GapMind for catabolism of small carbon sources

 

propionate catabolism in Dokdonella koreensis DS-123

Best path

putP, 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
putP propionate transporter; proline:Na+ symporter
prpE propionyl-CoA synthetase I596_RS03300 I596_RS00340
prpC 2-methylcitrate synthase I596_RS03335 I596_RS12560
prpD 2-methylcitrate dehydratase I596_RS14135
acn (2R,3S)-2-methylcitrate dehydratase I596_RS07590 I596_RS07575
prpB 2-methylisocitrate lyase I596_RS00395 I596_RS03320
Alternative steps:
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) I596_RS07575
dddA 3-hydroxypropionate dehydrogenase I596_RS04725
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase I596_RS12940 I596_RS04715
iolA malonate semialdehyde dehydrogenase (CoA-acylating) I596_RS04705 I596_RS02225
lctP propionate permease
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit I596_RS05545
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit I596_RS05545
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components I596_RS05545
mctC propionate:H+ symporter
mctP propionate permease
pccA propionyl-CoA carboxylase, alpha subunit I596_RS08895 I596_RS01860
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit I596_RS01860 I596_RS08895
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit I596_RS05360
pco propanyl-CoA oxidase I596_RS15145 I596_RS15670
prpF methylaconitate isomerase
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