GapMind for catabolism of small carbon sources

 

D-xylose catabolism in Caldicellulosiruptor hydrothermalis 108

Best path

xylF, xylG, xylH, xylA, xylB

Rules

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 (20 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
xylF ABC transporter for xylose, substrate binding component xylF CALHY_RS00525 CALHY_RS00505
xylG ABC transporter for xylose, ATP-binding component xylG CALHY_RS00530 CALHY_RS00570
xylH ABC transporter for xylose, permease component xylH CALHY_RS00535 CALHY_RS03455
xylA xylose isomerase CALHY_RS10405
xylB xylulokinase CALHY_RS10535 CALHY_RS00630
Alternative steps:
aldA (glycol)aldehyde dehydrogenase
aldox-large (glycol)aldehyde oxidoreductase, large subunit
aldox-med (glycol)aldehyde oxidoreductase, medium subunit
aldox-small (glycol)aldehyde oxidoreductase, small subunit
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 CALHY_RS04750 CALHY_RS07950
DKDP-aldolase 2-dehydro-3-deoxy-D-arabinonate aldolase CALHY_RS08105
DKDP-dehydrog D-2-keto-3-deoxypentoate dehydrogenase CALHY_RS02575 CALHY_RS08000
dopDH 2,5-dioxopentanonate dehydrogenase
Echvi_1871 sodium/xylose cotransporter
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 CALHY_RS11070
gtsC xylose ABC transporter, permease component 2 GtsC CALHY_RS12095
gtsD xylose ABC transporter, ATPase component GtsD CALHY_RS04750 CALHY_RS07950
gyaR glyoxylate reductase CALHY_RS00645 CALHY_RS02550
HDOP-hydrol 5-hydroxy-2,4-dioxopentanonate hydrolase CALHY_RS02540 CALHY_RS09440
kdaD 2-keto-3-deoxy-D-arabinonate dehydratase
xad D-xylonate dehydratase CALHY_RS10090
xdh D-xylose dehydrogenase CALHY_RS08000 CALHY_RS12190
xdhA xylitol dehydrogenase CALHY_RS10725 CALHY_RS09990
xylC xylonolactonase
xylE_Tm ABC transporter for xylose, substrate binding component xylE CALHY_RS02485 CALHY_RS03465
xylF_Tm ABC transporter for xylose, permease component xylF CALHY_RS03455 CALHY_RS02480
xylK_Tm ABC transporter for xylose, ATP binding component xylK CALHY_RS03450 CALHY_RS00570
xylT D-xylose transporter
xyrA xylitol reductase CALHY_RS11095

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.

Links

Downloads

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