xylitol catabolism in Ochrobactrum rhizosphaerae PR17

GapMind for catabolism of small carbon sources

xylitol catabolism in Ochrobactrum rhizosphaerae PR17

Best path

PS417_12065, PS417_12060, PS417_12055, xdhA, xylB

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

19 steps (14 with candidates)

Or see definitions of steps

Step	Description	Best candidate	2nd candidate
PS417_12065	xylitol ABC transporter, ATPase component	CEV32_RS14910	CEV32_RS01950
PS417_12060	xylitol ABC transporter, permease component	CEV32_RS06955	CEV32_RS01955
PS417_12055	xylitol ABC transporter, substrate-binding component
xdhA	xylitol dehydrogenase	CEV32_RS06880	CEV32_RS01740
xylB	xylulokinase	CEV32_RS01110	CEV32_RS06950
Alternative steps:
Dshi_0546	xylitol ABC transporter, ATPase component	CEV32_RS03925	CEV32_RS02050
Dshi_0547	xylitol ABC transporter, substrate-binding component
Dshi_0548	xylitol ABC transporter, permease component 1	CEV32_RS20100	CEV32_RS19870
Dshi_0549	xylitol ABC transporter, permease component 2	CEV32_RS15685	CEV32_RS01925
EIIA-Axl	xylitol PTS, enzyme IIA (EIIA-Axl)	CEV32_RS02405
EIIB-Axl	xylitol PTS, enzyme IIB (EIIB-Axl)	CEV32_RS02400
EIIC-Axl	xylitol PTS, enzyme IIC (EIIC-Axl)	CEV32_RS02410
fruI	xylitol PTS, enzyme IIABC (FruI)
HSERO_RS17000	xylitol ABC transporter, substrate-binding component
HSERO_RS17005	xylitol ABC transporter, permease component 1	CEV32_RS15680	CEV32_RS20100
HSERO_RS17010	xylitol ABC transporter, permease component 2	CEV32_RS15685	CEV32_RS01925
HSERO_RS17020	xylitol ABC transporter, ATPase component	CEV32_RS20110	CEV32_RS19880
PLT5	xylitol:H+ symporter PLT5
x5p-reductase	D-xylulose-5-phosphate 2-reductase	CEV32_RS01740	CEV32_RS03355

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

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

Related tools

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