GapMind for catabolism of small carbon sources

 

Definition of glycerol catabolism

As rules and steps, or see full text

Rules

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).

Steps

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)

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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