GapMind for catabolism of small carbon sources

 

Finding step fruI for D-fructose catabolism in Pseudomonas fluorescens FW300-N1B4

3 candidates for fruI: fructose-specific PTS system (fructose 1-phosphate forming), EI, Hpr, and EII-A components

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
hi Pf1N1B4_1146 Phosphoenolpyruvate-protein phosphotransferase of PTS system (EC 2.7.3.9) Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized) 100% 100% 1825.1 D-trehalose PTS system, I, HPr, and IIA components 44% 512.3
med Pf1N1B4_833 PTS system, glucose-specific IIA component / Phosphotransferase system, phosphocarrier protein HPr / Phosphoenolpyruvate-protein phosphotransferase of PTS system (EC 2.7.3.9) Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized) 41% 87% 525.4 trehalose-specific PTS system, I, HPr, and IIA components 80% 1275.0
lo Pf1N1B4_2284 FIG001592: Phosphocarrier protein kinase/phosphorylase, nitrogen regulation associated Fructose-specific PTS system, I, HPr, and IIA components (characterized) 37% 58% 342.4 Phosphoenolpyruvate-dependent phosphotransferase system; Enzyme I-Ntr; EINtr; Phosphotransferase system, enzyme I; EC 2.7.3.9 42% 584.3

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 fruI

Or cluster all characterized fruI proteins

This GapMind analysis is from Aug 02 2021. The underlying query database was built on Aug 02 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, 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