Definition of xylitol catabolism

GapMind for catabolism of small carbon sources

Definition of xylitol catabolism

# Xylitol utilization in GapMind is based on
# the MetaCyc pathway via xylitol dehydrogenase (metacyc:LARABITOLUTIL-PWY)
# or on utilization via a phosphotransferase system and
# D-xylulose-5-phosphate 2-reductase (PMID:27553222).

# Fused (one-component) PTS system, EII-ABC, from Streptococcus mutans.
# A fairly close homolog from Streptococcus agalactiae is annotated
# as a fructose PTS (fru1), but does not seem to have been characterized,
# and could well be a xylitol PTS as well.
fruI	xylitol PTS, enzyme IIABC (FruI)	curated:TCDB::Q1LZ59	ignore:TCDB::Q3K0G6

# PTS systems form D-xylitol-5-phsophate
xylitol-PTS: fruI

# A three-part PTS system. Axl is short for arabitol and xylitol.
EIIA-Axl	xylitol PTS, enzyme IIA (EIIA-Axl)	curated:TCDB::Q71WA4
EIIB-Axl	xylitol PTS, enzyme IIB (EIIB-Axl)	curated:TCDB::Q71WA5
EIIC-Axl	xylitol PTS, enzyme IIC (EIIC-Axl)	curated:TCDB::Q71WA6
xylitol-PTS: EIIA-Axl EIIB-Axl EIIC-Axl

# 4-component ABC transporter in Dinoroseobacter shibae.
Dshi_0546	xylitol ABC transporter, ATPase component	curated:reanno::Dino:3607124
Dshi_0547	xylitol ABC transporter, substrate-binding component	curated:reanno::Dino:3607125
Dshi_0548	xylitol ABC transporter, permease component 1	curated:reanno::Dino:3607126
Dshi_0549	xylitol ABC transporter, permease component 2	curated:reanno::Dino:3607127

# Transporters and PTS systems were identified using
# query: transporter:xylitol
xylitol-transport: Dshi_0546 Dshi_0547 Dshi_0548 Dshi_0549

# 4-component ABC transporter in Herbaspirillum seropedicae
HSERO_RS17000	xylitol ABC transporter, substrate-binding component	uniprot:D8IPH7
HSERO_RS17005	xylitol ABC transporter, permease component 1	uniprot:D8IPH8
HSERO_RS17010	xylitol ABC transporter, permease component 2	uniprot:D8IPH9
HSERO_RS17020	xylitol ABC transporter, ATPase component	uniprot:D8IPI1
xylitol-transport: HSERO_RS17000 HSERO_RS17005 HSERO_RS17010 HSERO_RS17020

# 3-component ABC transporter in Pseudomonas simiae WCS417
PS417_12065	xylitol ABC transporter, ATPase component	uniprot:A0A1N7TX47
PS417_12060	xylitol ABC transporter, permease component	uniprot:A0A1N7UKA9
PS417_12055	xylitol ABC transporter, substrate-binding component	uniprot:A0A1N7UEK0
xylitol-transport: PS417_12065 PS417_12060 PS417_12055

PLT5	xylitol:H+ symporter PLT5	curated:CharProtDB::CH_091483	curated:TCDB::Q1XF07
xylitol-transport: PLT5

# xdhA is xylitol dehydrogenase
# xylB is D-xylulokinase
import xylose.steps:xdhA xylB

# In the MetaCyc pathway, the dehydrogenase xdhA forms
# D-xylulose and the kinase xylB forms D-xylulose-5-phosphate, which is
# an intermediate in the pentose phosphate pathway.
all: xylitol-transport xdhA xylB

# The D-xylulose-5-phosphate 2-reductase activity is probably provided by
# lmo2663 and/or lmo2664, but it possible that these enzymes produce D-arabitol-1-phosphate instead
# (PMID:27553222). These enzymes are related to D-arabitol-phosphate
# dehydrogenase (arpD) from Streptococcus avium.
# (lmo2663 = uniprot:Q8Y414; lmo2664 = uniprot:Q8Y413)
x5p-reductase	D-xylulose-5-phosphate 2-reductase	uniprot:Q8Y414	uniprot:Q8Y413

# Utilization via a PTS system is not described in MetaCyc, but is
# thought to involve a D-xylulose-5-phosphate 2-reductase (in
# reverse) that forms D-xylulose-5-phosphate,
# which is consumed by the pentose phosphate pathway (PMID:3104310, PMID:27553222).
all: xylitol-PTS x5p-reductase

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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