GapMind for catabolism of small carbon sources

 

D-mannitol catabolism in Klebsiella michiganensis M5al

Best path

gutB, gutE, gutA, mtlD

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 (15 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
gutB mannitol PTS system, EII-A component GutB BWI76_RS22225
gutE mannitol PTS system, EII-BC1 component GutE BWI76_RS22220
gutA mannitol PTS system, EII-C2 component GutA BWI76_RS22215
mtlD mannitol-1-phosphate 5-dehydrogenase BWI76_RS27165 BWI76_RS01720
Alternative steps:
cmtA mannitol phosphotransferase system, EII-CB component CmtA/MtlF BWI76_RS27160
cmtB mannitol phosphotransferase system, EII-A component CmtB/MtlF BWI76_RS27160 BWI76_RS19735
mak mannose kinase BWI76_RS27555 BWI76_RS22415
manA mannose-6-phosphate isomerase BWI76_RS16280
mt1d mannitol 1-dehydrogenase BWI76_RS03320 BWI76_RS03140
mt2d mannitol 2-dehydrogenase BWI76_RS19755 BWI76_RS05645
mtlA mannitol phosphotransferase system, EII-CBA components BWI76_RS27160
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) BWI76_RS17835 BWI76_RS01820
mtlK polyol ABC transporter, ATP component MtlK/SmoG BWI76_RS01840 BWI76_RS06690
PLT5 polyol transporter PLT5 BWI76_RS03110
scrK fructokinase BWI76_RS07325 BWI76_RS14875

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 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