GapMind for catabolism of small carbon sources

 

glycerol catabolism in Nocardiopsis baichengensis YIM 90130

Best path

glpF, glpK, glpD, tpi

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 (14 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
glpF glycerol facilitator glpF C892_RS0110390 C892_RS0117300
glpK glycerol kinase C892_RS0110385 C892_RS0114335
glpD glycerol 3-phosphate dehydrogenase (monomeric) C892_RS0116650 C892_RS0120455
tpi triose-phosphate isomerase C892_RS0126430 C892_RS0126425
Alternative steps:
aqp-3 glycerol porter aqp-3
dhaD glycerol dehydrogenase C892_RS0111405 C892_RS0105375
dhaK dihydroxyacetone:PEP phosphotransferase, subunit K C892_RS0111110 C892_RS0121990
dhaK' dihydroxyacetone kinase, ATP dependent (monomeric) C892_RS0121990 C892_RS0111110
dhaL dihydroxyacetone:PEP phosphotransferase, subunit L C892_RS0111105 C892_RS0121990
dhaM dihydroxyacetone:PEP phosphotransferase, subunit M C892_RS0111115
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 C892_RS0110390
glpO glycerol 3-phosphate oxidase C892_RS0116650 C892_RS0120455
glpP glycerol ABC transporter, permease component 1 (GlpP)
glpQ glycerol ABC transporter, permease component 2 (GlpQ) C892_RS0123145 C892_RS0119340
glpS glycerol ABC transporter, ATPase component 1 (GlpS) C892_RS0124970 C892_RS0103640
glpT glycerol ABC transporter, ATPase component 2 (GlpT) C892_RS0124950 C892_RS0103640
glpV glycerol ABC transporter, substrate-binding component GlpV
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.

Links

Downloads

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