GapMind for catabolism of small carbon sources

 

D-xylose catabolism in Brucella inopinata BO1

Best path

xylF, xylG, xylH, 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 (22 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
xylF ABC transporter for xylose, substrate binding component xylF BIBO1_RS18910 BIBO1_RS15350
xylG ABC transporter for xylose, ATP-binding component xylG BIBO1_RS18905 BIBO1_RS15355
xylH ABC transporter for xylose, permease component xylH BIBO1_RS18900 BIBO1_RS15360
xylA xylose isomerase BIBO1_RS14080
xylB xylulokinase BIBO1_RS14085
Alternative steps:
aldA (glycol)aldehyde dehydrogenase BIBO1_RS11605 BIBO1_RS17145
aldox-large (glycol)aldehyde oxidoreductase, large subunit
aldox-med (glycol)aldehyde oxidoreductase, medium subunit BIBO1_RS13270
aldox-small (glycol)aldehyde oxidoreductase, small subunit BIBO1_RS13270
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 BIBO1_RS16280 BIBO1_RS16955
DKDP-aldolase 2-dehydro-3-deoxy-D-arabinonate aldolase BIBO1_RS14505
DKDP-dehydrog D-2-keto-3-deoxypentoate dehydrogenase BIBO1_RS12800 BIBO1_RS08590
dopDH 2,5-dioxopentanonate dehydrogenase BIBO1_RS10860 BIBO1_RS11605
Echvi_1871 sodium/xylose cotransporter
gal2 galactose/glucose/xylose uniporter
glcB malate synthase BIBO1_RS11635 BIBO1_RS18635
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 BIBO1_RS12775 BIBO1_RS17945
gyaR glyoxylate reductase BIBO1_RS06720 BIBO1_RS11805
HDOP-hydrol 5-hydroxy-2,4-dioxopentanonate hydrolase BIBO1_RS12805 BIBO1_RS19775
kdaD 2-keto-3-deoxy-D-arabinonate dehydratase
xad D-xylonate dehydratase BIBO1_RS18925 BIBO1_RS10395
xdh D-xylose dehydrogenase BIBO1_RS06485 BIBO1_RS15630
xdhA xylitol dehydrogenase BIBO1_RS08590 BIBO1_RS11530
xylC xylonolactonase
xylE_Tm ABC transporter for xylose, substrate binding component xylE
xylF_Tm ABC transporter for xylose, permease component xylF BIBO1_RS11585 BIBO1_RS18545
xylK_Tm ABC transporter for xylose, ATP binding component xylK BIBO1_RS19475 BIBO1_RS18905
xylT D-xylose transporter
xyrA xylitol reductase BIBO1_RS15685

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