GapMind for catabolism of small carbon sources

 

propionate catabolism in Belnapia rosea CPCC 100156

Best path

lctP, prpE, prpC, prpD, acn, prpB

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
lctP propionate permease BLR02_RS20815
prpE propionyl-CoA synthetase BLR02_RS09295 BLR02_RS17730
prpC 2-methylcitrate synthase BLR02_RS19010 BLR02_RS05735
prpD 2-methylcitrate dehydratase BLR02_RS19020
acn (2R,3S)-2-methylcitrate dehydratase BLR02_RS06435
prpB 2-methylisocitrate lyase BLR02_RS15615 BLR02_RS04390
Alternative steps:
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) BLR02_RS06435
dddA 3-hydroxypropionate dehydrogenase BLR02_RS18510 BLR02_RS02205
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase BLR02_RS23955 BLR02_RS08090
iolA malonate semialdehyde dehydrogenase (CoA-acylating) BLR02_RS18460 BLR02_RS07320
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
mctP propionate permease
pccA propionyl-CoA carboxylase, alpha subunit BLR02_RS03535 BLR02_RS01010
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit BLR02_RS01010 BLR02_RS23135
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit BLR02_RS03535
pccB propionyl-CoA carboxylase, beta subunit BLR02_RS03530 BLR02_RS23125
pco propanyl-CoA oxidase BLR02_RS06730
prpF methylaconitate isomerase BLR02_RS04850 BLR02_RS20970
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 24 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