GapMind for catabolism of small carbon sources

 

glycerol catabolism in Pantoea rwandensis LMG 26275

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 HA51_RS16115 HA51_RS24965
glpK glycerol kinase HA51_RS16120 HA51_RS14795
glpD glycerol 3-phosphate dehydrogenase (monomeric) HA51_RS17640 HA51_RS13405
tpi triose-phosphate isomerase HA51_RS16145 HA51_RS21490
Alternative steps:
aqp-3 glycerol porter aqp-3
dhaD glycerol dehydrogenase HA51_RS10360 HA51_RS03095
dhaK dihydroxyacetone:PEP phosphotransferase, subunit K HA51_RS12925 HA51_RS18525
dhaK' dihydroxyacetone kinase, ATP dependent (monomeric) HA51_RS18525 HA51_RS12925
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 HA51_RS17640 HA51_RS13405
glpP glycerol ABC transporter, permease component 1 (GlpP) HA51_RS03320
glpQ glycerol ABC transporter, permease component 2 (GlpQ)
glpS glycerol ABC transporter, ATPase component 1 (GlpS) HA51_RS18870 HA51_RS03335
glpT glycerol ABC transporter, ATPase component 2 (GlpT) HA51_RS18870 HA51_RS03335
glpV glycerol ABC transporter, substrate-binding component GlpV
PLT5 glycerol:H+ symporter PLT5 HA51_RS04135 HA51_RS00995
stl1 glycerol:H+ symporter Stl1p HA51_RS21365
TIPa glycerol facilitator TIPa HA51_RS24965 HA51_RS16115
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.

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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