GapMind for catabolism of small carbon sources


Definition of D-mannitol catabolism

As rules and steps, or see full text


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).


mtlA: mannitol phosphotransferase system, EII-CBA components

cmtA: mannitol phosphotransferase system, EII-CB component CmtA/MtlF

cmtB: mannitol phosphotransferase system, EII-A component CmtB/MtlF

gutB: mannitol PTS system, EII-A component GutB

gutE: mannitol PTS system, EII-BC1 component GutE

gutA: mannitol PTS system, EII-C2 component GutA

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

PLT5: polyol transporter PLT5

mtlD: mannitol-1-phosphate 5-dehydrogenase

mt1d: mannitol 1-dehydrogenase

mak: mannose kinase

manA: mannose-6-phosphate isomerase

mt2d: mannitol 2-dehydrogenase

scrK: fructokinase



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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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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