GapMind for catabolism of small carbon sources

 

propionate catabolism in Knoellia flava TL1

Best path

mctC, 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 (17 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
mctC propionate:H+ symporter N798_RS12935
prpE propionyl-CoA synthetase N798_RS01975 N798_RS12905
pccA propionyl-CoA carboxylase, alpha subunit N798_RS09750 N798_RS16330
pccB propionyl-CoA carboxylase, beta subunit N798_RS09605 N798_RS09655
epi methylmalonyl-CoA epimerase N798_RS16035
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit N798_RS05935 N798_RS15965
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit N798_RS05935 N798_RS15965
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase N798_RS04670
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) N798_RS04670
dddA 3-hydroxypropionate dehydrogenase
hpcD 3-hydroxypropionyl-CoA dehydratase N798_RS14785 N798_RS16580
iolA malonate semialdehyde dehydrogenase (CoA-acylating) N798_RS06805 N798_RS09860
lctP propionate permease N798_RS07055
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components N798_RS05935 N798_RS05435
mctP propionate permease N798_RS06185
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit N798_RS09750 N798_RS16330
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase N798_RS07895 N798_RS03280
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase N798_RS13855 N798_RS06285
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase
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