GapMind for catabolism of small carbon sources

 

Finding step manP for D-mannose catabolism in Klebsiella michiganensis M5al

4 candidates for manP: mannose PTS system, EII-CBA components

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
med BWI76_RS19725 PTS fructose transporter subunit EIIBC protein-Npi-phosphohistidine-D-mannose phosphotransferase (EC 2.7.1.191) (characterized) 44% 70% 377.1 PTS system fructose-specific EIIB'BC component; EIIB'BC-Fru; EC 2.7.1.202 89% 974.5
lo BWI76_RS24865 PTS family enzyme IIB'BC, fructose-specific protein-Npi-phosphohistidine-D-mannose phosphotransferase (EC 2.7.1.191) (characterized) 39% 70% 339 PTS family enzyme IIB'BC, fructose-specific, component of The tagatose-specific PTS transporter/kinase, TagIIA-TPr/TagIIB'BC (tagatose-1-P forming) 94% 888.3
lo BWI76_RS10670 PTS fructose transporter subunit IIC protein-Npi-phosphohistidine-D-mannose phosphotransferase (EC 2.7.1.191) (characterized) 44% 51% 268.9 Fructose-like permease IIC component 2; PTS system fructose-like EIIC component 2 86% 617.1
lo BWI76_RS27570 phosphotransferase system, fructose-specific IIC component protein-Npi-phosphohistidine-D-mannose phosphotransferase (EC 2.7.1.191) (characterized) 39% 52% 236.5 Putative PTS enzyme-II fructose, component of The FrzABC PTS putative transporter (promotes bacterial fitness under stress conditions and promotes fimbrial (fim) gene expression indirectly (Rouquet et al., 2009). Might transport D-tagatose, D-psicose and/or D-sorbose, or a disaccharide of these (Rouquet et al. 2009); involved in environmental sensing, host adaptation and virulence 95% 694.9

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

Also see fitness data for the candidates

Definition of step manP

Or cluster all characterized manP proteins

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, 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