D-xylose catabolism in Phyllobacterium endophyticum PEPV15

GapMind for catabolism of small carbon sources

D-xylose catabolism in Phyllobacterium endophyticum PEPV15

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	CU100_RS21650	CU100_RS03130
xylG	ABC transporter for xylose, ATP-binding component xylG	CU100_RS21645	CU100_RS06140
xylH	ABC transporter for xylose, permease component xylH	CU100_RS21640	CU100_RS22485
xylA	xylose isomerase	CU100_RS03115
xylB	xylulokinase	CU100_RS03120	CU100_RS22585
Alternative steps:
aldA	(glycol)aldehyde dehydrogenase	CU100_RS14940	CU100_RS08050
aldox-large	(glycol)aldehyde oxidoreductase, large subunit	CU100_RS04825	CU100_RS14675
aldox-med	(glycol)aldehyde oxidoreductase, medium subunit	CU100_RS04830	CU100_RS14695
aldox-small	(glycol)aldehyde oxidoreductase, small subunit	CU100_RS14690	CU100_RS04820
araS	component of Arabinose, fructose, xylose porter
araT	component of Arabinose, fructose, xylose porter
araU	component of Arabinose, fructose, xylose porter	CU100_RS17355
araV	component of Arabinose, fructose, xylose porter	CU100_RS19320	CU100_RS02485
DKDP-aldolase	2-dehydro-3-deoxy-D-arabinonate aldolase	CU100_RS13875
DKDP-dehydrog	D-2-keto-3-deoxypentoate dehydrogenase	CU100_RS24915	CU100_RS24550
dopDH	2,5-dioxopentanonate dehydrogenase	CU100_RS26485	CU100_RS26265
Echvi_1871	sodium/xylose cotransporter
gal2	galactose/glucose/xylose uniporter
glcB	malate synthase	CU100_RS03955	CU100_RS01445
glcP	glucose/mannose/xylose:H+ symporter
gtsA	xylose ABC transporter, periplasmic substrate-binding component GtsA	CU100_RS02575	CU100_RS17275
gtsB	xylose ABC transporter, permease component 1 GtsB	CU100_RS02580	CU100_RS17270
gtsC	xylose ABC transporter, permease component 2 GtsC	CU100_RS02585	CU100_RS17265
gtsD	xylose ABC transporter, ATPase component GtsD	CU100_RS20770	CU100_RS02590
gyaR	glyoxylate reductase	CU100_RS04245	CU100_RS20605
HDOP-hydrol	5-hydroxy-2,4-dioxopentanonate hydrolase	CU100_RS02455	CU100_RS26230
kdaD	2-keto-3-deoxy-D-arabinonate dehydratase	CU100_RS24115
xad	D-xylonate dehydratase	CU100_RS02465	CU100_RS21080
xdh	D-xylose dehydrogenase	CU100_RS16385	CU100_RS01840
xdhA	xylitol dehydrogenase	CU100_RS26385	CU100_RS03640
xylC	xylonolactonase	CU100_RS11445	CU100_RS11440
xylE_Tm	ABC transporter for xylose, substrate binding component xylE	CU100_RS11265	CU100_RS15985
xylF_Tm	ABC transporter for xylose, permease component xylF	CU100_RS15980	CU100_RS06145
xylK_Tm	ABC transporter for xylose, ATP binding component xylK	CU100_RS24845	CU100_RS11270
xylT	D-xylose transporter
xyrA	xylitol reductase	CU100_RS06155	CU100_RS01830

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.

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

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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