GapMind for catabolism of small carbon sources

 

glycerol catabolism in Klebsiella michiganensis M5al

Best path

glpF, dhaD, dhaK, dhaL, dhaM, 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 (16 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
glpF glycerol facilitator glpF BWI76_RS27510 BWI76_RS23100
dhaD glycerol dehydrogenase BWI76_RS24585 BWI76_RS00815
dhaK dihydroxyacetone:PEP phosphotransferase, subunit K BWI76_RS24595 BWI76_RS24610
dhaL dihydroxyacetone:PEP phosphotransferase, subunit L BWI76_RS24600
dhaM dihydroxyacetone:PEP phosphotransferase, subunit M BWI76_RS24605
tpi triose-phosphate isomerase BWI76_RS27465 BWI76_RS23980
Alternative steps:
aqp-3 glycerol porter aqp-3
dhaK' dihydroxyacetone kinase, ATP dependent (monomeric) BWI76_RS24610 BWI76_RS24595
fps1 glycerol uptake/efflux facilitator protein
glpA glycerol 3-phosphate dehydrogenase subunit A BWI76_RS19965
glpB glycerol 3-phosphate dehydrogenase subunit B BWI76_RS19970
glpC glycerol 3-phosphate dehydrogenase subunit C
glpD glycerol 3-phosphate dehydrogenase (monomeric) BWI76_RS26190
glpF' glycerol facilitator-aquaporin
glpK glycerol kinase BWI76_RS27515 BWI76_RS07670
glpO glycerol 3-phosphate oxidase BWI76_RS26190
glpP glycerol ABC transporter, permease component 1 (GlpP)
glpQ glycerol ABC transporter, permease component 2 (GlpQ)
glpS glycerol ABC transporter, ATPase component 1 (GlpS) BWI76_RS03120 BWI76_RS26290
glpT glycerol ABC transporter, ATPase component 2 (GlpT) BWI76_RS26290 BWI76_RS06690
glpV glycerol ABC transporter, substrate-binding component GlpV
PLT5 glycerol:H+ symporter PLT5 BWI76_RS03110
stl1 glycerol:H+ symporter Stl1p
TIPa glycerol facilitator TIPa BWI76_RS09585
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.

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 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