Definition of L-arabinose catabolism

GapMind for catabolism of small carbon sources

Definition of L-arabinose catabolism

# L-arabinose utilization in GapMind is based on MetaCyc pathways
# L-arabinose degradation I, via xylulose 5-phosphate (metacyc:ARABCAT-PWY);
# III, oxidation to 2-oxoglutarate (metacyc:PWY-5517);
# and IV, via glycolaldehyde (metacyc:PWY-7295).
# Pathway II via xylitol and xylulose is not represented in GapMind
# because it is not reported in prokaryotes (metacyc:PWY-5515).

# ABC transporters:
# GguAB-ChvE from Agrobacterium tumefaciens/radiobacter
# AraFGH from E. coli
# AraSTUV from Sulfolobus solfataricus
# XacGHIJKJ from Haloferax volcanii
# XylFGH from Sulfolobus acidocaldarius

gguA	L-arabinose ABC transporter, ATPase component GguA	curated:TCDB::O05176
gguB	L-arabinose ABC transporter, permease component GguB	curated:TCDB::O05177
# The related protein sbpA (P54083) binds arabinose
chvE	L-arabinose ABC transporter, substrate-binding component ChvE	curated:TCDB::P25548	ignore:SwissProt::P54083

# Transporters were identified using
# query: transporter:arabinose:L-arabinose:L-arabinofuranose:L-arabinopyranose:beta-L-arabinose:CPD-12045:CPD-12046
arabinose-transport: gguA gguB chvE

araF	L-arabinose ABC transporter, substrate-binding component AraF	curated:SwissProt::P02924
araG	L-arabinose ABC transporter, ATPase component AraG	curated:SwissProt::P0AAF3
araH	L-arabinose ABC transporter, permease component AraH	curated:CharProtDB::CH_014278
arabinose-transport: araF araG araH

araS	L-arabinose ABC transporter, substrate-binding component AraS	curated:TCDB::Q97UF5
araT	L-arabinose ABC transporter, permease component 1 (AraT)	curated:TCDB::Q97UF4
araU	L-arabinose ABC transporter, permease component 2 (AraU)	curated:TCDB::Q97UF3
araV	L-arabinose ABC transporter, ATPase component AraV	curated:TCDB::Q97UF2
arabinose-transport: araS araT araU araV

xacG	L-arabinose ABC transporter, substrate-binding component XacG	uniprot:D4GP35
xacH	L-arabinose ABC transporter, permease component 1 (XacH)	uniprot:D4GP36
xacI	L-arabinose ABC transporter, permease component 2 (XacI)	uniprot:D4GP37 
xacJ	L-arabinose ABC transporter, ATPase component 1 (XacJ)	uniprot:D4GP38 
xacK	L-arabinose ABC transporter, ATPase component 2 (XacK)	uniprot:D4GP39 
arabinose-transport: xacG xacH xacI xacJ xacK

xylFsa	L-arabinose ABC transporter, substrate-binding component XylF	uniprot:Q4J710 
xylGsa	L-arabinose ABC transporter, ATPase component XylG	uniprot:P0DTT6 
xylHsa	L-arabinose ABC transporter, permease component XylH	uniprot:Q4J711 
arabinose-transport: xylFsa xylGsa xylHsa

# Rodionov et al proposed that the Shewanella arabinose transporter is araUVWZ; this was confirmed
# by fitness data for Shewana3_2073:2076
araUsh	L-arabinose ABC transporter, substrate-binding component AraU(Sh)	uniprot:A0KWY4
araVsh	L-arabinose ABC transporter, ATPase component AraV(Sh)	uniprot:A0KWY5
araWsh	L-arabinose ABC transporter, permease component 1 AraW(Sh)	uniprot:A0KWY6
araZsh	L-arabinose ABC transporter, permease component 2 AraZ(Sh)	uniprot:A0KWY7
arabinose-transport: araUsh araVsh araWsh araZsh

# homomeric transporters

araE	L-arabinose:H+ symporter	curated:SwissProt::P0AE24	curated:SwissProt::P96710	curated:TCDB::C4B4V9
arabinose-transport: araE

# In the RB-TnSeq data, BT0355 is very important for L-arabinose utilization, and this does
# not seem to be a polar effect (the effect is found on both strands).
# In contrast, PMC5061871 reported a subtle effect of deleting BT0355 on L-arabinose utilization,
# but found that it was required for arabinobiose utilization.
BT0355	L-arabinose:Na+ symporter	uniprot:Q8AAV7	
arabinose-transport: BT0355

