GapMind for catabolism of small carbon sources

 

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

3 candidates for manY: mannose PTS system, EII-C component ManY/ManM

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
hi BWI76_RS17895 PTS mannose/fructose/sorbose transporter subunit IIC mannose permease IIC component (characterized) 94% 100% 488.4 PTS system sorbose-specific EIIC component; EIIC-Sor; Sorbose permease IIC component 61% 327.4
med BWI76_RS01730 PTS mannose/fructose/sorbose transporter subunit IIC mannose permease IIC component (characterized) 62% 100% 335.5 PTS system sorbose-specific EIIC component; EIIC-Sor; Sorbose permease IIC component 94% 474.6
lo BWI76_RS03965 PTS sugar transporter Mannose-specific PTS system, IIC component, component of Mannose enzyme II complex, IIAB, IIC, IID. IIC/IID serve allows entry of some bacteriocins including pediocin (class IIa) and lactococcin A (class IIc) (Kjos et al., 2011). Transports and phosphorylates Glucose, Mannose and Glucosamine (characterized) 31% 97% 121.3 PTS sugar transporter, component of PTS uptake system for glucoselysine and fructoselysine, GfrABCD 83% 415.6

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 manY

Or cluster all characterized manY proteins

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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