Definition of xylitol catabolism

GapMind for catabolism of small carbon sources

Definition of xylitol catabolism

As rules and steps, or see full text

Rules

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

all:

xylitol-transport, xdhA and xylB
or xylitol-PTS and x5p-reductase
Comment: 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. 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).

xylitol-transport:

Dshi_0546, Dshi_0547, Dshi_0548 and Dshi_0549
or HSERO_RS17000, HSERO_RS17005, HSERO_RS17010 and HSERO_RS17020
or PS417_12065, PS417_12060 and PS417_12055
or PLT5
Comment: Transporters and PTS systems were identified using query: transporter:xylitol

xylitol-PTS:

fruI
or EIIA-Axl, EIIB-Axl and EIIC-Axl
Comment: PTS systems form D-xylitol-5-phsophate

Steps

fruI: xylitol PTS, enzyme IIABC (FruI)

Curated sequence Q1LZ59: The fructose inducible fructose/xylitol porter, FruI
Ignore hits to Q3K0G6 when looking for 'other' hits (Chromosomal fructose Enzyme IIABC (Fru1) of 654 aas; in an operon with fructose-1-P kinase)
Comment: 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.
Total: 1 characterized proteins

EIIA-Axl: xylitol PTS, enzyme IIA (EIIA-Axl)

Curated sequence Q71WA4: PTS system, IIA component, component of Pentitol [arabitol (arabinitol, lyxitol)/xylitol] PTS permease, IICBA (encoded within an operon that also encodes a polyol-P dehydrogenase, a ribose-5-P isomerase, a ribulose 5-P-3-epimerase, and a BlgG-type PTS antiterminator) (Saklani-Jusforgues et al., 2001; Kentache T et al., 2016, in press)
Comment: A three-part PTS system. Axl is short for arabitol and xylitol.
Total: 1 characterized proteins

EIIB-Axl: xylitol PTS, enzyme IIB (EIIB-Axl)

Curated sequence Q71WA5: Putative PTS system, galactitol-specific, IIB component, component of Pentitol [arabitol (arabinitol, lyxitol)/xylitol] PTS permease, IICBA (encoded within an operon that also encodes a polyol-P dehydrogenase, a ribose-5-P isomerase, a ribulose 5-P-3-epimerase, and a BlgG-type PTS antiterminator) (Saklani-Jusforgues et al., 2001; Kentache T et al., 2016, in press)
Total: 1 characterized proteins

EIIC-Axl: xylitol PTS, enzyme IIC (EIIC-Axl)

Curated sequence Q71WA6: PTS system, galactitol-specific, IIC component, component of Pentitol [arabitol (arabinitol, lyxitol)/xylitol] PTS permease, IICBA (encoded within an operon that also encodes a polyol-P dehydrogenase, a ribose-5-P isomerase, a ribulose 5-P-3-epimerase, and a BlgG-type PTS antiterminator) (Saklani-Jusforgues et al., 2001; Kentache T et al., 2016, in press)
Total: 1 characterized proteins

Dshi_0546: xylitol ABC transporter, ATPase component

Curated sequence 3607124: ABC transporter for Xylitol, ATPase component
Comment: 4-component ABC transporter in Dinoroseobacter shibae.
Total: 1 characterized proteins

Dshi_0547: xylitol ABC transporter, substrate-binding component

Curated sequence 3607125: ABC transporter for Xylitol, periplasmic substrate-binding component
Total: 1 characterized proteins

Dshi_0548: xylitol ABC transporter, permease component 1

Curated sequence 3607126: ABC transporter for Xylitol, permease component 1
Total: 1 characterized proteins

Dshi_0549: xylitol ABC transporter, permease component 2

Curated sequence 3607127: ABC transporter for Xylitol, permease component 2
Total: 1 characterized proteins

HSERO_RS17000: xylitol ABC transporter, substrate-binding component

UniProt sequence D8IPH7: SubName: Full=ABC-type sugar transport system, periplasmic component protein {ECO:0000313|EMBL:ADJ64874.1};
Comment: 4-component ABC transporter in Herbaspirillum seropedicae
Total: 1 characterized proteins

HSERO_RS17005: xylitol ABC transporter, permease component 1

UniProt sequence D8IPH8: SubName: Full=ABC-type sugar transport system, permease component protein {ECO:0000313|EMBL:ADJ64875.1};
Total: 1 characterized proteins

HSERO_RS17010: xylitol ABC transporter, permease component 2

UniProt sequence D8IPH9: SubName: Full=ABC-type sugar transport system, permease component protein {ECO:0000313|EMBL:ADJ64876.1};
Total: 1 characterized proteins

