GapMind for catabolism of small carbon sources

 

D-xylose catabolism in Polaromonas naphthalenivorans CJ2

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 (22 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
gtsA xylose ABC transporter, periplasmic substrate-binding component GtsA PNAP_RS18440 PNAP_RS02600
gtsB xylose ABC transporter, permease component 1 GtsB PNAP_RS18450
gtsC xylose ABC transporter, permease component 2 GtsC PNAP_RS18455
gtsD xylose ABC transporter, ATPase component GtsD PNAP_RS18460 PNAP_RS01135
xylA xylose isomerase
xylB xylulokinase
Alternative steps:
aldA (glycol)aldehyde dehydrogenase PNAP_RS13165 PNAP_RS15070
aldox-large (glycol)aldehyde oxidoreductase, large subunit
aldox-med (glycol)aldehyde oxidoreductase, medium subunit PNAP_RS05155
aldox-small (glycol)aldehyde oxidoreductase, small subunit PNAP_RS13460 PNAP_RS05155
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 PNAP_RS18460 PNAP_RS07720
DKDP-aldolase 2-dehydro-3-deoxy-D-arabinonate aldolase PNAP_RS05990
DKDP-dehydrog D-2-keto-3-deoxypentoate dehydrogenase PNAP_RS06215 PNAP_RS11540
dopDH 2,5-dioxopentanonate dehydrogenase PNAP_RS07980 PNAP_RS13310
Echvi_1871 sodium/xylose cotransporter
gal2 galactose/glucose/xylose uniporter
glcB malate synthase PNAP_RS18410
glcP glucose/mannose/xylose:H+ symporter
gyaR glyoxylate reductase PNAP_RS08100 PNAP_RS07420
HDOP-hydrol 5-hydroxy-2,4-dioxopentanonate hydrolase PNAP_RS03065 PNAP_RS12360
kdaD 2-keto-3-deoxy-D-arabinonate dehydratase
xad D-xylonate dehydratase PNAP_RS13320 PNAP_RS08485
xdh D-xylose dehydrogenase PNAP_RS06215 PNAP_RS10650
xdhA xylitol dehydrogenase PNAP_RS11540 PNAP_RS10390
xylC xylonolactonase PNAP_RS00605 PNAP_RS07950
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 PNAP_RS13005 PNAP_RS17575
xylG ABC transporter for xylose, ATP-binding component xylG PNAP_RS20195 PNAP_RS05160
xylH ABC transporter for xylose, permease component xylH PNAP_RS20205 PNAP_RS13005
xylK_Tm ABC transporter for xylose, ATP binding component xylK PNAP_RS20195 PNAP_RS05160
xylT D-xylose transporter
xyrA xylitol reductase

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