GapMind for catabolism of small carbon sources

 

D-xylose catabolism in Paraburkholderia bryophila 376MFSha3.1

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 H281DRAFT_03877 H281DRAFT_02713
xylG ABC transporter for xylose, ATP-binding component xylG H281DRAFT_03878 H281DRAFT_02712
xylH ABC transporter for xylose, permease component xylH H281DRAFT_03879 H281DRAFT_02714
xylA xylose isomerase H281DRAFT_03876
xylB xylulokinase H281DRAFT_04153 H281DRAFT_04167
Alternative steps:
aldA (glycol)aldehyde dehydrogenase H281DRAFT_00972 H281DRAFT_03540
aldox-large (glycol)aldehyde oxidoreductase, large subunit H281DRAFT_02182 H281DRAFT_02676
aldox-med (glycol)aldehyde oxidoreductase, medium subunit H281DRAFT_02674 H281DRAFT_01140
aldox-small (glycol)aldehyde oxidoreductase, small subunit H281DRAFT_02181 H281DRAFT_02675
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 H281DRAFT_01260 H281DRAFT_02040
DKDP-aldolase 2-dehydro-3-deoxy-D-arabinonate aldolase H281DRAFT_00509
DKDP-dehydrog D-2-keto-3-deoxypentoate dehydrogenase H281DRAFT_03529 H281DRAFT_06507
dopDH 2,5-dioxopentanonate dehydrogenase H281DRAFT_01155 H281DRAFT_05316
Echvi_1871 sodium/xylose cotransporter
gal2 galactose/glucose/xylose uniporter
glcB malate synthase H281DRAFT_00963 H281DRAFT_00576
glcP glucose/mannose/xylose:H+ symporter
gtsA xylose ABC transporter, periplasmic substrate-binding component GtsA H281DRAFT_00166 H281DRAFT_01454
gtsB xylose ABC transporter, permease component 1 GtsB H281DRAFT_00167 H281DRAFT_01453
gtsC xylose ABC transporter, permease component 2 GtsC H281DRAFT_00168 H281DRAFT_01452
gtsD xylose ABC transporter, ATPase component GtsD H281DRAFT_00169 H281DRAFT_03749
gyaR glyoxylate reductase H281DRAFT_04333 H281DRAFT_06500
HDOP-hydrol 5-hydroxy-2,4-dioxopentanonate hydrolase H281DRAFT_02528 H281DRAFT_03528
kdaD 2-keto-3-deoxy-D-arabinonate dehydratase H281DRAFT_05918 H281DRAFT_03528
xad D-xylonate dehydratase H281DRAFT_05919 H281DRAFT_02329
xdh D-xylose dehydrogenase H281DRAFT_06300 H281DRAFT_02753
xdhA xylitol dehydrogenase H281DRAFT_04147 H281DRAFT_01517
xylC xylonolactonase H281DRAFT_06301 H281DRAFT_05978
xylE_Tm ABC transporter for xylose, substrate binding component xylE H281DRAFT_02713 H281DRAFT_03378
xylF_Tm ABC transporter for xylose, permease component xylF H281DRAFT_02714 H281DRAFT_00427
xylK_Tm ABC transporter for xylose, ATP binding component xylK H281DRAFT_00426 H281DRAFT_03380
xylT D-xylose transporter
xyrA xylitol reductase H281DRAFT_00358 H281DRAFT_03668

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