GapMind for catabolism of small carbon sources

 

xylitol catabolism in Nocardiopsis gilva YIM 90087

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 (12 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
PLT5 xylitol:H+ symporter PLT5 CDO52_RS15385
xdhA xylitol dehydrogenase CDO52_RS02195 CDO52_RS11130
xylB xylulokinase CDO52_RS16690 CDO52_RS17970
Alternative steps:
Dshi_0546 xylitol ABC transporter, ATPase component CDO52_RS13845 CDO52_RS13825
Dshi_0547 xylitol ABC transporter, substrate-binding component
Dshi_0548 xylitol ABC transporter, permease component 1 CDO52_RS17260 CDO52_RS16290
Dshi_0549 xylitol ABC transporter, permease component 2 CDO52_RS17265 CDO52_RS11100
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 CDO52_RS17260
HSERO_RS17010 xylitol ABC transporter, permease component 2 CDO52_RS17265 CDO52_RS20665
HSERO_RS17020 xylitol ABC transporter, ATPase component CDO52_RS13845 CDO52_RS13825
PS417_12055 xylitol ABC transporter, substrate-binding component
PS417_12060 xylitol ABC transporter, permease component CDO52_RS22215 CDO52_RS18105
PS417_12065 xylitol ABC transporter, ATPase component CDO52_RS21125 CDO52_RS18110
x5p-reductase D-xylulose-5-phosphate 2-reductase CDO52_RS17250 CDO52_RS21860

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