GapMind for catabolism of small carbon sources


propionate catabolism in Azospirillum brasilense Sp245

Best path

lctP, prpE, pccA, pccB, epi, mcm-large, mcm-small

Also see fitness data for the top candidates


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
lctP propionate permease AZOBR_RS25125
prpE propionyl-CoA synthetase AZOBR_RS00270 AZOBR_RS06340
pccA propionyl-CoA carboxylase, alpha subunit AZOBR_RS21105 AZOBR_RS22285
pccB propionyl-CoA carboxylase, beta subunit AZOBR_RS21100 AZOBR_RS22295
epi methylmalonyl-CoA epimerase AZOBR_RS07250
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit AZOBR_RS24250 AZOBR_RS21115
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit AZOBR_RS24250 AZOBR_RS21115
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase AZOBR_RS17090 AZOBR_RS02985
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) AZOBR_RS02985
dddA 3-hydroxypropionate dehydrogenase AZOBR_RS26815
hpcD 3-hydroxypropionyl-CoA dehydratase AZOBR_RS26485 AZOBR_RS01260
iolA malonate semialdehyde dehydrogenase (CoA-acylating) AZOBR_RS22500 AZOBR_RS29750
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components AZOBR_RS24250 AZOBR_RS21115
mctC propionate:H+ symporter AZOBR_RS02940 AZOBR_RS19235
mctP propionate permease
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit AZOBR_RS21105 AZOBR_RS12015
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit AZOBR_RS22285
pco propanyl-CoA oxidase AZOBR_RS19670
prpB 2-methylisocitrate lyase AZOBR_RS02405 AZOBR_RS27820
prpC 2-methylcitrate synthase AZOBR_RS24300 AZOBR_RS25925
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase AZOBR_RS24310 AZOBR_RS28105
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 (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