D-xylose catabolism in Rhizobium johnstonii 3841

GapMind for catabolism of small carbon sources

D-xylose catabolism in Rhizobium johnstonii 3841

Best path

Rules

Overview: Xylose degradation in GapMind is based on MetaCyc pathways I via D-xylulose (link), II via xylitol (link), III or V via 2-dehydro-3-deoxy-D-arabinonate (DKDP) dehydratase (link, link), IV via DKDP aldolase (link), as well as another pathway via DKDP dehydrogenase (PMC6336799).

all:

xylose-transport, xylA and xylB
or xylose-transport, xyrA, xdhA and xylB
or xylose-transport, xdh, xylC, xad, kdaD and dopDH
or xylose-transport, xdh, xylC, xad, DKDP-aldolase, glycolaldehyde-dehydrogenase, gyaR and glcB
or xylose-transport, xdh, xylC, xad, DKDP-dehydrog, HDOP-hydrol, gyaR and glcB
Comment: In pathway I, isomerase xylA forms D-xylulose and kinase xylB forms D-xylulose 5-phosphate, an intermediate in the pentose phosphate pathway. In pathway II, the reductase xyrA forms xylitol, the dehydrogenase xdhA forms xylitol, and the kinase xylB forms D-xylulose 5-phosphate. (This pathway is only reported in fungi.) In pathway III or V, dehydrogenase xdh forms xylonolactone, lactonase xylC forms D-xylonate, dehydratase xad forms 2-dehydro-3-deoxy-D-arabinonate, dehydratase kdaD forms 2,5-dioxopentanoate (also known as α-ketoglutarate semialdehyde), and dopDH forms 2-oxoglutarate, an intermediate in the TCA cycle. (Pathway III has a 1,4-lactone intermediate, while pathway V has a 1,5-lactone intermediate; GapMind does not distinguish these.) In pathway IV, xdh and xylC form D-xylonate, dehydratase xad forms 2-dehydro-3-deoxy-D-arabinonate (DKDP), and an aldolase forms pyruvate and glycolaldehyde; glycolaldehyde is oxidized to glycolate and to glyoxylate, and assimilated by malate synthase (glcB). Alternatively, after DKDP is formed, a dehydrogenase forms 5-hydroxy,2-4-dioxopentanonate (HDOP), and a hydrolase forms pyruvate and glycolate (PMC6336799); the glycolate is oxidized to glyoxylate and converted to malate.

glycolaldehyde-dehydrogenase:

aldA
or aldox-large, aldox-med and aldox-small

xylose-transport:

xylT
or gal2
or glcP
or Echvi_1871
or xylF, xylG and xylH
or xylF_Tm, xylE_Tm and xylK_Tm
or araV, araU, araT and araS
or gtsA, gtsB, gtsC and gtsD
Comment: Transporters were identified using query: transporter:D-xylose:xylose:CPD-15377

36 steps (30 with candidates)

Or see definitions of steps

Step	Description	Best candidate	2nd candidate
xylF	ABC transporter for xylose, substrate binding component xylF	RL_RS18635	RL_RS18670
xylG	ABC transporter for xylose, ATP-binding component xylG	RL_RS18630	RL_RS23960
xylH	ABC transporter for xylose, permease component xylH	RL_RS18625	RL_RS19815
xylA	xylose isomerase	RL_RS21535
xylB	xylulokinase	RL_RS21540	RL_RS36725
Alternative steps:
aldA	(glycol)aldehyde dehydrogenase	RL_RS00540	RL_RS28045
aldox-large	(glycol)aldehyde oxidoreductase, large subunit
aldox-med	(glycol)aldehyde oxidoreductase, medium subunit	RL_RS18385
aldox-small	(glycol)aldehyde oxidoreductase, small subunit	RL_RS25285	RL_RS34435
araS	component of Arabinose, fructose, xylose porter
araT	component of Arabinose, fructose, xylose porter	RL_RS08605
araU	component of Arabinose, fructose, xylose porter	RL_RS33030	RL_RS22570
araV	component of Arabinose, fructose, xylose porter	RL_RS17260	RL_RS33780
DKDP-aldolase	2-dehydro-3-deoxy-D-arabinonate aldolase	RL_RS07805	RL_RS35540
DKDP-dehydrog	D-2-keto-3-deoxypentoate dehydrogenase	RL_RS32780	RL_RS05075
dopDH	2,5-dioxopentanonate dehydrogenase	RL_RS18615	RL_RS11875
Echvi_1871	sodium/xylose cotransporter
gal2	galactose/glucose/xylose uniporter
glcB	malate synthase	RL_RS00270	RL_RS24195
glcP	glucose/mannose/xylose:H+ symporter
gtsA	xylose ABC transporter, periplasmic substrate-binding component GtsA	RL_RS09500	RL_RS21915
gtsB	xylose ABC transporter, permease component 1 GtsB	RL_RS21910	RL_RS14435
gtsC	xylose ABC transporter, permease component 2 GtsC	RL_RS21905	RL_RS09510
gtsD	xylose ABC transporter, ATPase component GtsD	RL_RS19665	RL_RS21900
gyaR	glyoxylate reductase	RL_RS00780	RL_RS29355
HDOP-hydrol	5-hydroxy-2,4-dioxopentanonate hydrolase	RL_RS00080
kdaD	2-keto-3-deoxy-D-arabinonate dehydratase	RL_RS27325	RL_RS00080
xad	D-xylonate dehydratase	RL_RS19450	RL_RS18610
xdh	D-xylose dehydrogenase	RL_RS00480	RL_RS04790
xdhA	xylitol dehydrogenase	RL_RS31695	RL_RS29350
xylC	xylonolactonase	RL_RS36795	RL_RS30660
xylE_Tm	ABC transporter for xylose, substrate binding component xylE	RL_RS12625	RL_RS12260
xylF_Tm	ABC transporter for xylose, permease component xylF	RL_RS02695	RL_RS34865
xylK_Tm	ABC transporter for xylose, ATP binding component xylK	RL_RS12630	RL_RS23960
xylT	D-xylose transporter
xyrA	xylitol reductase	RL_RS36710	RL_RS23475

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 Apr 09 2024. 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 2024 update 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