GapMind for catabolism of small carbon sources

 

glycerol catabolism in Sinorhizobium meliloti 1021

Best path

glpS, glpT, glpP, glpQ, glpV, 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 (16 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
glpS glycerol ABC transporter, ATPase component 1 (GlpS) SMc02519 SM_b20972
glpT glycerol ABC transporter, ATPase component 2 (GlpT) SMc02518 SM_b21216
glpP glycerol ABC transporter, permease component 1 (GlpP) SMc02517 SM_b21220
glpQ glycerol ABC transporter, permease component 2 (GlpQ) SMc02516 SMa1341
glpV glycerol ABC transporter, substrate-binding component GlpV SMc02514
glpK glycerol kinase SM_b21009
glpD glycerol 3-phosphate dehydrogenase (monomeric) SMc02520 SMc01620
tpi triose-phosphate isomerase SMc01023 SMc01614
Alternative steps:
aqp-3 glycerol porter aqp-3
dhaD glycerol dehydrogenase SMc02038 SMc02041
dhaK dihydroxyacetone:PEP phosphotransferase, subunit K SM_b20312 SM_b20314
dhaK' dihydroxyacetone kinase, ATP dependent (monomeric) SM_b20767 SM_b20314
dhaL dihydroxyacetone:PEP phosphotransferase, subunit L SM_b20307 SM_b20313
dhaM dihydroxyacetone:PEP phosphotransferase, subunit M
fps1 glycerol uptake/efflux facilitator protein
glpA glycerol 3-phosphate dehydrogenase subunit A SMc02520
glpB glycerol 3-phosphate dehydrogenase subunit B
glpC glycerol 3-phosphate dehydrogenase subunit C
glpF glycerol facilitator glpF SMa0627 SMc01870
glpF' glycerol facilitator-aquaporin
glpO glycerol 3-phosphate oxidase SMc02520 SMc01620
PLT5 glycerol:H+ symporter PLT5
stl1 glycerol:H+ symporter Stl1p
TIPa glycerol facilitator TIPa SMc01870
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 (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