GapMind for catabolism of small carbon sources


D-xylose catabolism in Pseudomonas fluorescens FW300-N2E2

Best path

xylF, xylG, xylH, 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 (27 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
xylF ABC transporter for xylose, substrate binding component xylF Pf6N2E2_1455
xylG ABC transporter for xylose, ATP-binding component xylG Pf6N2E2_1456 Pf6N2E2_523
xylH ABC transporter for xylose, permease component xylH Pf6N2E2_1457 Pf6N2E2_524
xylA xylose isomerase Pf6N2E2_1454
xylB xylulokinase Pf6N2E2_805
Alternative steps:
aldA (glycol)aldehyde dehydrogenase Pf6N2E2_1102 Pf6N2E2_1751
aldox-large (glycol)aldehyde oxidoreductase, large subunit
aldox-med (glycol)aldehyde oxidoreductase, medium subunit
aldox-small (glycol)aldehyde oxidoreductase, small subunit Pf6N2E2_1203 Pf6N2E2_5938
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 Pf6N2E2_1960 Pf6N2E2_807
DKDP-aldolase 2-dehydro-3-deoxy-D-arabinonate aldolase Pf6N2E2_2747 Pf6N2E2_3203
DKDP-dehydrog D-2-keto-3-deoxypentoate dehydrogenase Pf6N2E2_1663 Pf6N2E2_1004
dopDH 2,5-dioxopentanonate dehydrogenase Pf6N2E2_612 Pf6N2E2_3298
Echvi_1871 sodium/xylose cotransporter
gal2 galactose/glucose/xylose uniporter
glcB malate synthase Pf6N2E2_4752
glcP glucose/mannose/xylose:H+ symporter
gtsA xylose ABC transporter, periplasmic substrate-binding component GtsA Pf6N2E2_2892
gtsB xylose ABC transporter, permease component 1 GtsB Pf6N2E2_2891
gtsC xylose ABC transporter, permease component 2 GtsC Pf6N2E2_2890
gtsD xylose ABC transporter, ATPase component GtsD Pf6N2E2_2889 Pf6N2E2_1649
gyaR glyoxylate reductase Pf6N2E2_5310 Pf6N2E2_627
HDOP-hydrol 5-hydroxy-2,4-dioxopentanonate hydrolase Pf6N2E2_865 Pf6N2E2_1662
kdaD 2-keto-3-deoxy-D-arabinonate dehydratase Pf6N2E2_1667 Pf6N2E2_862
xad D-xylonate dehydratase Pf6N2E2_1668 Pf6N2E2_609
xdh D-xylose dehydrogenase Pf6N2E2_1839 Pf6N2E2_1004
xdhA xylitol dehydrogenase Pf6N2E2_5889 Pf6N2E2_1375
xylC xylonolactonase Pf6N2E2_5966 Pf6N2E2_488
xylE_Tm ABC transporter for xylose, substrate binding component xylE
xylF_Tm ABC transporter for xylose, permease component xylF Pf6N2E2_524 Pf6N2E2_5970
xylK_Tm ABC transporter for xylose, ATP binding component xylK Pf6N2E2_523 Pf6N2E2_1008
xylT D-xylose transporter Pf6N2E2_883
xyrA xylitol reductase Pf6N2E2_1443 Pf6N2E2_1615

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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