GapMind for catabolism of small carbon sources

 

D-xylose catabolism in Pseudomonas fluorescens GW456-L13

Best path

gtsA, gtsB, gtsC, gtsD, xylA, xylB

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 (23 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
gtsA xylose ABC transporter, periplasmic substrate-binding component GtsA PfGW456L13_1894
gtsB xylose ABC transporter, permease component 1 GtsB PfGW456L13_1895
gtsC xylose ABC transporter, permease component 2 GtsC PfGW456L13_1896
gtsD xylose ABC transporter, ATPase component GtsD PfGW456L13_1897 PfGW456L13_3039
xylA xylose isomerase
xylB xylulokinase PfGW456L13_3037
Alternative steps:
aldA (glycol)aldehyde dehydrogenase PfGW456L13_3932 PfGW456L13_495
aldox-large (glycol)aldehyde oxidoreductase, large subunit
aldox-med (glycol)aldehyde oxidoreductase, medium subunit
aldox-small (glycol)aldehyde oxidoreductase, small subunit PfGW456L13_3353 PfGW456L13_2091
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 PfGW456L13_3039 PfGW456L13_1897
DKDP-aldolase 2-dehydro-3-deoxy-D-arabinonate aldolase PfGW456L13_4507 PfGW456L13_3832
DKDP-dehydrog D-2-keto-3-deoxypentoate dehydrogenase PfGW456L13_3453 PfGW456L13_2058
dopDH 2,5-dioxopentanonate dehydrogenase PfGW456L13_5044 PfGW456L13_3316
Echvi_1871 sodium/xylose cotransporter
gal2 galactose/glucose/xylose uniporter
glcB malate synthase PfGW456L13_1139
glcP glucose/mannose/xylose:H+ symporter
gyaR glyoxylate reductase PfGW456L13_4945 PfGW456L13_2948
HDOP-hydrol 5-hydroxy-2,4-dioxopentanonate hydrolase PfGW456L13_3411 PfGW456L13_3405
kdaD 2-keto-3-deoxy-D-arabinonate dehydratase
xad D-xylonate dehydratase PfGW456L13_3320 PfGW456L13_3725
xdh D-xylose dehydrogenase PfGW456L13_3401 PfGW456L13_2522
xdhA xylitol dehydrogenase PfGW456L13_3657 PfGW456L13_2058
xylC xylonolactonase PfGW456L13_2118
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 PfGW456L13_2122 PfGW456L13_3910
xylG ABC transporter for xylose, ATP-binding component xylG PfGW456L13_2121 PfGW456L13_3911
xylH ABC transporter for xylose, permease component xylH PfGW456L13_2122 PfGW456L13_3910
xylK_Tm ABC transporter for xylose, ATP binding component xylK PfGW456L13_2121 PfGW456L13_3911
xylT D-xylose transporter
xyrA xylitol reductase PfGW456L13_2966 PfGW456L13_2401

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