GapMind for catabolism of small carbon sources

 

xylitol catabolism in Ruegeria conchae TW15

Best path

PLT5, xdhA, xylB

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).

19 steps (10 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
PLT5 xylitol:H+ symporter PLT5
xdhA xylitol dehydrogenase G7G_RS0116430 G7G_RS0120430
xylB xylulokinase G7G_RS0115560
Alternative steps:
Dshi_0546 xylitol ABC transporter, ATPase component G7G_RS0111275 G7G_RS0105580
Dshi_0547 xylitol ABC transporter, substrate-binding component
Dshi_0548 xylitol ABC transporter, permease component 1 G7G_RS0110565 G7G_RS0115545
Dshi_0549 xylitol ABC transporter, permease component 2 G7G_RS0120420 G7G_RS0115540
EIIA-Axl xylitol PTS, enzyme IIA (EIIA-Axl)
EIIB-Axl xylitol PTS, enzyme IIB (EIIB-Axl)
EIIC-Axl xylitol PTS, enzyme IIC (EIIC-Axl)
fruI xylitol PTS, enzyme IIABC (FruI)
HSERO_RS17000 xylitol ABC transporter, substrate-binding component
HSERO_RS17005 xylitol ABC transporter, permease component 1
HSERO_RS17010 xylitol ABC transporter, permease component 2 G7G_RS0115540 G7G_RS0110560
HSERO_RS17020 xylitol ABC transporter, ATPase component G7G_RS0110555 G7G_RS0121175
PS417_12055 xylitol ABC transporter, substrate-binding component
PS417_12060 xylitol ABC transporter, permease component G7G_RS0100410 G7G_RS22595
PS417_12065 xylitol ABC transporter, ATPase component G7G_RS0100415 G7G_RS0100435
x5p-reductase D-xylulose-5-phosphate 2-reductase G7G_RS0113540

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 24 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:

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