GapMind for catabolism of small carbon sources

 

glycerol catabolism in Dyella japonica UNC79MFTsu3.2

Best path

glpF, glpK, glpD, tpi

Also see fitness data for the top candidates

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).

25 steps (11 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
glpF glycerol facilitator glpF N515DRAFT_3908 N515DRAFT_1366
glpK glycerol kinase N515DRAFT_3907
glpD glycerol 3-phosphate dehydrogenase (monomeric) N515DRAFT_3909
tpi triose-phosphate isomerase N515DRAFT_1376 N515DRAFT_4291
Alternative steps:
aqp-3 glycerol porter aqp-3
dhaD glycerol dehydrogenase N515DRAFT_1006 N515DRAFT_2399
dhaK dihydroxyacetone:PEP phosphotransferase, subunit K
dhaK' dihydroxyacetone kinase, ATP dependent (monomeric)
dhaL dihydroxyacetone:PEP phosphotransferase, subunit L
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-aquaporin
glpO glycerol 3-phosphate oxidase N515DRAFT_3909
glpP glycerol ABC transporter, permease component 1 (GlpP)
glpQ glycerol ABC transporter, permease component 2 (GlpQ)
glpS glycerol ABC transporter, ATPase component 1 (GlpS) N515DRAFT_4212 N515DRAFT_1562
glpT glycerol ABC transporter, ATPase component 2 (GlpT) N515DRAFT_4212 N515DRAFT_1562
glpV glycerol ABC transporter, substrate-binding component GlpV
PLT5 glycerol:H+ symporter PLT5 N515DRAFT_1228 N515DRAFT_0382
stl1 glycerol:H+ symporter Stl1p N515DRAFT_1228
TIPa glycerol facilitator TIPa N515DRAFT_1366
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.

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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