GapMind for catabolism of small carbon sources

 

D-xylose catabolism in Marinobacter adhaerens HP15

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 (16 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
gtsA xylose ABC transporter, periplasmic substrate-binding component GtsA HP15_2958
gtsB xylose ABC transporter, permease component 1 GtsB HP15_2957
gtsC xylose ABC transporter, permease component 2 GtsC HP15_2956
gtsD xylose ABC transporter, ATPase component GtsD HP15_2955 HP15_939
xylA xylose isomerase
xylB xylulokinase
Alternative steps:
aldA (glycol)aldehyde dehydrogenase HP15_2020 HP15_3626
aldox-large (glycol)aldehyde oxidoreductase, large subunit
aldox-med (glycol)aldehyde oxidoreductase, medium subunit
aldox-small (glycol)aldehyde oxidoreductase, small subunit HP15_1257 HP15_1561
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 HP15_2955 HP15_4062
DKDP-aldolase 2-dehydro-3-deoxy-D-arabinonate aldolase
DKDP-dehydrog D-2-keto-3-deoxypentoate dehydrogenase HP15_2724 HP15_4143
dopDH 2,5-dioxopentanonate dehydrogenase HP15_2020 HP15_3626
Echvi_1871 sodium/xylose cotransporter
gal2 galactose/glucose/xylose uniporter
glcB malate synthase HP15_2188
glcP glucose/mannose/xylose:H+ symporter
gyaR glyoxylate reductase HP15_2931 HP15_2554
HDOP-hydrol 5-hydroxy-2,4-dioxopentanonate hydrolase HP15_2550 HP15_38
kdaD 2-keto-3-deoxy-D-arabinonate dehydratase
xad D-xylonate dehydratase HP15_3363 HP15_595
xdh D-xylose dehydrogenase HP15_1586 HP15_2213
xdhA xylitol dehydrogenase HP15_1707 HP15_2784
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
xylG ABC transporter for xylose, ATP-binding component xylG
xylH ABC transporter for xylose, permease component xylH
xylK_Tm ABC transporter for xylose, ATP binding component xylK
xylT D-xylose transporter
xyrA xylitol reductase HP15_2827 HP15_833

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