GapMind for catabolism of small carbon sources

 

D-mannitol catabolism in Pedobacter sp. GW460-11-11-14-LB5

Best path

mtlA, mtlD

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
mtlA mannitol phosphotransferase system, EII-CBA components
mtlD mannitol-1-phosphate 5-dehydrogenase
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
manA mannose-6-phosphate isomerase CA265_RS13185 CA265_RS08895
mt1d mannitol 1-dehydrogenase CA265_RS12755
mt2d mannitol 2-dehydrogenase CA265_RS15450 CA265_RS00760
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 CA265_RS15880 CA265_RS07485
PLT5 polyol transporter PLT5 CA265_RS23325
scrK fructokinase CA265_RS18205

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 (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