GapMind for catabolism of small carbon sources

 

propionate catabolism in Burkholderia phytofirmans PsJN

Best path

mctC, prpE, prpC, acnD, prpF, acn, prpB

Also see fitness data for the top candidates

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
mctC propionate:H+ symporter BPHYT_RS11800 BPHYT_RS25605
prpE propionyl-CoA synthetase BPHYT_RS07000 BPHYT_RS13830
prpC 2-methylcitrate synthase BPHYT_RS33965 BPHYT_RS30150
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) BPHYT_RS30145 BPHYT_RS33980
prpF methylaconitate isomerase BPHYT_RS30140 BPHYT_RS27420
acn (2R,3S)-2-methylcitrate dehydratase BPHYT_RS30145 BPHYT_RS10160
prpB 2-methylisocitrate lyase BPHYT_RS12285 BPHYT_RS26855
Alternative steps:
dddA 3-hydroxypropionate dehydrogenase BPHYT_RS19495 BPHYT_RS21745
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase BPHYT_RS25360 BPHYT_RS17335
iolA malonate semialdehyde dehydrogenase (CoA-acylating) BPHYT_RS19500 BPHYT_RS28825
lctP propionate permease BPHYT_RS13235
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit BPHYT_RS02085
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit BPHYT_RS02305
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components BPHYT_RS02085
mctP propionate permease BPHYT_RS22245 BPHYT_RS06030
pccA propionyl-CoA carboxylase, alpha subunit BPHYT_RS23275 BPHYT_RS17015
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit BPHYT_RS17015 BPHYT_RS25975
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit BPHYT_RS23265
pco propanyl-CoA oxidase BPHYT_RS11475 BPHYT_RS03780
prpD 2-methylcitrate dehydratase BPHYT_RS33975
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 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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