GapMind for catabolism of small carbon sources

 

D-xylose catabolism in Pseudomonas putida KT2440

Best path

gtsA, gtsB, gtsC, gtsD, xdh, xylC, xad, kdaD, dopDH

Also see fitness data for the top candidates

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
gtsA xylose ABC transporter, periplasmic substrate-binding component GtsA PP_1015
gtsB xylose ABC transporter, permease component 1 GtsB PP_1016
gtsC xylose ABC transporter, permease component 2 GtsC PP_1017
gtsD xylose ABC transporter, ATPase component GtsD PP_1018 PP_0411
xdh D-xylose dehydrogenase PP_1946 PP_1817
xylC xylonolactonase PP_3180 PP_1170
xad D-xylonate dehydratase PP_5128
kdaD 2-keto-3-deoxy-D-arabinonate dehydratase PP_2836
dopDH 2,5-dioxopentanonate dehydrogenase PP_3602 PP_1256
Alternative steps:
aldA (glycol)aldehyde dehydrogenase PP_0213 PP_1481
aldox-large (glycol)aldehyde oxidoreductase, large subunit
aldox-med (glycol)aldehyde oxidoreductase, medium subunit PP_3309
aldox-small (glycol)aldehyde oxidoreductase, small subunit PP_3308 PP_3947
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 PP_1018 PP_1484
DKDP-aldolase 2-dehydro-3-deoxy-D-arabinonate aldolase PP_1237
DKDP-dehydrog D-2-keto-3-deoxypentoate dehydrogenase PP_1817 PP_1951
Echvi_1871 sodium/xylose cotransporter
gal2 galactose/glucose/xylose uniporter
glcB malate synthase PP_0356
glcP glucose/mannose/xylose:H+ symporter
gyaR glyoxylate reductase PP_1261 PP_3376
HDOP-hydrol 5-hydroxy-2,4-dioxopentanonate hydrolase PP_5153 PP_1709
xdhA xylitol dehydrogenase PP_0552 PP_1946
xylA xylose isomerase
xylB xylulokinase
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 PP_2456
xylG ABC transporter for xylose, ATP-binding component xylG PP_2759 PP_2455
xylH ABC transporter for xylose, permease component xylH PP_2761 PP_2456
xylK_Tm ABC transporter for xylose, ATP binding component xylK PP_2759 PP_2455
xylT D-xylose transporter
xyrA xylitol reductase PP_2368 PP_3671

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 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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