A3GO_RS0115400
iolA malonate semialdehyde dehydrogenase (CoA-acylating) A3GO_RS0108930 A3GO_RS0120300
lctP propionate permease
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components A3GO_RS0103970 A3GO_RS0114395
mctC propionate:H+ symporter
mctP propionate permease
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit A3GO_RS0103980 A3GO_RS0119025
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase A3GO_RS0115815 A3GO_RS0114380
prpB 2-methylisocitrate lyase A3GO_RS0109300 A3GO_RS0103960
prpC 2-methylcitrate synthase A3GO_RS0103745 A3GO_RS0101980
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase A3GO_RS0100145
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 Apr 09 2024. 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:

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