Arabidopsis thaliana (Mouse-ear cress)

Arabidopsis thaliana is a small flowering plant native to Eurasia. A. thaliana is considered a weed; it is found by roadsides and in disturbed lands.

A winter annual with a relatively short life cycle, Arabidopsis is a popular model organism in plant biology and genetics. For a complex multicellular eukaryote, A. thaliana has a relatively small genome of approximately 135 megabase pairs. It was the first plant to have its genome sequenced, and is a popular tool for understanding the molecular biology of many plant traits, including flower development and light sensing.

The genome of A. thaliana was sequenced in 2000.

"Arabidopsis thaliana", Wikipedia: The Free Encyclopedia

Protein models in Repository

From left to right: i) The number of proteins in the reference proteome of Arabidopsis thaliana, ii) the number of unique protein sequences for which at least one model is available, iii) the total number of models and iv) a coverage bar plot is shown.
The bar plot shows the coverage for every protein in the reference proteome of Arabidopsis thaliana 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.

For information on the latest proteome for Arabidopsis thaliana, please visit UniProtKB.

You can easily download the latest protein sequences for Arabidopsis thaliana proteome here. Please note this download is for the current UniProtKB release, which may be different to release 2020_02 that was used for the most up to date SWISS-MODEL Repository.

Proteins in proteomeSequences modelledModels
27,46320,67037,584

Detailed coverage numbers are obtained by hovering the mouse over one of the boxes.

Structural Coverage

The plot shows the evolution over years (x-axis) of the fraction of Arabidopsis thaliana 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 proteins in the structure database (templates). Alignments with low sequence identity are displayed in light blue, whereas alignments with high sequence identity are depicted in dark blue. The SWISS-MODEL Template Library is used as database of templates. Only target-template alignments found by HHblits and only residues with atom coordinates are considered.

Residue Coverage

This chart shows the percentage of residues in the Arabidopsis thaliana proteome which are covered by experimental structures and the enhancement of coverage by homology modelling by the SWISS-MODEL pipeline. Experimental residue coverage is determined using SIFTS mapping. For residues which are not covered by experimental structures (including where there are no atom records in SIFTS mapping) the model coverage bars are coloured by QMEANDisCo local quality score.

Oligomeric State

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.

Single Chain2-mer3-mer4-mer5-mer6-mer7-mer8-mer9-mer10-mer11-mer12-mer14-mer15-mer16-mer20-mer24-mer26-mer35-mer39-mer60-mer62-mer
32,1753,983352588162685330125237201611612115
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