Definition of L-fucose catabolism

GapMind for catabolism of small carbon sources

Definition of L-fucose catabolism

# Fucose degradation in GapMind is based on
# the MetaCyc pathway via L-fuculose (metacyc:FUCCAT-PWY)
# or the oxidative pathway via 2,4-diketo-3-deoxy-L-fuconate (KDF) hydrolase (PMC6336799).

# BT1277 (G8JZT2) is distantly related and important for fucose utilization
fucP	L-fucose:H+ symporter FucP	curated:SwissProt::P11551	uniprot:G8JZT2

# Transporters were identified using
# query: transporter:L-fucose:L-fucopyranose:CPD-10329:CPD0-1107:CPD-15619
fucose-transport: fucP

# A 4-part ABC transporter was annotated in Sinorhizobium meliloti
# based on fitness data and also from expression data.
# Expression of the substrate-binding component (SM_b21103) 
# is induced by L-fucose or D-fucose (PMC1635973)

SM_b21103	ABC transporter for L-fucose, substrate-binding component	curated:reanno::Smeli:SM_b21103
SM_b21104	ABC transporter for L-fucose, permease component 1	curated:reanno::Smeli:SM_b21104
SM_b21105	ABC transporter for L-fucose, permease component 2	curated:reanno::Smeli:SM_b21105
SM_b21106	ABC transporter for L-fucose, ATPase component	curated:reanno::Smeli:SM_b21106
fucose-transport: SM_b21103 SM_b21104 SM_b21105 SM_b21106

# A 3-part ABC transporter was identified in Burkholderia phytofirmans
# based on fitness data
BPHYT_RS34250	ABC transporter for L-fucose, substrate-binding component	uniprot:B2T9W0
BPHYT_RS34245	ABC transporter for L-fucose, ATPase component	uniprot:B2T9V9
BPHYT_RS34240	ABC transporter for L-fucose, permease component	uniprot:B2T9V8
fucose-transport: BPHYT_RS34250 BPHYT_RS34245 BPHYT_RS34240

# A 3-part ABC transporter was identified in Herbaspirillum
# seropedicae based on fitness data
HSERO_RS05250	ABC transporter for L-fucose, ATPase component	uniprot:D8J111
HSERO_RS05255	ABC transporter for L-fucose, permease component	uniprot:D8J112
HSERO_RS05260	ABC transporter for L-fucose, substrate-binding component	uniprot:D8J113
fucose-transport: HSERO_RS05250 HSERO_RS05255 HSERO_RS05260

# BT1276 (Q8A896) is important for fucose utilization
fucU	L-fucose mutarotase FucU	EC:5.1.3.29	uniprot:Q8A896
fucI	L-fucose isomerase FucI	EC:5.3.1.25
# BT2175 (G8JZS7) is important for fucose utilization
fucK	L-fuculose kinase FucK	EC:2.7.1.51	uniprot:G8JZS7
# BT2174 (G8JZT1) is important for fucose utilization
fucA	L-fuculose-phosphate aldolase FucA	EC:4.1.2.17	uniprot:G8JZT1

import rhamnose.steps:aldA fucO
# Lactaldehyde can be oxidized to lactate (aldA) or reduced to propanediol (fucO).
# Either of these can be excreted.
lactaldehyde-conversion: aldA
lactaldehyde-conversion: fucO

import fructose.steps:tpi # triose-phsophate isomerase

# In the L-fucuolose pathway, mutarotase fucU converts the beta-pyranose to
# the alpha-pyranose form, isomerase fucI produces L-fuculose, kinase fucK forms L-fuculose
# 1-phosphate, and aldolase fucA produces glycerone phosphate and
# (S)-lactaldehyde. Lactaldehyde might be oxidized to lactate and
# secreted (or oxidized to pyruvate), or, it might be reduced to
# propane-1,2-diol and secreted; tpi converts glycerone-phosphate to
# glyceraldehyde 3-phosphate.
all: fucose-transport fucU fucI fucK fucA tpi lactaldehyde-conversion

# C785_RS21215 (A0A2E7P8M8) was shown to be a L-fucose dehydrogenase (PMC6336799)
fdh	L-fucose 1-dehydrogenase	EC:1.1.1.122	uniprot:A0A2E7P8M8

# BmulJ_04915 (A0A0H3KNC4) is the biochemically characterized enzyme, see PMID:23214453.
# HSERO_RS05265 (D8J114) and BPHYT_RS34220 (B2T9V4) are important for fucose utilization
fuconolactonase	L-fucono-1,5-lactonase	uniprot:A0A0H3KNC4	curated:reanno::Smeli:SM_b21101	uniprot:A0A0H3KNC4	uniprot:D8J114	uniprot:B2T9V4

# HSERO_RS05235 (D8J108) is important for fucose utilization.
# Ignore the putative accessory protein BPHYT_RS34235.
fucD	L-fuconate dehydratase	EC:4.2.1.68	uniprot:D8J108	ignore:reanno::BFirm:BPHYT_RS34235

# No EC number, but XCC4067 (Q8P3K4) is annotated in SwissProt based on PMID:17144652.
# C785_RS13675 (A0A4P7ABK7) was also shown to have this acivity (PMC6336799)
# HSERO_RS19365	(D8IS13) and BPHYT_RS34215 (B2T9V3) are important for fucose utilization
# (The substrate for EC 1.1.1.401 (2-dehydro-3-deoxy-L-rhamnonate 4-dehydrogenase)
#  has the other stereochemistry at position 4.)
fucDH	2-keto-3-deoxy-L-fuconate 4-dehydrogenase	curated:SwissProt::Q8P3K4	uniprot:A0A4P7ABK7	uniprot:D8IS13	uniprot:B2T9V3

# C785_RS20550 (A0A2E7P912) was shown to be a L-2-keto-3-deoxyfuconate  (L-KDF) hydrolase by PMC6336799.
# HSERO_RS06355 (D8INW0) is important for fucose utilization.
# Q39BA7 is rather closely related but is reported to be a ureidoglycolate lyase.
# metacyc MONOMER-16233 is misannotated as a dehydrogenase in MetaCyc -- it is the hydrolase.
KDF-hydrolase	2,4-diketo-3-deoxy-L-fuconate hydrolase	uniprot:A0A2E7P912	curated:reanno::BFirm:BPHYT_RS34210	curated:reanno::Smeli:SM_b21112	uniprot:D8INW0	ignore:SwissProt::Q39BA7	curated:metacyc::MONOMER-16233

# In the oxidative pathway, mutarotase fucU forms the
# beta-pyranose form, fucose dehydrogenase (fdh) forms L-fucono-1,5-lactone,
# a lactonase forms L-fuconate, dehydratase fucD forms 2-keto-3-deoxy-L-fuconate,
# dehydrogenase fucDH forms 2,4-diketo-3-deoxy-L-fuconate (KDF, also known as
# 2,4-diketo-3-deoxy-L-rhamnonate), and a hydrolase forms lactate and
# pyruvate. The lactate could be secreted or oxidized to pyruvate.
all: fucose-transport fucU fdh fuconolactonase fucD fucDH KDF-hydrolase

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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