GapMind for catabolism of small carbon sources

 

xylitol catabolism in Dyella japonica UNC79MFTsu3.2

Best path

PLT5, xdhA, xylB

Also see fitness data for the top candidates

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 (11 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
PLT5 xylitol:H+ symporter PLT5 N515DRAFT_1228 N515DRAFT_0382
xdhA xylitol dehydrogenase N515DRAFT_0039 N515DRAFT_1006
xylB xylulokinase N515DRAFT_3230
Alternative steps:
Dshi_0546 xylitol ABC transporter, ATPase component N515DRAFT_4212 N515DRAFT_1562
Dshi_0547 xylitol ABC transporter, substrate-binding component
Dshi_0548 xylitol ABC transporter, permease component 1 N515DRAFT_3134
Dshi_0549 xylitol ABC transporter, permease component 2 N515DRAFT_3133
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
HSERO_RS17020 xylitol ABC transporter, ATPase component N515DRAFT_4212 N515DRAFT_1562
PS417_12055 xylitol ABC transporter, substrate-binding component N515DRAFT_2412 N515DRAFT_3231
PS417_12060 xylitol ABC transporter, permease component N515DRAFT_2415 N515DRAFT_2414
PS417_12065 xylitol ABC transporter, ATPase component N515DRAFT_3232 N515DRAFT_2413
x5p-reductase D-xylulose-5-phosphate 2-reductase N515DRAFT_0039 N515DRAFT_2489

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