GapMind for catabolism of small carbon sources

 

xylitol catabolism in Chromobacterium vaccinii MWU205

Best path

fruI, x5p-reductase

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 (9 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
fruI xylitol PTS, enzyme IIABC (FruI) VL52_RS18010
x5p-reductase D-xylulose-5-phosphate 2-reductase VL52_RS13400
Alternative steps:
Dshi_0546 xylitol ABC transporter, ATPase component VL52_RS12740 VL52_RS04920
Dshi_0547 xylitol ABC transporter, substrate-binding component
Dshi_0548 xylitol ABC transporter, permease component 1
Dshi_0549 xylitol ABC transporter, permease component 2 VL52_RS04910
EIIA-Axl xylitol PTS, enzyme IIA (EIIA-Axl)
EIIB-Axl xylitol PTS, enzyme IIB (EIIB-Axl)
EIIC-Axl xylitol PTS, enzyme IIC (EIIC-Axl)
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 VL52_RS12740 VL52_RS04920
PLT5 xylitol:H+ symporter PLT5
PS417_12055 xylitol ABC transporter, substrate-binding component VL52_RS18725
PS417_12060 xylitol ABC transporter, permease component VL52_RS18720
PS417_12065 xylitol ABC transporter, ATPase component VL52_RS18715 VL52_RS07675
xdhA xylitol dehydrogenase VL52_RS13400 VL52_RS17095
xylB xylulokinase

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