GapMind for catabolism of small carbon sources


D-xylose catabolism in Pseudomonas fluorescens FW300-N1B4

Best path

gtsA, gtsB, gtsC, gtsD, xylA, xylB

Also see fitness data for the top candidates


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).

36 steps (23 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
gtsA xylose ABC transporter, periplasmic substrate-binding component GtsA Pf1N1B4_596
gtsB xylose ABC transporter, permease component 1 GtsB Pf1N1B4_595
gtsC xylose ABC transporter, permease component 2 GtsC Pf1N1B4_594
gtsD xylose ABC transporter, ATPase component GtsD Pf1N1B4_593 Pf1N1B4_4847
xylA xylose isomerase
xylB xylulokinase Pf1N1B4_4845
Alternative steps:
aldA (glycol)aldehyde dehydrogenase Pf1N1B4_5695 Pf1N1B4_4931
aldox-large (glycol)aldehyde oxidoreductase, large subunit
aldox-med (glycol)aldehyde oxidoreductase, medium subunit
aldox-small (glycol)aldehyde oxidoreductase, small subunit Pf1N1B4_4870 Pf1N1B4_4583
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 Pf1N1B4_3974 Pf1N1B4_4847
DKDP-aldolase 2-dehydro-3-deoxy-D-arabinonate aldolase Pf1N1B4_3332 Pf1N1B4_5813
DKDP-dehydrog D-2-keto-3-deoxypentoate dehydrogenase Pf1N1B4_512 Pf1N1B4_4954
dopDH 2,5-dioxopentanonate dehydrogenase Pf1N1B4_1109 Pf1N1B4_4624
Echvi_1871 sodium/xylose cotransporter
gal2 galactose/glucose/xylose uniporter
glcB malate synthase Pf1N1B4_2478
glcP glucose/mannose/xylose:H+ symporter
gyaR glyoxylate reductase Pf1N1B4_1004 Pf1N1B4_4763
HDOP-hydrol 5-hydroxy-2,4-dioxopentanonate hydrolase Pf1N1B4_2275
kdaD 2-keto-3-deoxy-D-arabinonate dehydratase
xad D-xylonate dehydratase Pf1N1B4_4621 Pf1N1B4_398
xdh D-xylose dehydrogenase Pf1N1B4_4943 Pf1N1B4_451
xdhA xylitol dehydrogenase Pf1N1B4_512 Pf1N1B4_5039
xylC xylonolactonase Pf1N1B4_413 Pf1N1B4_4510
xylE_Tm ABC transporter for xylose, substrate binding component xylE
xylF ABC transporter for xylose, substrate binding component xylF
xylF_Tm ABC transporter for xylose, permease component xylF Pf1N1B4_4287 Pf1N1B4_409
xylG ABC transporter for xylose, ATP-binding component xylG Pf1N1B4_4286 Pf1N1B4_410
xylH ABC transporter for xylose, permease component xylH Pf1N1B4_4287 Pf1N1B4_409
xylK_Tm ABC transporter for xylose, ATP binding component xylK Pf1N1B4_4286 Pf1N1B4_410
xylT D-xylose transporter
xyrA xylitol reductase Pf1N1B4_4693 Pf1N1B4_128

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.



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:

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:

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:

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:

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