Definition of glycerol catabolism

GapMind for catabolism of small carbon sources

Definition of glycerol catabolism

# Glycerol utilization in GapMind is based on MetaCyc pathways
# glycerol degradation I via glycerol kinase (metacyc:PWY-4261),
# II via dihydroxyacetone kinase (metacyc:PWY-6131),
# or V via dihydroxyacetone:PEP phosphotransferase (metacyc:GLYCEROLMETAB-PWY).
# Two fermentative pathways are not included because they do not lead to
# carbon incorporation (metacyc:PWY-6130, metacyc:PWY-7003).

# ABC transporters:

# GlpSTPQV from Rhizobium leguminosarum
# and a related system from Acidovorax GW101-3H11.
# GlpS/GlpT are similar to each other; GlpS is more similar to Ac3H11_791 and GlpT to Ac3H11_792.
glpS	glycerol ABC transporter, ATPase component 1 (GlpS)	curated:TCDB::G3LHY8	curated:reanno::acidovorax_3H11:Ac3H11_791
glpT	glycerol ABC transporter, ATPase component 2 (GlpT)	curated:TCDB::G3LHY9	curated:reanno::acidovorax_3H11:Ac3H11_792
glpP	glycerol ABC transporter, permease component 1 (GlpP)	curated:TCDB::G3LHZ0	curated:reanno::acidovorax_3H11:Ac3H11_793
glpQ	glycerol ABC transporter, permease component 2 (GlpQ)	curated:TCDB::G3LHZ1	curated:reanno::acidovorax_3H11:Ac3H11_794
glpV	glycerol ABC transporter, substrate-binding component GlpV	curated:TCDB::G3LHZ3	curated:reanno::acidovorax_3H11:Ac3H11_796

# Transporters were identified using
# query: transporter:glycerol and
# glycerol-3-phosphate transporters were manually removed from the results
glycerol-transport: glpS glpT glpP glpQ glpV

# Other transporters:

# Ignore an uncharacterized homolog from Archaeoglobus
glpF	glycerol facilitator glpF	curated:CharProtDB::CH_024677	curated:CharProtDB::CH_091207	curated:CharProtDB::CH_091783	curated:SwissProt::F9UMX3	curated:SwissProt::F9UST3	curated:SwissProt::F9USY3	curated:SwissProt::F9UTW9	curated:SwissProt::F9UUB3	curated:SwissProt::P47862	curated:TCDB::F6QEC2	curated:TCDB::P08995	curated:TCDB::P18156	curated:TCDB::P52280	curated:TCDB::Q6Q1Q6	curated:TCDB::Q8WPZ6	curated:TCDB::Q9C4Z5	ignore:TCDB::O28846
glycerol-transport: glpF

aqp-3	glycerol porter aqp-3	curated:TCDB::E3UMZ6	curated:TCDB::729057658	curated:TCDB::E3UMZ5	curated:TCDB::E3UN01
glycerol-transport: aqp-3

stl1	glycerol:H+ symporter Stl1p	curated:CharProtDB::CH_091379	curated:CharProtDB::CH_122745	curated:TCDB::C4QVV9
glycerol-transport: stl1

glpF'	glycerol facilitator-aquaporin	curated:CharProtDB::CH_012828
glycerol-transport: glpF'

fps1	glycerol uptake/efflux facilitator protein	curated:CharProtDB::CH_091157
glycerol-transport: fps1

PLT5	glycerol:H+ symporter PLT5	curated:CharProtDB::CH_091483
glycerol-transport: PLT5

YFL054C	glycrol facilitator protein	curated:CharProtDB::CH_091497
glycerol-transport: YFL054C

TIPa	glycerol facilitator TIPa	curated:TCDB::Q9XG70
glycerol-transport: TIPa

# Two human HHAT-type proteins are related to glycerol transporters but it is not so clear
# that they are characterized as transporters; ignored.
# And a porin from Pseudomonas aeruginosa was ignored.
# Aquaporin NIP2-1 from Arabidopsis was ignored because it was described as having "minimal" glycerol transport.
# Ignored two putative transporters from Listeria innocua, Lin0367/Lin0368, which are not characterized.

glpK	glycerol kinase	EC:2.7.1.30

# Fitness data identified SMc02520 (Q92LM5) as the glycerol-3-phosphate dehydrogenase in Sinorhizobium meliloti.
glpD	glycerol 3-phosphate dehydrogenase (monomeric)	curated:SwissProt::P18158	curated:BRENDA::P13035	curated:BRENDA::P35571	curated:BRENDA::P43304	curated:BRENDA::Q06B39	curated:BRENDA::Q64521	curated:CharProtDB::CH_091834	curated:SwissProt::P32191	curated:SwissProt::Q8SR40	curated:SwissProt::Q9SS48	curated:CharProtDB::CH_122883	uniprot:Q92LM5

