GapMind for catabolism of small carbon sources


glycerol catabolism in Paraburkholderia bryophila 376MFSha3.1

Best path

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

Also see fitness data for the top candidates


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 (17 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
glpS glycerol ABC transporter, ATPase component 1 (GlpS) H281DRAFT_03734 H281DRAFT_01451
glpT glycerol ABC transporter, ATPase component 2 (GlpT) H281DRAFT_03733 H281DRAFT_05701
glpP glycerol ABC transporter, permease component 1 (GlpP) H281DRAFT_03732 H281DRAFT_05891
glpQ glycerol ABC transporter, permease component 2 (GlpQ) H281DRAFT_03731 H281DRAFT_05890
glpV glycerol ABC transporter, substrate-binding component GlpV H281DRAFT_03729
glpK glycerol kinase H281DRAFT_04229 H281DRAFT_04146
glpD glycerol 3-phosphate dehydrogenase (monomeric) H281DRAFT_04228
tpi triose-phosphate isomerase H281DRAFT_04564 H281DRAFT_04190
Alternative steps:
aqp-3 glycerol porter aqp-3 H281DRAFT_05734
dhaD glycerol dehydrogenase H281DRAFT_03803 H281DRAFT_05508
dhaK dihydroxyacetone:PEP phosphotransferase, subunit K H281DRAFT_02702 H281DRAFT_05885
dhaK' dihydroxyacetone kinase, ATP dependent (monomeric) H281DRAFT_05885 H281DRAFT_02702
dhaL dihydroxyacetone:PEP phosphotransferase, subunit L H281DRAFT_05886 H281DRAFT_02701
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 H281DRAFT_04230 H281DRAFT_05734
glpF' glycerol facilitator-aquaporin H281DRAFT_04230
glpO glycerol 3-phosphate oxidase H281DRAFT_04228
PLT5 glycerol:H+ symporter PLT5
stl1 glycerol:H+ symporter Stl1p
TIPa glycerol facilitator TIPa H281DRAFT_05734
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 17 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 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