GapMind for catabolism of small carbon sources

 

glycerol catabolism in Streptacidiphilus oryzae TH49

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 (16 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
glpF glycerol facilitator glpF BS73_RS34080 BS73_RS10550
glpK glycerol kinase BS73_RS34075 BS73_RS10555
glpD glycerol 3-phosphate dehydrogenase (monomeric) BS73_RS23040 BS73_RS10545
tpi triose-phosphate isomerase BS73_RS12430 BS73_RS16890
Alternative steps:
aqp-3 glycerol porter aqp-3 BS73_RS24920
dhaD glycerol dehydrogenase BS73_RS34250 BS73_RS00110
dhaK dihydroxyacetone:PEP phosphotransferase, subunit K BS73_RS33670 BS73_RS16870
dhaK' dihydroxyacetone kinase, ATP dependent (monomeric) BS73_RS16870 BS73_RS33670
dhaL dihydroxyacetone:PEP phosphotransferase, subunit L BS73_RS33665 BS73_RS16870
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 BS73_RS23040 BS73_RS10545
glpP glycerol ABC transporter, permease component 1 (GlpP) BS73_RS24190
glpQ glycerol ABC transporter, permease component 2 (GlpQ) BS73_RS33855
glpS glycerol ABC transporter, ATPase component 1 (GlpS) BS73_RS18100 BS73_RS14235
glpT glycerol ABC transporter, ATPase component 2 (GlpT) BS73_RS18100 BS73_RS14235
glpV glycerol ABC transporter, substrate-binding component GlpV
PLT5 glycerol:H+ symporter PLT5 BS73_RS21865 BS73_RS21860
stl1 glycerol:H+ symporter Stl1p
TIPa glycerol facilitator TIPa BS73_RS24920
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