# Glycerol 3-phosphate dehydrogenase includes EC:1.1.5.3, EC:1.1.1.8, and  EC:1.1.1.94.
# 1.1.5.3 is flavin- or quinone-dependent and may be heteromeric.
# 1.1.1.8/1.1.1.94 are NAD(P)H dependent and the forward reaction is thermodynamically unfavorable,
#   so they are not included here.
g3p-dehydrogenase: glpD

glpA	glycerol 3-phosphate dehydrogenase subunit A	curated:SwissProt::D4GQU6	curated:SwissProt::D4GYI2	curated:ecocyc::ANGLYC3PDEHYDROGSUBUNITA-MONOMER
glpB	glycerol 3-phosphate dehydrogenase subunit B	curated:ecocyc::ANGLYC3PDEHYDROGSUBUNITB-MONOMER
glpC	glycerol 3-phosphate dehydrogenase subunit C	curated:ecocyc::ANGLYC3PDEHYDROGSUBUNITC-MONOMER
g3p-dehydrogenase: glpA glpB glpC glpD

glpO	glycerol 3-phosphate oxidase	EC:1.1.3.21

# An oxygen-dependent enzyme, glycerol-3-phosphate oxidase, can also form glycerone phosphate.
g3p-dehydrogenase: glpO

import fructose.steps:tpi

dhaD	glycerol dehydrogenase	EC:1.1.1.6

# There's another glycerol dehydrogenase, EC 1.1.1.72, forming glyceraldehyde;
# this is not reported to be involved in glycerol catabolism in prokaryotes,
# and is not described here

# most prokaryotic dihydroxyacetone kinases are heteromeric and use phosophoenolpyruvate
# rather than ATP as the phosphoryl donor (EC 2.7.1.121)
# This is a PTS-like system that relies on EI and Hpr proteins to phosphorylate the dhaM subunit
# The BRENDA entry does not actually seem to be characterized, not clear if it is dhaK or dhaK'
dhaK	dihydroxyacetone:PEP phosphotransferase, subunit K	curated:BRENDA::P76015	curated:SwissProt::Q92EU2	curated:SwissProt::Q9CIV8	ignore_other:2.7.1.121	ignore:BRENDA::A0A1D3TV19
dhaL	dihydroxyacetone:PEP phosphotransferase, subunit L	curated:BRENDA::P76014	curated:SwissProt::Q92EU3	curated:SwissProt::Q9CIV7	ignore_other:2.7.1.121
dhaM	dihydroxyacetone:PEP phosphotransferase, subunit M	curated:SwissProt::Q92ET9	curated:SwissProt::Q9CIV6	curated:BRENDA::P37349	curated:CharProtDB::CH_000735	curated:SwissProt::A0A0H3H456	curated:SwissProt::D4GL26	curated:SwissProt::P0DN88	ignore_other:2.7.1.121

# These dihydroxyacetone kinases utilize ATP directly; these are mostly eukaryotic, but also
# include a system from Citrobacter (also known as dhaK)
dhaK'	dihydroxyacetone kinase, ATP dependent (monomeric)	curated:BRENDA::P43550	curated:BRENDA::P54838	curated:BRENDA::Q3LXA3	curated:CharProtDB::CH_008528	curated:CharProtDB::CH_124545	curated:SwissProt::F1RKQ4	curated:SwissProt::Q4KLZ6	curated:metacyc::MONOMER-13163	curated:metacyc::MONOMER-16996	ignore_other:2.7.1.29

# In pathway V, the three-subunit phosphotranfserase dhaKLM phosphorylates dihydroxyacetone,
# with phosphoenolpyruvate as the donor.
# In pathway II, a kinase (also known as dhaK, here dhaK') phosphorylates dihydroxyacetone.
dhkinase: dhaK dhaL dhaM
dhkinase: dhaK'

# Pathway I involves glycerol kinase glpK and glycerol-3-phosphate dehydrogenase;
# the glycerone phosphate can be converted to glyceraldehyde-3-phosphate by triose-phosphate isomerase.
all: glycerol-transport glpK g3p-dehydrogenase tpi

# In pathways II or V, the dehydrogenase dhaD forms dihydroxyacetone, which is phosphorylated and isomerized
# to glyceraldehyde 3-phosphate.
all: glycerol-transport dhaD dhkinase tpi

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources