D-xylose catabolism in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

D-xylose catabolism in Dinoroseobacter shibae DFL-12

Best path

Also see fitness data for the top candidates

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 (27 with candidates)

Or see definitions of steps

Step	Description	Best candidate	2nd candidate
xylT	D-xylose transporter
xylA	xylose isomerase	Dshi_1996
xylB	xylulokinase	Dshi_1997	Dshi_1235
Alternative steps:
aldA	(glycol)aldehyde dehydrogenase	Dshi_2887	Dshi_1425
aldox-large	(glycol)aldehyde oxidoreductase, large subunit	Dshi_2659	Dshi_4202
aldox-med	(glycol)aldehyde oxidoreductase, medium subunit	Dshi_1210	Dshi_4200
aldox-small	(glycol)aldehyde oxidoreductase, small subunit	Dshi_1211	Dshi_2660
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	Dshi_2017	Dshi_3141
DKDP-aldolase	2-dehydro-3-deoxy-D-arabinonate aldolase	Dshi_0149
DKDP-dehydrog	D-2-keto-3-deoxypentoate dehydrogenase	Dshi_0553	Dshi_2182
dopDH	2,5-dioxopentanonate dehydrogenase	Dshi_0577	Dshi_2442
Echvi_1871	sodium/xylose cotransporter	Dshi_3906	Dshi_3904
gal2	galactose/glucose/xylose uniporter
glcB	malate synthase	Dshi_1227	Dshi_2874
glcP	glucose/mannose/xylose:H+ symporter
gtsA	xylose ABC transporter, periplasmic substrate-binding component GtsA
gtsB	xylose ABC transporter, permease component 1 GtsB
gtsC	xylose ABC transporter, permease component 2 GtsC	Dshi_1246	Dshi_1650
gtsD	xylose ABC transporter, ATPase component GtsD	Dshi_1416	Dshi_2017
gyaR	glyoxylate reductase	Dshi_2970	Dshi_2643
HDOP-hydrol	5-hydroxy-2,4-dioxopentanonate hydrolase	Dshi_2542	Dshi_0967
kdaD	2-keto-3-deoxy-D-arabinonate dehydratase	Dshi_2542
xad	D-xylonate dehydratase	Dshi_1244	Dshi_0129
xdh	D-xylose dehydrogenase	Dshi_1243	Dshi_3712
xdhA	xylitol dehydrogenase	Dshi_0551	Dshi_4159
xylC	xylonolactonase	Dshi_1240
xylE_Tm	ABC transporter for xylose, substrate binding component xylE
xylF	ABC transporter for xylose, substrate binding component xylF	Dshi_2000
xylF_Tm	ABC transporter for xylose, permease component xylF	Dshi_2432	Dshi_2431
xylG	ABC transporter for xylose, ATP-binding component xylG	Dshi_2433	Dshi_0530
xylH	ABC transporter for xylose, permease component xylH	Dshi_2431	Dshi_1999
xylK_Tm	ABC transporter for xylose, ATP binding component xylK	Dshi_2433	Dshi_0530
xyrA	xylitol reductase	Dshi_0539

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 17 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