GapMind for catabolism of small carbon sources


D-xylose catabolism in Pseudomonas simiae WCS417

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 (27 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
gtsA xylose ABC transporter, periplasmic substrate-binding component GtsA PS417_22145
gtsB xylose ABC transporter, permease component 1 GtsB PS417_22140
gtsC xylose ABC transporter, permease component 2 GtsC PS417_22135
gtsD xylose ABC transporter, ATPase component GtsD PS417_22130 PS417_12700
xylA xylose isomerase PS417_10945
xylB xylulokinase PS417_12690 PS417_13655
Alternative steps:
aldA (glycol)aldehyde dehydrogenase PS417_00895 PS417_05945
aldox-large (glycol)aldehyde oxidoreductase, large subunit
aldox-med (glycol)aldehyde oxidoreductase, medium subunit PS417_24365
aldox-small (glycol)aldehyde oxidoreductase, small subunit PS417_24370 PS417_13030
araS component of Arabinose, fructose, xylose porter
araT component of Arabinose, fructose, xylose porter
araU component of Arabinose, fructose, xylose porter PS417_22135
araV component of Arabinose, fructose, xylose porter PS417_12700 PS417_22130
DKDP-aldolase 2-dehydro-3-deoxy-D-arabinonate aldolase PS417_14640
DKDP-dehydrog D-2-keto-3-deoxypentoate dehydrogenase PS417_11520 PS417_21340
dopDH 2,5-dioxopentanonate dehydrogenase PS417_11015 PS417_04200
Echvi_1871 sodium/xylose cotransporter
gal2 galactose/glucose/xylose uniporter
glcB malate synthase PS417_26040
glcP glucose/mannose/xylose:H+ symporter
gyaR glyoxylate reductase PS417_04730 PS417_12555
HDOP-hydrol 5-hydroxy-2,4-dioxopentanonate hydrolase PS417_18185 PS417_17835
kdaD 2-keto-3-deoxy-D-arabinonate dehydratase
xad D-xylonate dehydratase PS417_11000 PS417_00165
xdh D-xylose dehydrogenase PS417_11045 PS417_17895
xdhA xylitol dehydrogenase PS417_17720 PS417_12045
xylC xylonolactonase PS417_07255 PS417_11020
xylE_Tm ABC transporter for xylose, substrate binding component xylE
xylF ABC transporter for xylose, substrate binding component xylF PS417_10940
xylF_Tm ABC transporter for xylose, permease component xylF PS417_12060 PS417_17725
xylG ABC transporter for xylose, ATP-binding component xylG PS417_10935 PS417_11890
xylH ABC transporter for xylose, permease component xylH PS417_10930 PS417_12060
xylK_Tm ABC transporter for xylose, ATP binding component xylK PS417_11890 PS417_17730
xylT D-xylose transporter
xyrA xylitol reductase PS417_13335 PS417_10670

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