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:
- xylitol-PTS:
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
Dshi_0548: xylitol ABC transporter, permease component 1
Dshi_0549: xylitol ABC transporter, permease component 2
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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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:
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