GapMind for catabolism of small carbon sources


Definition of glycerol catabolism

As rules and steps, or see full text


Overview: Glycerol utilization in GapMind is based on MetaCyc pathways glycerol degradation I via glycerol kinase (link), II via dihydroxyacetone kinase (link), or V via dihydroxyacetone:PEP phosphotransferase (link). Two fermentative pathways are not included because they do not lead to carbon incorporation (link, link).


glpS: glycerol ABC transporter, ATPase component 1 (GlpS)

glpT: glycerol ABC transporter, ATPase component 2 (GlpT)

glpP: glycerol ABC transporter, permease component 1 (GlpP)

glpQ: glycerol ABC transporter, permease component 2 (GlpQ)

glpV: glycerol ABC transporter, substrate-binding component GlpV

glpF: glycerol facilitator glpF

aqp-3: glycerol porter aqp-3

stl1: glycerol:H+ symporter Stl1p

glpF': glycerol facilitator-aquaporin

fps1: glycerol uptake/efflux facilitator protein

PLT5: glycerol:H+ symporter PLT5

YFL054C: glycrol facilitator protein

TIPa: glycerol facilitator TIPa

glpK: glycerol kinase

glpD: glycerol 3-phosphate dehydrogenase (monomeric)

glpA: glycerol 3-phosphate dehydrogenase subunit A

glpB: glycerol 3-phosphate dehydrogenase subunit B

glpC: glycerol 3-phosphate dehydrogenase subunit C

glpO: glycerol 3-phosphate oxidase

tpi: triose-phosphate isomerase

dhaD: glycerol dehydrogenase

dhaK: dihydroxyacetone:PEP phosphotransferase, subunit K

dhaL: dihydroxyacetone:PEP phosphotransferase, subunit L

dhaM: dihydroxyacetone:PEP phosphotransferase, subunit M

dhaK': dihydroxyacetone kinase, ATP dependent (monomeric)



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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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