GapMind for catabolism of small carbon sources

 

D-xylose catabolism in Pseudomonas benzenivorans DSM 8628

Best path

gtsA, gtsB, gtsC, gtsD, xylA, xylB

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 (23 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
gtsA xylose ABC transporter, periplasmic substrate-binding component GtsA BLS63_RS18140
gtsB xylose ABC transporter, permease component 1 GtsB BLS63_RS18135
gtsC xylose ABC transporter, permease component 2 GtsC BLS63_RS18130
gtsD xylose ABC transporter, ATPase component GtsD BLS63_RS18125 BLS63_RS17880
xylA xylose isomerase
xylB xylulokinase
Alternative steps:
aldA (glycol)aldehyde dehydrogenase BLS63_RS26230 BLS63_RS15725
aldox-large (glycol)aldehyde oxidoreductase, large subunit BLS63_RS06640
aldox-med (glycol)aldehyde oxidoreductase, medium subunit BLS63_RS06645
aldox-small (glycol)aldehyde oxidoreductase, small subunit BLS63_RS06650 BLS63_RS02625
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 BLS63_RS17880 BLS63_RS18125
DKDP-aldolase 2-dehydro-3-deoxy-D-arabinonate aldolase BLS63_RS06945
DKDP-dehydrog D-2-keto-3-deoxypentoate dehydrogenase BLS63_RS12140 BLS63_RS15580
dopDH 2,5-dioxopentanonate dehydrogenase BLS63_RS03170 BLS63_RS14235
Echvi_1871 sodium/xylose cotransporter
gal2 galactose/glucose/xylose uniporter
glcB malate synthase BLS63_RS18835 BLS63_RS04200
glcP glucose/mannose/xylose:H+ symporter
gyaR glyoxylate reductase BLS63_RS03155 BLS63_RS17655
HDOP-hydrol 5-hydroxy-2,4-dioxopentanonate hydrolase BLS63_RS14245 BLS63_RS16590
kdaD 2-keto-3-deoxy-D-arabinonate dehydratase
xad D-xylonate dehydratase BLS63_RS16475
xdh D-xylose dehydrogenase BLS63_RS06695 BLS63_RS12140
xdhA xylitol dehydrogenase BLS63_RS14255 BLS63_RS19025
xylC xylonolactonase BLS63_RS03215
xylE_Tm ABC transporter for xylose, substrate binding component xylE BLS63_RS04620
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 BLS63_RS14020
xylH ABC transporter for xylose, permease component xylH
xylK_Tm ABC transporter for xylose, ATP binding component xylK BLS63_RS14020
xylT D-xylose transporter
xyrA xylitol reductase BLS63_RS12250 BLS63_RS20560

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