GapMind for catabolism of small carbon sources

 

D-xylose catabolism in Burkholderia phytofirmans PsJN

Best path

xylF, xylG, xylH, xylA, xylB

Also see fitness data for the top candidates

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 (29 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
xylF ABC transporter for xylose, substrate binding component xylF BPHYT_RS32820
xylG ABC transporter for xylose, ATP-binding component xylG BPHYT_RS32815 BPHYT_RS27185
xylH ABC transporter for xylose, permease component xylH BPHYT_RS32810 BPHYT_RS16055
xylA xylose isomerase BPHYT_RS32825
xylB xylulokinase BPHYT_RS16080 BPHYT_RS16155
Alternative steps:
aldA (glycol)aldehyde dehydrogenase BPHYT_RS09875 BPHYT_RS34305
aldox-large (glycol)aldehyde oxidoreductase, large subunit BPHYT_RS01765
aldox-med (glycol)aldehyde oxidoreductase, medium subunit BPHYT_RS10830 BPHYT_RS01760
aldox-small (glycol)aldehyde oxidoreductase, small subunit BPHYT_RS01770 BPHYT_RS10825
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 BPHYT_RS32360 BPHYT_RS09400
DKDP-aldolase 2-dehydro-3-deoxy-D-arabinonate aldolase BPHYT_RS12615 BPHYT_RS29250
DKDP-dehydrog D-2-keto-3-deoxypentoate dehydrogenase BPHYT_RS34215 BPHYT_RS16940
dopDH 2,5-dioxopentanonate dehydrogenase BPHYT_RS10925 BPHYT_RS28455
Echvi_1871 sodium/xylose cotransporter
gal2 galactose/glucose/xylose uniporter
glcB malate synthase BPHYT_RS31665 BPHYT_RS09815
glcP glucose/mannose/xylose:H+ symporter
gtsA xylose ABC transporter, periplasmic substrate-binding component GtsA BPHYT_RS00415 BPHYT_RS05025
gtsB xylose ABC transporter, permease component 1 GtsB BPHYT_RS05030 BPHYT_RS29185
gtsC xylose ABC transporter, permease component 2 GtsC BPHYT_RS05035 BPHYT_RS29180
gtsD xylose ABC transporter, ATPase component GtsD BPHYT_RS05040 BPHYT_RS35680
gyaR glyoxylate reductase BPHYT_RS14520 BPHYT_RS20960
HDOP-hydrol 5-hydroxy-2,4-dioxopentanonate hydrolase BPHYT_RS28740 BPHYT_RS34210
kdaD 2-keto-3-deoxy-D-arabinonate dehydratase BPHYT_RS28765 BPHYT_RS34210
xad D-xylonate dehydratase BPHYT_RS31695 BPHYT_RS19730
xdh D-xylose dehydrogenase BPHYT_RS16920 BPHYT_RS34945
xdhA xylitol dehydrogenase BPHYT_RS16050 BPHYT_RS23440
xylC xylonolactonase BPHYT_RS16915 BPHYT_RS24170
xylE_Tm ABC transporter for xylose, substrate binding component xylE BPHYT_RS27195
xylF_Tm ABC transporter for xylose, permease component xylF BPHYT_RS16055 BPHYT_RS20745
xylK_Tm ABC transporter for xylose, ATP binding component xylK BPHYT_RS20740 BPHYT_RS27185
xylT D-xylose transporter
xyrA xylitol reductase BPHYT_RS08410 BPHYT_RS35150

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.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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