GapMind for catabolism of small carbon sources


glycerol catabolism in Belnapia rosea CPCC 100156

Best path

glpS, glpT, glpP, glpQ, glpV, glpK, glpD, tpi


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).

25 steps (13 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
glpS glycerol ABC transporter, ATPase component 1 (GlpS) BLR02_RS19245 BLR02_RS22760
glpT glycerol ABC transporter, ATPase component 2 (GlpT) BLR02_RS19240 BLR02_RS07875
glpP glycerol ABC transporter, permease component 1 (GlpP) BLR02_RS19235
glpQ glycerol ABC transporter, permease component 2 (GlpQ) BLR02_RS19230
glpV glycerol ABC transporter, substrate-binding component GlpV BLR02_RS19220
glpK glycerol kinase BLR02_RS19215
glpD glycerol 3-phosphate dehydrogenase (monomeric) BLR02_RS19250
tpi triose-phosphate isomerase BLR02_RS03220 BLR02_RS05985
Alternative steps:
aqp-3 glycerol porter aqp-3
dhaD glycerol dehydrogenase BLR02_RS05380 BLR02_RS04880
dhaK dihydroxyacetone:PEP phosphotransferase, subunit K BLR02_RS05295
dhaK' dihydroxyacetone kinase, ATP dependent (monomeric) BLR02_RS05295
dhaL dihydroxyacetone:PEP phosphotransferase, subunit L BLR02_RS05295
dhaM dihydroxyacetone:PEP phosphotransferase, subunit M
fps1 glycerol uptake/efflux facilitator protein
glpA glycerol 3-phosphate dehydrogenase subunit A
glpB glycerol 3-phosphate dehydrogenase subunit B
glpC glycerol 3-phosphate dehydrogenase subunit C
glpF glycerol facilitator glpF
glpF' glycerol facilitator-aquaporin
glpO glycerol 3-phosphate oxidase BLR02_RS19250
PLT5 glycerol:H+ symporter PLT5
stl1 glycerol:H+ symporter Stl1p
TIPa glycerol facilitator TIPa
YFL054C glycrol facilitator protein

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.



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