GapMind for catabolism of small carbon sources

 

D-xylose catabolism in Pseudomonas fluorescens FW300-N2E3

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 (22 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
gtsA xylose ABC transporter, periplasmic substrate-binding component GtsA AO353_03395
gtsB xylose ABC transporter, permease component 1 GtsB AO353_03390
gtsC xylose ABC transporter, permease component 2 GtsC AO353_03385
gtsD xylose ABC transporter, ATPase component GtsD AO353_03380 AO353_25130
xylA xylose isomerase
xylB xylulokinase AO353_25905
Alternative steps:
aldA (glycol)aldehyde dehydrogenase AO353_28230 AO353_11505
aldox-large (glycol)aldehyde oxidoreductase, large subunit
aldox-med (glycol)aldehyde oxidoreductase, medium subunit
aldox-small (glycol)aldehyde oxidoreductase, small subunit AO353_23430 AO353_01425
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 AO353_25895 AO353_25130
DKDP-aldolase 2-dehydro-3-deoxy-D-arabinonate aldolase AO353_17670
DKDP-dehydrog D-2-keto-3-deoxypentoate dehydrogenase AO353_01660 AO353_21770
dopDH 2,5-dioxopentanonate dehydrogenase AO353_05300 AO353_14870
Echvi_1871 sodium/xylose cotransporter
gal2 galactose/glucose/xylose uniporter
glcB malate synthase AO353_07560
glcP glucose/mannose/xylose:H+ symporter
gyaR glyoxylate reductase AO353_04850 AO353_26885
HDOP-hydrol 5-hydroxy-2,4-dioxopentanonate hydrolase AO353_24305 AO353_08500
kdaD 2-keto-3-deoxy-D-arabinonate dehydratase
xad D-xylonate dehydratase AO353_08345
xdh D-xylose dehydrogenase AO353_23170 AO353_01660
xdhA xylitol dehydrogenase AO353_25145 AO353_01660
xylC xylonolactonase
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 AO353_21390 AO353_20825
xylG ABC transporter for xylose, ATP-binding component xylG AO353_21385 AO353_20820
xylH ABC transporter for xylose, permease component xylH AO353_21390 AO353_20825
xylK_Tm ABC transporter for xylose, ATP binding component xylK AO353_21385 AO353_20820
xylT D-xylose transporter
xyrA xylitol reductase AO353_28090 AO353_14720

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 (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 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