GapMind for catabolism of small carbon sources

 

D-xylose catabolism in Sphingomonas histidinilytica UM2

Best path

xylT, xdh, xylC, xad, DKDP-dehydrog, HDOP-hydrol, gyaR, glcB

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 (17 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
xylT D-xylose transporter
xdh D-xylose dehydrogenase B5X82_RS02960 B5X82_RS19760
xylC xylonolactonase B5X82_RS19865 B5X82_RS02675
xad D-xylonate dehydratase B5X82_RS24850 B5X82_RS25810
DKDP-dehydrog D-2-keto-3-deoxypentoate dehydrogenase B5X82_RS19900 B5X82_RS02810
HDOP-hydrol 5-hydroxy-2,4-dioxopentanonate hydrolase B5X82_RS15800 B5X82_RS15985
gyaR glyoxylate reductase B5X82_RS09620 B5X82_RS23755
glcB malate synthase B5X82_RS05215 B5X82_RS15170
Alternative steps:
aldA (glycol)aldehyde dehydrogenase B5X82_RS11705 B5X82_RS22960
aldox-large (glycol)aldehyde oxidoreductase, large subunit B5X82_RS11780 B5X82_RS17460
aldox-med (glycol)aldehyde oxidoreductase, medium subunit B5X82_RS11770 B5X82_RS16145
aldox-small (glycol)aldehyde oxidoreductase, small subunit B5X82_RS11775 B5X82_RS16150
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 B5X82_RS14905 B5X82_RS22845
DKDP-aldolase 2-dehydro-3-deoxy-D-arabinonate aldolase B5X82_RS17540
dopDH 2,5-dioxopentanonate dehydrogenase B5X82_RS15880 B5X82_RS11705
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 B5X82_RS14905 B5X82_RS22845
kdaD 2-keto-3-deoxy-D-arabinonate dehydratase
xdhA xylitol dehydrogenase B5X82_RS02710 B5X82_RS16245
xylA xylose isomerase
xylB xylulokinase
xylE_Tm ABC transporter for xylose, substrate binding component xylE
xylF ABC transporter for xylose, substrate binding component xylF
xylF_Tm ABC transporter for xylose, permease component xylF
xylG ABC transporter for xylose, ATP-binding component xylG
xylH ABC transporter for xylose, permease component xylH
xylK_Tm ABC transporter for xylose, ATP binding component xylK
xyrA xylitol reductase B5X82_RS13785 B5X82_RS22190

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 24 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:

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