GapMind for catabolism of small carbon sources

 

propionate catabolism in Marinobacter guineae M3B

Best path

putP, prpE, prpC, acnD, prpF, 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 (20 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
putP propionate transporter; proline:Na+ symporter CLH62_RS03100
prpE propionyl-CoA synthetase CLH62_RS16445 CLH62_RS02220
prpC 2-methylcitrate synthase CLH62_RS01920 CLH62_RS18550
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) CLH62_RS01915 CLH62_RS12705
prpF methylaconitate isomerase CLH62_RS01910
acn (2R,3S)-2-methylcitrate dehydratase CLH62_RS01915 CLH62_RS03005
prpB 2-methylisocitrate lyase CLH62_RS01925
Alternative steps:
dddA 3-hydroxypropionate dehydrogenase CLH62_RS05315 CLH62_RS11820
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase CLH62_RS05465 CLH62_RS15970
iolA malonate semialdehyde dehydrogenase (CoA-acylating) CLH62_RS05310 CLH62_RS15980
lctP propionate permease
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit CLH62_RS14370
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit CLH62_RS14385
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components CLH62_RS14370
mctC propionate:H+ symporter CLH62_RS20085
mctP propionate permease
pccA propionyl-CoA carboxylase, alpha subunit CLH62_RS15455 CLH62_RS04865
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit CLH62_RS13790 CLH62_RS04865
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit CLH62_RS06390
pccB propionyl-CoA carboxylase, beta subunit CLH62_RS15445 CLH62_RS04850
pco propanyl-CoA oxidase CLH62_RS10225
prpD 2-methylcitrate dehydratase CLH62_RS01880
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