GapMind for catabolism of small carbon sources

 

D-mannitol catabolism in Shewanella amazonensis SB2B

Best path

PLT5, mt2d, scrK

Also see fitness data for the top candidates

Rules

Overview: Mannitol degradation in GapMind is based on MetaCyc pathway mannitol degradation I via a phosphotransferase system (link), pathway II via mannitol 1-dehydrogenase (link), or another oxidative pathway with mannitol 2-dehydrogenase (PMID:8254318).

17 steps (6 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
PLT5 polyol transporter PLT5
mt2d mannitol 2-dehydrogenase Sama_0097 Sama_1980
scrK fructokinase Sama_0561 Sama_0291
Alternative steps:
cmtA mannitol phosphotransferase system, EII-CB component CmtA/MtlF
cmtB mannitol phosphotransferase system, EII-A component CmtB/MtlF
gutA mannitol PTS system, EII-C2 component GutA
gutB mannitol PTS system, EII-A component GutB
gutE mannitol PTS system, EII-BC1 component GutE
mak mannose kinase Sama_2231 Sama_1405
manA mannose-6-phosphate isomerase Sama_2243
mt1d mannitol 1-dehydrogenase Sama_2709
mtlA mannitol phosphotransferase system, EII-CBA components
mtlD mannitol-1-phosphate 5-dehydrogenase
mtlE polyol ABC transporter, substrate-binding component MtlE/SmoE
mtlF polyol ABC transporter, permease component 1 (MtlF/SmoF)
mtlG polyol ABC transporter, permease component 2 (MtlG/SmoG)
mtlK polyol ABC transporter, ATP component MtlK/SmoG Sama_2641 Sama_0668

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, 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