GapMind for catabolism of small carbon sources

 

Definition of xylitol catabolism

As rules and steps, or see full text

Rules

Overview: Xylitol utilization in GapMind is based on the MetaCyc pathway via xylitol dehydrogenase (link) or on utilization via a phosphotransferase system and D-xylulose-5-phosphate 2-reductase (PMID:27553222).

Steps

fruI: xylitol PTS, enzyme IIABC (FruI)

EIIA-Axl: xylitol PTS, enzyme IIA (EIIA-Axl)

EIIB-Axl: xylitol PTS, enzyme IIB (EIIB-Axl)

EIIC-Axl: xylitol PTS, enzyme IIC (EIIC-Axl)

Dshi_0546: xylitol ABC transporter, ATPase component

Dshi_0547: xylitol ABC transporter, substrate-binding component

Dshi_0548: xylitol ABC transporter, permease component 1

Dshi_0549: xylitol ABC transporter, permease component 2

HSERO_RS17000: xylitol ABC transporter, substrate-binding component

HSERO_RS17005: xylitol ABC transporter, permease component 1

HSERO_RS17010: xylitol ABC transporter, permease component 2

HSERO_RS17020: xylitol ABC transporter, ATPase component

PS417_12065: xylitol ABC transporter, ATPase component

PS417_12060: xylitol ABC transporter, permease component

PS417_12055: xylitol ABC transporter, substrate-binding component

PLT5: xylitol:H+ symporter PLT5

xdhA: xylitol dehydrogenase

xylB: xylulokinase

x5p-reductase: D-xylulose-5-phosphate 2-reductase

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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