GapMind for catabolism of small carbon sources

 

D-xylose catabolism in Dyella japonica UNC79MFTsu3.2

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 (24 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
xylF ABC transporter for xylose, substrate binding component xylF N515DRAFT_3231
xylG ABC transporter for xylose, ATP-binding component xylG N515DRAFT_3232 N515DRAFT_2413
xylH ABC transporter for xylose, permease component xylH N515DRAFT_3233 N515DRAFT_2415
xylA xylose isomerase N515DRAFT_3229
xylB xylulokinase N515DRAFT_3230
Alternative steps:
aldA (glycol)aldehyde dehydrogenase N515DRAFT_3729 N515DRAFT_2488
aldox-large (glycol)aldehyde oxidoreductase, large subunit
aldox-med (glycol)aldehyde oxidoreductase, medium subunit
aldox-small (glycol)aldehyde oxidoreductase, small subunit N515DRAFT_2295 N515DRAFT_4010
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 N515DRAFT_4212 N515DRAFT_1562
DKDP-aldolase 2-dehydro-3-deoxy-D-arabinonate aldolase N515DRAFT_1147
DKDP-dehydrog D-2-keto-3-deoxypentoate dehydrogenase N515DRAFT_1253 N515DRAFT_0334
dopDH 2,5-dioxopentanonate dehydrogenase N515DRAFT_0954 N515DRAFT_3729
Echvi_1871 sodium/xylose cotransporter
gal2 galactose/glucose/xylose uniporter
glcB malate synthase N515DRAFT_4124
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 N515DRAFT_3133
gtsD xylose ABC transporter, ATPase component GtsD N515DRAFT_4212 N515DRAFT_1562
gyaR glyoxylate reductase N515DRAFT_0108 N515DRAFT_3581
HDOP-hydrol 5-hydroxy-2,4-dioxopentanonate hydrolase N515DRAFT_1252
kdaD 2-keto-3-deoxy-D-arabinonate dehydratase
xad D-xylonate dehydratase N515DRAFT_2409 N515DRAFT_0569
xdh D-xylose dehydrogenase N515DRAFT_1230 N515DRAFT_1253
xdhA xylitol dehydrogenase N515DRAFT_0039 N515DRAFT_1006
xylC xylonolactonase N515DRAFT_1229
xylE_Tm ABC transporter for xylose, substrate binding component xylE
xylF_Tm ABC transporter for xylose, permease component xylF N515DRAFT_2415 N515DRAFT_3233
xylK_Tm ABC transporter for xylose, ATP binding component xylK N515DRAFT_3232 N515DRAFT_2413
xylT D-xylose transporter N515DRAFT_1228 N515DRAFT_0382
xyrA xylitol reductase N515DRAFT_3546 N515DRAFT_4192

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