GapMind for catabolism of small carbon sources

 

D-xylose catabolism in Rhizobium leguminosarum bv. trifolii WSM1325

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 (29 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
xylF ABC transporter for xylose, substrate binding component xylF RLEG_RS15670 RLEG_RS15710
xylG ABC transporter for xylose, ATP-binding component xylG RLEG_RS15665 RLEG_RS20700
xylH ABC transporter for xylose, permease component xylH RLEG_RS15660 RLEG_RS16900
xylA xylose isomerase RLEG_RS18315
xylB xylulokinase RLEG_RS18320 RLEG_RS25575
Alternative steps:
aldA (glycol)aldehyde dehydrogenase RLEG_RS21595 RLEG_RS24785
aldox-large (glycol)aldehyde oxidoreductase, large subunit
aldox-med (glycol)aldehyde oxidoreductase, medium subunit RLEG_RS15465
aldox-small (glycol)aldehyde oxidoreductase, small subunit RLEG_RS23140 RLEG_RS15465
araS component of Arabinose, fructose, xylose porter
araT component of Arabinose, fructose, xylose porter
araU component of Arabinose, fructose, xylose porter RLEG_RS25820 RLEG_RS19345
araV component of Arabinose, fructose, xylose porter RLEG_RS14315 RLEG_RS21560
DKDP-aldolase 2-dehydro-3-deoxy-D-arabinonate aldolase RLEG_RS05610 RLEG_RS24005
DKDP-dehydrog D-2-keto-3-deoxypentoate dehydrogenase RLEG_RS29855 RLEG_RS03025
dopDH 2,5-dioxopentanonate dehydrogenase RLEG_RS15650 RLEG_RS28155
Echvi_1871 sodium/xylose cotransporter
gal2 galactose/glucose/xylose uniporter
glcB malate synthase RLEG_RS21360 RLEG_RS20885
glcP glucose/mannose/xylose:H+ symporter
gtsA xylose ABC transporter, periplasmic substrate-binding component GtsA RLEG_RS07325 RLEG_RS18705
gtsB xylose ABC transporter, permease component 1 GtsB RLEG_RS18700 RLEG_RS07330
gtsC xylose ABC transporter, permease component 2 GtsC RLEG_RS18695 RLEG_RS11530
gtsD xylose ABC transporter, ATPase component GtsD RLEG_RS16765 RLEG_RS18690
gyaR glyoxylate reductase RLEG_RS21870 RLEG_RS16385
HDOP-hydrol 5-hydroxy-2,4-dioxopentanonate hydrolase RLEG_RS21170 RLEG_RS30500
kdaD 2-keto-3-deoxy-D-arabinonate dehydratase RLEG_RS33140 RLEG_RS21170
xad D-xylonate dehydratase RLEG_RS16525 RLEG_RS15645
xdh D-xylose dehydrogenase RLEG_RS21530 RLEG_RS02715
xdhA xylitol dehydrogenase RLEG_RS27655 RLEG_RS34700
xylC xylonolactonase RLEG_RS25640
xylE_Tm ABC transporter for xylose, substrate binding component xylE RLEG_RS09720 RLEG_RS09435
xylF_Tm ABC transporter for xylose, permease component xylF RLEG_RS00785 RLEG_RS23605
xylK_Tm ABC transporter for xylose, ATP binding component xylK RLEG_RS09725 RLEG_RS22820
xylT D-xylose transporter
xyrA xylitol reductase RLEG_RS25560 RLEG_RS20215

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 Apr 09 2024. 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