GapMind for catabolism of small carbon sources


D-xylose catabolism in Marinomonas arctica 328

Best path

xylF, xylG, xylH, xylA, xylB


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 DK187_RS20550 DK187_RS04280
xylG ABC transporter for xylose, ATP-binding component xylG DK187_RS20555 DK187_RS04275
xylH ABC transporter for xylose, permease component xylH DK187_RS20560 DK187_RS04270
xylA xylose isomerase DK187_RS04225
xylB xylulokinase DK187_RS04265 DK187_RS13485
Alternative steps:
aldA (glycol)aldehyde dehydrogenase DK187_RS02405 DK187_RS15780
aldox-large (glycol)aldehyde oxidoreductase, large subunit
aldox-med (glycol)aldehyde oxidoreductase, medium subunit DK187_RS18130
aldox-small (glycol)aldehyde oxidoreductase, small subunit DK187_RS18130
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 DK187_RS16035 DK187_RS08910
DKDP-aldolase 2-dehydro-3-deoxy-D-arabinonate aldolase DK187_RS13010
DKDP-dehydrog D-2-keto-3-deoxypentoate dehydrogenase DK187_RS13080 DK187_RS05415
dopDH 2,5-dioxopentanonate dehydrogenase DK187_RS15865 DK187_RS20580
Echvi_1871 sodium/xylose cotransporter
gal2 galactose/glucose/xylose uniporter
glcB malate synthase DK187_RS13940
glcP glucose/mannose/xylose:H+ symporter
gtsA xylose ABC transporter, periplasmic substrate-binding component GtsA DK187_RS03300 DK187_RS17240
gtsB xylose ABC transporter, permease component 1 GtsB DK187_RS03295 DK187_RS17245
gtsC xylose ABC transporter, permease component 2 GtsC DK187_RS03290 DK187_RS17250
gtsD xylose ABC transporter, ATPase component GtsD DK187_RS03285 DK187_RS04605
gyaR glyoxylate reductase DK187_RS10550 DK187_RS16380
HDOP-hydrol 5-hydroxy-2,4-dioxopentanonate hydrolase DK187_RS05505 DK187_RS19500
kdaD 2-keto-3-deoxy-D-arabinonate dehydratase
xad D-xylonate dehydratase DK187_RS20575 DK187_RS11915
xdh D-xylose dehydrogenase DK187_RS11910 DK187_RS20570
xdhA xylitol dehydrogenase DK187_RS14770 DK187_RS02445
xylC xylonolactonase DK187_RS11895 DK187_RS03545
xylE_Tm ABC transporter for xylose, substrate binding component xylE DK187_RS19175
xylF_Tm ABC transporter for xylose, permease component xylF DK187_RS05065 DK187_RS04235
xylK_Tm ABC transporter for xylose, ATP binding component xylK DK187_RS16470 DK187_RS20555
xylT D-xylose transporter
xyrA xylitol reductase DK187_RS13020 DK187_RS09090

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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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