GapMind for catabolism of small carbon sources


D-xylose catabolism in Algoriphagus machipongonensis PR1

Best path

Echvi_1871, 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 (19 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
Echvi_1871 sodium/xylose cotransporter ALPR1_RS12485 ALPR1_RS16525
xylA xylose isomerase ALPR1_RS12475
xylB xylulokinase ALPR1_RS12480
Alternative steps:
aldA (glycol)aldehyde dehydrogenase ALPR1_RS01205 ALPR1_RS06860
aldox-large (glycol)aldehyde oxidoreductase, large subunit
aldox-med (glycol)aldehyde oxidoreductase, medium subunit
aldox-small (glycol)aldehyde oxidoreductase, small subunit ALPR1_RS12140 ALPR1_RS01975
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 ALPR1_RS06390 ALPR1_RS04965
DKDP-aldolase 2-dehydro-3-deoxy-D-arabinonate aldolase ALPR1_RS17120
DKDP-dehydrog D-2-keto-3-deoxypentoate dehydrogenase ALPR1_RS17925 ALPR1_RS13840
dopDH 2,5-dioxopentanonate dehydrogenase ALPR1_RS03515 ALPR1_RS01205
gal2 galactose/glucose/xylose uniporter
glcB malate synthase
glcP glucose/mannose/xylose:H+ symporter
gtsA xylose ABC transporter, periplasmic substrate-binding component GtsA
gtsB xylose ABC transporter, permease component 1 GtsB
gtsC xylose ABC transporter, permease component 2 GtsC
gtsD xylose ABC transporter, ATPase component GtsD ALPR1_RS06390 ALPR1_RS13410
gyaR glyoxylate reductase ALPR1_RS12870 ALPR1_RS11040
HDOP-hydrol 5-hydroxy-2,4-dioxopentanonate hydrolase ALPR1_RS13845
kdaD 2-keto-3-deoxy-D-arabinonate dehydratase ALPR1_RS00910
xad D-xylonate dehydratase ALPR1_RS18915 ALPR1_RS16225
xdh D-xylose dehydrogenase ALPR1_RS04245 ALPR1_RS14805
xdhA xylitol dehydrogenase ALPR1_RS16070 ALPR1_RS08420
xylC xylonolactonase ALPR1_RS03685
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
xylG ABC transporter for xylose, ATP-binding component xylG
xylH ABC transporter for xylose, permease component xylH
xylK_Tm ABC transporter for xylose, ATP binding component xylK
xylT D-xylose transporter ALPR1_RS12850 ALPR1_RS10185
xyrA xylitol reductase ALPR1_RS12360 ALPR1_RS14305

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