GapMind for catabolism of small carbon sources

 

D-xylose catabolism in Jeotgalibacillus soli P9

Best path

xylT, 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 (24 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
xylT D-xylose transporter
xylA xylose isomerase
xylB xylulokinase KP78_RS17820
Alternative steps:
aldA (glycol)aldehyde dehydrogenase KP78_RS01230 KP78_RS11775
aldox-large (glycol)aldehyde oxidoreductase, large subunit KP78_RS12240
aldox-med (glycol)aldehyde oxidoreductase, medium subunit KP78_RS12250
aldox-small (glycol)aldehyde oxidoreductase, small subunit KP78_RS12255 KP78_RS12660
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 KP78_RS09000 KP78_RS04790
DKDP-aldolase 2-dehydro-3-deoxy-D-arabinonate aldolase KP78_RS01485 KP78_RS11655
DKDP-dehydrog D-2-keto-3-deoxypentoate dehydrogenase KP78_RS12140 KP78_RS11215
dopDH 2,5-dioxopentanonate dehydrogenase KP78_RS13035 KP78_RS01230
Echvi_1871 sodium/xylose cotransporter
gal2 galactose/glucose/xylose uniporter
glcB malate synthase KP78_RS04030
glcP glucose/mannose/xylose:H+ symporter
gtsA xylose ABC transporter, periplasmic substrate-binding component GtsA
gtsB xylose ABC transporter, permease component 1 GtsB KP78_RS09990
gtsC xylose ABC transporter, permease component 2 GtsC KP78_RS06190 KP78_RS04785
gtsD xylose ABC transporter, ATPase component GtsD KP78_RS09000 KP78_RS04790
gyaR glyoxylate reductase KP78_RS13065 KP78_RS06275
HDOP-hydrol 5-hydroxy-2,4-dioxopentanonate hydrolase KP78_RS09315 KP78_RS07310
kdaD 2-keto-3-deoxy-D-arabinonate dehydratase
xad D-xylonate dehydratase KP78_RS07070
xdh D-xylose dehydrogenase KP78_RS11215 KP78_RS07015
xdhA xylitol dehydrogenase KP78_RS05185 KP78_RS05180
xylC xylonolactonase
xylE_Tm ABC transporter for xylose, substrate binding component xylE KP78_RS04880
xylF ABC transporter for xylose, substrate binding component xylF
xylF_Tm ABC transporter for xylose, permease component xylF KP78_RS04875 KP78_RS05685
xylG ABC transporter for xylose, ATP-binding component xylG KP78_RS04870 KP78_RS05680
xylH ABC transporter for xylose, permease component xylH KP78_RS04875 KP78_RS05685
xylK_Tm ABC transporter for xylose, ATP binding component xylK KP78_RS04870 KP78_RS05680
xyrA xylitol reductase KP78_RS04850 KP78_RS04175

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