GapMind for catabolism of small carbon sources

 

D-xylose catabolism in Echinicola vietnamensis KMM 6221, DSM 17526

Best path

Echvi_1871, 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 (22 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
Echvi_1871 sodium/xylose cotransporter Echvi_1871 Echvi_1880
xylA xylose isomerase Echvi_1876
xylB xylulokinase Echvi_1875
Alternative steps:
aldA (glycol)aldehyde dehydrogenase Echvi_0481 Echvi_3822
aldox-large (glycol)aldehyde oxidoreductase, large subunit
aldox-med (glycol)aldehyde oxidoreductase, medium subunit
aldox-small (glycol)aldehyde oxidoreductase, small subunit Echvi_4165
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 Echvi_1022 Echvi_3653
DKDP-aldolase 2-dehydro-3-deoxy-D-arabinonate aldolase Echvi_1276
DKDP-dehydrog D-2-keto-3-deoxypentoate dehydrogenase Echvi_2940 Echvi_4610
dopDH 2,5-dioxopentanonate dehydrogenase Echvi_3952 Echvi_0481
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
gtsC xylose ABC transporter, permease component 2 GtsC
gtsD xylose ABC transporter, ATPase component GtsD Echvi_2123 Echvi_1022
gyaR glyoxylate reductase Echvi_3936 Echvi_2777
HDOP-hydrol 5-hydroxy-2,4-dioxopentanonate hydrolase Echvi_2939
kdaD 2-keto-3-deoxy-D-arabinonate dehydratase
xad D-xylonate dehydratase Echvi_2055 Echvi_3769
xdh D-xylose dehydrogenase Echvi_2940 Echvi_3928
xdhA xylitol dehydrogenase Echvi_3219 Echvi_3928
xylC xylonolactonase
xylE_Tm ABC transporter for xylose, substrate binding component xylE
xylF ABC transporter for xylose, substrate binding component xylF Echvi_1284
xylF_Tm ABC transporter for xylose, permease component xylF Echvi_1280
xylG ABC transporter for xylose, ATP-binding component xylG Echvi_1282
xylH ABC transporter for xylose, permease component xylH Echvi_1280
xylK_Tm ABC transporter for xylose, ATP binding component xylK Echvi_1282
xylT D-xylose transporter Echvi_2805 Echvi_2810
xyrA xylitol reductase Echvi_3562 Echvi_4178

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