Definition of L-rhamnose catabolism

GapMind for catabolism of small carbon sources

Definition of L-rhamnose catabolism

# Rhamnose utilization in GapMind is based on MetaCyc pathway
# I via L-rhamnulose 1-phosphate aldolase (metacyc:RHAMCAT-PWY),
# pathway II via 2-keto-3-deoxy-L-rhamnonate aldolase (metacyc:PWY-6713),
# and pathway III via 2,4-diketo-3-deoxyrhamnonate hydrolase (metacyc:PWY-6714).

# Fitness data shows that the (distant) homolog in Bacteroides thetaiotaomicron (BT3765, Q8A1A1) is also
# a rhamnose transporter
rhaT	L-rhamnose:H+ symporter RhaT	curated:SwissProt::P27125	uniprot:Q8A1A1

# Transporters were identified usiung:
# query: transporter:L-rhamnose:rhamnose:L-rhamnofuranose:L-rhamnopyranose:CPD-16564:CPD-16565:CPD0-1112:CPD-15405
rhamnose-transport: rhaT

# 4-part ABC transporter rhaPQST. 
# In TCDB, the rhamnose transporter of Rhizobium leguminosarum is described as rhaSTP
# but rhaQ (Q7BSH2_RHILT) is also probably part of this system.
# The comment in TCDB also speculates about group translocation, because the R. leguminosarum
# system requires the rhamnose/rhamnulose kinase rhaK for activity; but
# in Sinorhizobium meliloti, which has a similar system,
# the rhaK protein has rhamnulokinase activity only
# (Rivers 2015, URL:https://mspace.lib.umanitoba.ca/handle/1993/30289).
rhaP	L-rhamnose ABC transporter, permease component 1 (RhaP)	curated:TCDB::Q7BSH3
rhaQ	L-rhamnose ABC transporter, permease component 2 (RhaQ)	uniprot:Q7BSH2
rhaS	L-rhamnose ABC transporter, substrate-binding component RhaS	curated:TCDB::Q7BSH5
# Because of the one-component transporter rhaT, the ATPase component is named rhaT' in GapMind.
rhaT'	L-rhamnose ABC transporter, ATPase component RhaT	curated:TCDB::Q7BSH4
rhamnose-transport: rhaP rhaQ rhaS rhaT'

# Fitness data suggests Echvi_1617 is the rhamnose transporter.
# It is probably Na+ dependent, but this is uncertain.
Echvi_1617	L-rhamnose transporter	uniprot:L0FX46
rhamnose-transport: Echvi_1617

# In Burkholderia phytofirmans PsJN, a 3-part ABC transporter is involved
# in utilization of L-rhamnose, L-fucose, and xylitol
BPHYT_RS34250	L-rhamnose ABC transporter, substrate-binding component	uniprot:B2T9W0
BPHYT_RS34245	L-rhamnose ABC transporter, ATPase component	uniprot:B2T9V9
BPHYT_RS34240	L-rhamnose ABC transporter, permease component	uniprot:B2T9V8
rhamnose-transport: BPHYT_RS34250 BPHYT_RS34245 BPHYT_RS34240


rhaM	L-rhamnose mutarotase	EC:5.1.3.32
rhaA	L-rhamnose isomerase	EC:5.3.1.14
rhaB	L-rhamnulokinase	EC:2.7.1.5

# BT3766 (Q8A1A0) was confirmed by fitness data
rhaD	rhamnulose 1-phosphate aldolase	EC:4.1.2.19	uniprot:Q8A1A0

import fructose.steps:tpi # triose-phsophate isomerase

# The EC number is for the NAD dependent reaction.
# There's also a NADP dependent reaction, sometimes given this EC, sometimes not.
aldA	lactaldehyde dehydrogenase	EC:1.2.1.22	ignore_other:lactaldehyde dehydrogenase

# BT3767 (Q8A199) was confirmed by fitness data
fucO	L-lactaldehyde reductase	EC:1.1.1.77	uniprot:Q8A199

# Lactaldehyde might be oxidized to
# lactate and secreted (or oxidized to pyruvate); or, it might be
# reduced to propane-1,2-diol and secreted.
lactaldehyde-conversion: aldA
lactaldehyde-conversion: fucO

# In pathway I, the mutarotase rhaM forms
# beta-rhamnopyranose, isomerase rhaA forms rhamnulofuranose, kinase rhaB
# forms rhamnulose 1-phosphate, aldolase rhaD forms (S)-lactaldehyde and
# glycerone phosphate, and tpi converts glycerone phosphate to
# glyceraldehyde 3-phosphate. 
all: rhamnose-transport rhaM rhaA rhaB rhaD tpi lactaldehyde-conversion

# The rhamnofuranose dehydrogenase may be either NADH or NADPH dependent, or use either
LRA1	L-rhamnofuranose dehydrogenase	EC:1.1.1.378	EC:1.1.1.173	EC:1.1.1.377
LRA2	L-rhamnono-gamma-lactonase	EC:3.1.1.65
# Ignore BPHYT_RS34235, a putative accessory domain
LRA3	L-rhamnonate dehydratase	EC:4.2.1.90	ignore:reanno::BFirm:BPHYT_RS34235
LRA4	2-keto-3-deoxy-L-rhamnonate aldolase	EC:4.1.2.53

# In pathway II, the 1-dehydrogenase LRA1 forms L-rhamnono-1,4-lactone,
# the lactonase LRA2 forms L-rhamnonate, the dehydratase LRA3 forms
# 2-dehydro-3-deoxy-L-rhamnonate, and the aldolase LRA4 forms pyruvate and
# lactaldehyde.
all: rhamnose-transport LRA1 LRA2 LRA3 LRA4 lactaldehyde-conversion

# The enzyme from Sphingomonas strain SKA58 is Q1NEI6 not Q1NEI7; there is an error in MetaCyc.
# Q1NEI6 is annotated correctly in other resources
LRA5	2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase	EC:1.1.1.401	ignore:metacyc::MONOMER-16233

# EC:3.7.1.26 has been assigned but not linked to the characterized protein, which is
# EAT09363.1 or metacyc:MONOMER-16233 (PMID:19187228) -- but MONOMER-16233 is misannotated as
# a dehydrogenase.
# And, ignore uniprot:Q39BA7, which is very similar to LRA6 from Burkholderia phytofirmans PsJN
# but is reported to be a ureidoglycolate lyase (PMID:14506266).
LRA6	2,4-diketo-3-deoxyrhamnonate hydrolase	curated:metacyc::MONOMER-16233	term:L-2,4-diketo-3-deoxyrhamnonate hydrolase	term:2,4-diketo-3-deoxy-L-rhamnonate hydrolase	EC:3.7.1.26	ignore:SwissProt::Q39BA7

# In pathway III, rhamnose is also oxidized and dehydrated to
# 2-dehydro-3-deoxy-L-rhamnonate, but then, dehydrogenase LRA5 forms
# 2,4-didehydro-3-deoxy-L-rhamnonate and hydrolase LRA6 forms L-lactate
# and pyruvate.
all: rhamnose-transport LRA1 LRA2 LRA3 LRA5 LRA6

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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