HSERO_RS17020: xylitol ABC transporter, ATPase component

UniProt sequence D8IPI1: SubName: Full=ABC-type sugar transport system, ATPase component protein {ECO:0000313|EMBL:ADJ64878.1};
Total: 1 characterized proteins

PS417_12065: xylitol ABC transporter, ATPase component

UniProt sequence A0A1N7TX47: SubName: Full=D-ribose transporter ATP-binding protein {ECO:0000313|EMBL:AIB36300.1}; SubName: Full=Putative xylitol transport system ATP-binding protein {ECO:0000313|EMBL:SFB30631.1}; SubName: Full=Sugar ABC transporter ATP-binding protein {ECO:0000313|EMBL:PRW86400.1};
Comment: 3-component ABC transporter in Pseudomonas simiae WCS417
Total: 1 characterized proteins

PS417_12060: xylitol ABC transporter, permease component

UniProt sequence A0A1N7UKA9: SubName: Full=ABC transporter permease {ECO:0000313|EMBL:PRW86399.1}; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family {ECO:0000313|EMBL:SFB30651.1}; SubName: Full=Sugar ABC transporter permease {ECO:0000313|EMBL:AIB36299.1};
Total: 1 characterized proteins

PS417_12055: xylitol ABC transporter, substrate-binding component

UniProt sequence A0A1N7UEK0: SubName: Full=Putative xylitol transport system substrate-binding protein {ECO:0000313|EMBL:SFB30667.1}; SubName: Full=Sugar ABC transporter substrate-binding protein {ECO:0000313|EMBL:AIB36298.1};
Total: 1 characterized proteins

PLT5: xylitol:H+ symporter PLT5

Curated sequence CH_091483: polyol transporter 5. Polyol transporter 5; Protein POLYOL TRANSPORTER 5; AtPLT5; Sugar-proton symporter PLT5. The broad specificity sugar/sugar alcohol (myo-inositol, glycerol, ribose, sorbitol, mannitol, xylitol, erythritol, etc) H+ symporter, AtPLT5 (transports a wide range of hexoses, pentoses, tetroses, sugar alcohols and a sugar acid, but not disaccharides) (Reinders et al., 2005) (expressed in roots, leaves and floral organs)
Curated sequence Q1XF07: Polyol (xylitol):H+ symporter, PLT4
Total: 2 characterized proteins

xdhA: xylitol dehydrogenase

Curated proteins or TIGRFams with EC 1.1.1.9
Ignore hits to items matching 1.1.1.14 when looking for 'other' hits
Ignore hits to items matching xylulose reductase when looking for 'other' hits
Comment: L-iditol 2-dehydrogenases (EC 1.1.1.14) often act on xylitol as well, so are ignored. There's also some xylulose reductases annotated but without an EC number.
Total: 24 characterized proteins

xylB: xylulokinase

Curated proteins or TIGRFams with EC 2.7.1.17
UniProt sequence L0FZT0: SubName: Full=Pentulose/hexulose kinase {ECO:0000313|EMBL:AGA78130.1};
UniProt sequence Q97FW4: RecName: Full=Xylulose kinase {ECO:0000256|HAMAP-Rule:MF_02220, ECO:0000256|RuleBase:RU364073}; Short=Xylulokinase {ECO:0000256|HAMAP-Rule:MF_02220, ECO:0000256|RuleBase:RU364073}; EC=2.7.1.17 {ECO:0000256|HAMAP-Rule:MF_02220, ECO:0000256|RuleBase:RU364073};
UniProt sequence Q8A9M3: SubName: Full=Xylulose kinase (Xylulokinase) {ECO:0000313|EMBL:AAO75899.1};
Comment: Echvi_1875 (L0FZT0) is annotated as xylulose kinase and has its strongest phentoypes on xylose. CA_C2612 (Q97FW4) from Clostridium acetobutylicum was proven to be xylulose kinase (PMC2873477). BT0792 (Q8A9M3) has its strongest phenotypes on xylose.
Total: 1 HMMs and 21 characterized proteins

x5p-reductase: D-xylulose-5-phosphate 2-reductase

UniProt sequence Q8Y414: SubName: Full=Lmo2663 protein {ECO:0000313|EMBL:CAD00876.1};
UniProt sequence Q8Y413: SubName: Full=Lmo2664 protein {ECO:0000313|EMBL:CAD00877.1};
Comment: 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 = Q8Y414; lmo2664 = Q8Y413)
Total: 2 characterized proteins

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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, or view the source code.

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