GapMind for catabolism of small carbon sources

 

propionate catabolism in Pseudomonas litoralis 2SM5

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 (15 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
putP propionate transporter; proline:Na+ symporter BLU11_RS15570
prpE propionyl-CoA synthetase BLU11_RS00320 BLU11_RS01910
prpC 2-methylcitrate synthase BLU11_RS05820 BLU11_RS04740
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) BLU11_RS05825 BLU11_RS05430
prpF methylaconitate isomerase BLU11_RS05830
acn (2R,3S)-2-methylcitrate dehydratase BLU11_RS05825 BLU11_RS08620
prpB 2-methylisocitrate lyase BLU11_RS05815
Alternative steps:
dddA 3-hydroxypropionate dehydrogenase BLU11_RS15245
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase BLU11_RS15435 BLU11_RS12290
iolA malonate semialdehyde dehydrogenase (CoA-acylating) BLU11_RS18585 BLU11_RS12285
lctP propionate permease
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
mctC propionate:H+ symporter
mctP propionate permease
pccA propionyl-CoA carboxylase, alpha subunit BLU11_RS15495 BLU11_RS15720
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit BLU11_RS16535 BLU11_RS02630
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit BLU11_RS10715
pccB propionyl-CoA carboxylase, beta subunit BLU11_RS15485 BLU11_RS15710
pco propanyl-CoA oxidase BLU11_RS13665
prpD 2-methylcitrate dehydratase
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.

Links

Downloads

Related tools

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