# Echvi_1880 is specifically important for L-arabinose utilization
Echvi_1880	L-arabinose:Na+ symporter	uniprot:L0FZT5
arabinose-transport: Echvi_1880

# Ignore various arabinose exporters:
# yhhS, yfcJ, setC, ybdA, ydeA, ynfM, kgtP from E. coli; SotA from Erwinia;
# CmlA/MdfA from Pseudomonas aeruginosa
#
# Ignore AraNPQ-MsmX from B. subtilis, which is sometimes annotated as an arabinose transporter,
# but genetic studies suggests that it is involved in the transport of oligosaccharides of arabinose
# only (see PMC2950484)

araA	L-arabinose isomerase	EC:5.3.1.4
# BT0350 (Q8AAW2) is similar to the L-ribulokinase of Corynebacterium glutamicum (PMC2687266; C4B4W2)
# and is specifically improtant during growth on L-arabinose.
araB	ribulokinase	EC:2.7.1.16	uniprot:C4B4W2	uniprot:Q8AAW2
araD	L-ribulose-5-phosphate epimerase	EC:5.1.3.4
# araABD is pathway I.


# In pathway I, isomerase araA forms L-ribulose, kinase
# araB forms ribulose 5-phosphate, and epimerase araD
# forms D-xylulose 5-phosphate,
# which is an intermediate in the pentose phosphate pathway.
all: arabinose-transport araA araB araD

xacB	L-arabinose 1-dehydrogenase	EC:1.1.1.376	EC:1.1.1.46
# SMc00883 (Q92RN9) is specifically important for L-arabinose utilization and does not appear polar.
# (It has a vague annotation in SwissProt.)
# Similarly for Ac3H11_615 (A0A165IRV8)
xacC	L-arabinono-1,4-lactonase	EC:3.1.1.15	uniprot:Q92RN9	uniprot:A0A165IRV8	ignore:SwissProt::Q92RN9
# The function of Q92RP0 seems to be unknown so ignore it
xacD	L-arabinonate dehydratase	EC:4.2.1.25	ignore:SwissProt::Q92RP0
xacE	2-dehydro-3-deoxy-L-arabinonate dehydratase	EC:4.2.1.43
xacF	alpha-ketoglutarate semialdehyde dehydrogenase	EC:1.2.1.26

# In pathway III, the 1-dehydrogenase xacB
# (which acts on the furanose form, not the usual pyranose form?)
# forms  arabino-1,4-lactone, lactonase xacC forms arbinonate, two
# dehydratases form 2-dehydro-3-deoxy-L-arabinonate and 2,5-dioxopentanonate (α-ketoglutarate semialdehyde),
# and dehydrogenase xacF forms 2-oxoglutarate, which is an intermediate in the TCA cycle.
# (Fitness data suggests that L-arabinose 1-epimerase or mutarotase is also involved,
# perhaps in creating the correct epimer for the 1-dehydrogenase, but
# is not included in GapMind.)
all: arabinose-transport xacB xacC xacD xacE xacF

# gyaR = glyoxylate reductase / glycolate dehydrogenase
# glcB = malate synthase
import xylose.steps:glycolaldehyde-dehydrogenase gyaR glcB

# Q97U28 is the same protein but with 14 more N-terminal a.a., and is annotated with 4.1.2.55 only.
# And a similar enzyme from S. acidcaldarius is thought to perform this reaction as well (PMC2962468)
KDG-aldolase	2-dehydro-3-deoxy-L-arabinonate aldolase	EC:4.1.2.18	ignore:BRENDA::Q97U28	curated:BRENDA::Q4JC35

# Pathway IV begins as in pathway III, to
# 2-dehydro-3-deoxy-L-arabinonate, followed by KDG aldolase to
# pyruvate and glycolaldehyde; the glycolaldehyde is oxidized to
# glycolate and then to glyoxylate, and combined with acetyl-CoA by
# malate synthase, which is a TCA cycle intermediate.
# (Other pathways for glyxoylate assimilation are known but are not
#  represented here.)
all: arabinose-transport xacB xacC xacD KDG-aldolase glycolaldehyde-dehydrogenase gyaR glcB

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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