GapMind for catabolism of small carbon sources

 

propionate catabolism in Saccharomonospora cyanea NA-134

Best path

lctP, 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 (19 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lctP propionate permease SACCYDRAFT_RS21830
prpE propionyl-CoA synthetase SACCYDRAFT_RS21150 SACCYDRAFT_RS23100
pccA propionyl-CoA carboxylase, alpha subunit SACCYDRAFT_RS03395 SACCYDRAFT_RS19840
pccB propionyl-CoA carboxylase, beta subunit SACCYDRAFT_RS03415 SACCYDRAFT_RS19845
epi methylmalonyl-CoA epimerase SACCYDRAFT_RS18435
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit SACCYDRAFT_RS03315 SACCYDRAFT_RS16070
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit SACCYDRAFT_RS03315
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase SACCYDRAFT_RS14425
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) SACCYDRAFT_RS14425
dddA 3-hydroxypropionate dehydrogenase SACCYDRAFT_RS20575 SACCYDRAFT_RS15820
hpcD 3-hydroxypropionyl-CoA dehydratase SACCYDRAFT_RS18310 SACCYDRAFT_RS03705
iolA malonate semialdehyde dehydrogenase (CoA-acylating) SACCYDRAFT_RS20580 SACCYDRAFT_RS15225
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components SACCYDRAFT_RS03315 SACCYDRAFT_RS16070
mctC propionate:H+ symporter SACCYDRAFT_RS07000
mctP propionate permease
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit SACCYDRAFT_RS03395 SACCYDRAFT_RS19840
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit SACCYDRAFT_RS19840
pco propanyl-CoA oxidase SACCYDRAFT_RS20625 SACCYDRAFT_RS04895
prpB 2-methylisocitrate lyase SACCYDRAFT_RS18195 SACCYDRAFT_RS18415
prpC 2-methylcitrate synthase SACCYDRAFT_RS21740 SACCYDRAFT_RS21820
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 Apr 09 2024. 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