Pseudomonas aeruginosa is a common Gram-negative, rod-shaped bacterium that can cause disease in plants and animals, including humans. P. aeruginosa is found in soil, water, skin flora, and most man-made environments throughout the world.
P. aeruginosa is a prototypical "multidrug resistant" (MDR) pathogen recognised for its ubiquity and its intrinsically advanced antibiotic resistance mechanisms. It is of considerable medical importance due to its association with serious illnesses – especially nosocomial infections such as ventilator-associated pneumonia and various sepsis syndromes.
The genome of P. aeruginosa was first sequenced in 2001.
("Pseudomonas aeruginosa", Wikipedia: The Free Encyclopedia)
From left to right: i) The number of proteins in the reference proteome of Pseudomonas aeruginosa, ii) the total number of models, iii) the number of unique protein sequences for which at least one model is available and iv) a coverage bar plot is shown.
The bar plot shows the coverage for every protein in the reference proteome of Pseudomonas aeruginosa for which there is at least one model. Different colours (dark green to red boxes) represent the coverage of the targets. Targets with high coverage are represented in dark green (more than 80% of the target's length is covered by models), whereas low coverage is shown in red. The size of each box is proportional to the number of target sequences with a given coverage.
|Proteins in Proteome||Sequences modelled||Models||Sequence coverage of models|
The plot shows the evolution over years (x-axis) of the fraction of Pseudomonas aeruginosa reference proteome residues (y-axis) for which structural information is available. Different colors (light blue to dark blue) in the plot represent the quality of the sequence alignment between the reference proteome sequences (targets) and the sequences of the protein structure database (templates). Alignments with low sequence identity are displayed in light blue, whereas alignments with high sequence identity are depicted with dark blue in the plot. Target-template alignments were computed using HHblits. NR20 database was used to calculate profiles to search a database derived from all unique PDB protein sequences.
Global quality estimation of SWISS-MODEL Repository models is assessed by the QMEAN4 composite scoring function. The quality bar shows fractions of models divided into categories of varying quality. High QMEAN4 values correspond to high quality models (left side of the bar plot). Below -4.0 QMEAN4 values (right side of the plot), models are often no longer of reliable quality.
Detailed numbers are obtained by hovering the mouse over one of the boxes.
Many proteins form oligomeric structures either by self-assembly (homo-oligomeric) or by assembly with other proteins (hetero-oligomeric) to accomplish their function. In SWISS-MODEL Repository, the quaternary structure annotation of the template is used to model the target sequence in its oligomeric form. Currently our method is limited to the modelling of homo-oligomeric assemblies. The oligomeric state of the template is only considered if the interface is conserved.