GapMind for catabolism of small carbon sources

 

D-xylose catabolism in Pseudomonas fluorescens FW300-N2C3

Best path

xylF, xylG, xylH, 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 (29 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
xylF ABC transporter for xylose, substrate binding component xylF AO356_28505
xylG ABC transporter for xylose, ATP-binding component xylG AO356_28510 AO356_23205
xylH ABC transporter for xylose, permease component xylH AO356_28515 AO356_23210
xylA xylose isomerase AO356_28500
xylB xylulokinase AO356_27695
Alternative steps:
aldA (glycol)aldehyde dehydrogenase AO356_26145 AO356_26740
aldox-large (glycol)aldehyde oxidoreductase, large subunit AO356_26665
aldox-med (glycol)aldehyde oxidoreductase, medium subunit AO356_26660 AO356_15625
aldox-small (glycol)aldehyde oxidoreductase, small subunit AO356_26655 AO356_15620
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 AO356_00010 AO356_01640
DKDP-aldolase 2-dehydro-3-deoxy-D-arabinonate aldolase AO356_04530
DKDP-dehydrog D-2-keto-3-deoxypentoate dehydrogenase AO356_28740 AO356_20240
dopDH 2,5-dioxopentanonate dehydrogenase AO356_24600 AO356_07180
Echvi_1871 sodium/xylose cotransporter
gal2 galactose/glucose/xylose uniporter
glcB malate synthase AO356_14100
glcP glucose/mannose/xylose:H+ symporter
gtsA xylose ABC transporter, periplasmic substrate-binding component GtsA AO356_05195
gtsB xylose ABC transporter, permease component 1 GtsB AO356_05190
gtsC xylose ABC transporter, permease component 2 GtsC AO356_05185
gtsD xylose ABC transporter, ATPase component GtsD AO356_05180 AO356_27685
gyaR glyoxylate reductase AO356_16925 AO356_24675
HDOP-hydrol 5-hydroxy-2,4-dioxopentanonate hydrolase AO356_27435 AO356_28735
kdaD 2-keto-3-deoxy-D-arabinonate dehydratase AO356_27450 AO356_28755
xad D-xylonate dehydratase AO356_28760 AO356_24585
xdh D-xylose dehydrogenase AO356_19860 AO356_25515
xdhA xylitol dehydrogenase AO356_28545 AO356_19860
xylC xylonolactonase AO356_20235 AO356_23060
xylE_Tm ABC transporter for xylose, substrate binding component xylE
xylF_Tm ABC transporter for xylose, permease component xylF AO356_23210 AO356_20255
xylK_Tm ABC transporter for xylose, ATP binding component xylK AO356_23205 AO356_20250
xylT D-xylose transporter AO356_27270
xyrA xylitol reductase AO356_28450 AO356_23370

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, 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