D-xylose catabolism in Bradyrhizobium diazoefficiens USDA110

GapMind for catabolism of small carbon sources

D-xylose catabolism in Bradyrhizobium diazoefficiens USDA110

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 (28 with candidates)

Or see definitions of steps

Step	Description	Best candidate	2nd candidate
xylF	ABC transporter for xylose, substrate binding component xylF	BJA_RS15925	BJA_RS05700
xylG	ABC transporter for xylose, ATP-binding component xylG	BJA_RS15930	BJA_RS29285
xylH	ABC transporter for xylose, permease component xylH	BJA_RS15935	BJA_RS05695
xylA	xylose isomerase	BJA_RS05685
xylB	xylulokinase	BJA_RS05680	BJA_RS29290
Alternative steps:
aldA	(glycol)aldehyde dehydrogenase	BJA_RS04085	BJA_RS38580
aldox-large	(glycol)aldehyde oxidoreductase, large subunit	BJA_RS01685	BJA_RS19675
aldox-med	(glycol)aldehyde oxidoreductase, medium subunit	BJA_RS31600	BJA_RS17525
aldox-small	(glycol)aldehyde oxidoreductase, small subunit	BJA_RS01680	BJA_RS28670
araS	component of Arabinose, fructose, xylose porter
araT	component of Arabinose, fructose, xylose porter
araU	component of Arabinose, fructose, xylose porter
araV	component of Arabinose, fructose, xylose porter	BJA_RS19420	BJA_RS17985
DKDP-aldolase	2-dehydro-3-deoxy-D-arabinonate aldolase	BJA_RS36875	BJA_RS25565
DKDP-dehydrog	D-2-keto-3-deoxypentoate dehydrogenase	BJA_RS16540	BJA_RS19405
dopDH	2,5-dioxopentanonate dehydrogenase	BJA_RS29725	BJA_RS18690
Echvi_1871	sodium/xylose cotransporter
gal2	galactose/glucose/xylose uniporter
glcB	malate synthase	BJA_RS07540	BJA_RS34450
glcP	glucose/mannose/xylose:H+ symporter
gtsA	xylose ABC transporter, periplasmic substrate-binding component GtsA
gtsB	xylose ABC transporter, permease component 1 GtsB	BJA_RS24340
gtsC	xylose ABC transporter, permease component 2 GtsC	BJA_RS24345
gtsD	xylose ABC transporter, ATPase component GtsD	BJA_RS24350	BJA_RS19420
gyaR	glyoxylate reductase	BJA_RS03880	BJA_RS35810
HDOP-hydrol	5-hydroxy-2,4-dioxopentanonate hydrolase	BJA_RS32210	BJA_RS40065
kdaD	2-keto-3-deoxy-D-arabinonate dehydratase	BJA_RS15880
xad	D-xylonate dehydratase	BJA_RS19410	BJA_RS01895
xdh	D-xylose dehydrogenase	BJA_RS14080	BJA_RS16805
xdhA	xylitol dehydrogenase	BJA_RS28150	BJA_RS34615
xylC	xylonolactonase	BJA_RS17075	BJA_RS16710
xylE_Tm	ABC transporter for xylose, substrate binding component xylE	BJA_RS11085
xylF_Tm	ABC transporter for xylose, permease component xylF	BJA_RS11095	BJA_RS29280
xylK_Tm	ABC transporter for xylose, ATP binding component xylK	BJA_RS11090	BJA_RS13250
xylT	D-xylose transporter
xyrA	xylitol reductase	BJA_RS31685	BJA_RS26470

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