GapMind for catabolism of small carbon sources

 

glycerol catabolism in Cereibacter sphaeroides ATCC 17029

Best path

glpS, glpT, glpP, glpQ, glpV, 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 (13 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
glpS glycerol ABC transporter, ATPase component 1 (GlpS) RSPH17029_RS06720 RSPH17029_RS08750
glpT glycerol ABC transporter, ATPase component 2 (GlpT) RSPH17029_RS06715 RSPH17029_RS20290
glpP glycerol ABC transporter, permease component 1 (GlpP) RSPH17029_RS06710 RSPH17029_RS17170
glpQ glycerol ABC transporter, permease component 2 (GlpQ) RSPH17029_RS06705
glpV glycerol ABC transporter, substrate-binding component GlpV RSPH17029_RS06695
glpK glycerol kinase RSPH17029_RS06690 RSPH17029_RS14315
glpD glycerol 3-phosphate dehydrogenase (monomeric) RSPH17029_RS06725
tpi triose-phosphate isomerase RSPH17029_RS03035 RSPH17029_RS05860
Alternative steps:
aqp-3 glycerol porter aqp-3 RSPH17029_RS07200
dhaD glycerol dehydrogenase RSPH17029_RS15405 RSPH17029_RS05055
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 glpF RSPH17029_RS07200
glpF' glycerol facilitator-aquaporin
glpO glycerol 3-phosphate oxidase RSPH17029_RS06725
PLT5 glycerol:H+ symporter PLT5
stl1 glycerol:H+ symporter Stl1p
TIPa glycerol facilitator TIPa RSPH17029_RS07200
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 Apr 10 2024. 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:

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