GapMind for catabolism of small carbon sources


xylitol catabolism in Paraburkholderia bryophila 376MFSha3.1

Best path

PS417_12065, PS417_12060, PS417_12055, xdhA, xylB

Also see fitness data for the top candidates


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
PS417_12065 xylitol ABC transporter, ATPase component H281DRAFT_03380 H281DRAFT_01223
PS417_12060 xylitol ABC transporter, permease component H281DRAFT_02714 H281DRAFT_01120
PS417_12055 xylitol ABC transporter, substrate-binding component
xdhA xylitol dehydrogenase H281DRAFT_04147 H281DRAFT_01517
xylB xylulokinase H281DRAFT_04153 H281DRAFT_04167
Alternative steps:
Dshi_0546 xylitol ABC transporter, ATPase component H281DRAFT_04155 H281DRAFT_03749
Dshi_0547 xylitol ABC transporter, substrate-binding component
Dshi_0548 xylitol ABC transporter, permease component 1 H281DRAFT_05891 H281DRAFT_03746
Dshi_0549 xylitol ABC transporter, permease component 2 H281DRAFT_04157 H281DRAFT_03731
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 H281DRAFT_05890
HSERO_RS17020 xylitol ABC transporter, ATPase component H281DRAFT_03749 H281DRAFT_03228
PLT5 xylitol:H+ symporter PLT5
x5p-reductase D-xylulose-5-phosphate 2-reductase H281DRAFT_03586 H281DRAFT_01517

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.



Related tools

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