GapMind for catabolism of small carbon sources


D-xylose catabolism in Azospirillum brasilense Sp245

Best path

xylF, xylG, xylH, xdh, xylC, xad, DKDP-dehydrog, HDOP-hydrol, gyaR, glcB

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 (24 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
xylF ABC transporter for xylose, substrate binding component xylF AZOBR_RS31240
xylG ABC transporter for xylose, ATP-binding component xylG AZOBR_RS31245 AZOBR_RS31210
xylH ABC transporter for xylose, permease component xylH AZOBR_RS31250 AZOBR_RS31200
xdh D-xylose dehydrogenase AZOBR_RS11740 AZOBR_RS28175
xylC xylonolactonase AZOBR_RS31230 AZOBR_RS22710
xad D-xylonate dehydratase AZOBR_RS31260 AZOBR_RS25270
DKDP-dehydrog D-2-keto-3-deoxypentoate dehydrogenase AZOBR_RS04635 AZOBR_RS27005
HDOP-hydrol 5-hydroxy-2,4-dioxopentanonate hydrolase AZOBR_RS15905 AZOBR_RS26375
gyaR glyoxylate reductase AZOBR_RS01325 AZOBR_RS15695
glcB malate synthase AZOBR_RS03245 AZOBR_RS25430
Alternative steps:
aldA (glycol)aldehyde dehydrogenase AZOBR_RS19635 AZOBR_RS09720
aldox-large (glycol)aldehyde oxidoreductase, large subunit AZOBR_RS08560 AZOBR_RS06730
aldox-med (glycol)aldehyde oxidoreductase, medium subunit AZOBR_RS08555 AZOBR_RS29695
aldox-small (glycol)aldehyde oxidoreductase, small subunit AZOBR_RS08565 AZOBR_RS27485
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 AZOBR_RS24710 AZOBR_RS08840
DKDP-aldolase 2-dehydro-3-deoxy-D-arabinonate aldolase AZOBR_RS08420
dopDH 2,5-dioxopentanonate dehydrogenase AZOBR_RS18165 AZOBR_RS29750
Echvi_1871 sodium/xylose cotransporter
gal2 galactose/glucose/xylose uniporter
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 AZOBR_RS00060 AZOBR_RS27980
kdaD 2-keto-3-deoxy-D-arabinonate dehydratase AZOBR_RS18160 AZOBR_RS15905
xdhA xylitol dehydrogenase AZOBR_RS13230 AZOBR_RS29790
xylA xylose isomerase AZOBR_RS27920
xylB xylulokinase
xylE_Tm ABC transporter for xylose, substrate binding component xylE
xylF_Tm ABC transporter for xylose, permease component xylF AZOBR_RS27940 AZOBR_RS31200
xylK_Tm ABC transporter for xylose, ATP binding component xylK AZOBR_RS31245 AZOBR_RS31210
xylT D-xylose transporter
xyrA xylitol reductase AZOBR_RS21420 AZOBR_RS19710

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