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. 2023 Jan 6;51(D1):D1470-D1482.
doi: 10.1093/nar/gkac1014.

NLRscape: an atlas of plant NLR proteins

Eliza C Martin  1 , Catalin F Ion  1 , Florin Ifrimescu  1 , Laurentiu Spiridon  1 , Jaap Bakker  2 , Aska Goverse  2 , Andrei-J Petrescu  1
Affiliations

NLRscape: an atlas of plant NLR proteins

Eliza C Martin et al. Nucleic Acids Res. .

Abstract

NLRscape is a webserver that curates a collection of over 80 000 plant protein sequences identified in UniProtKB to contain NOD-like receptor signatures, and hosts in addition a number of tools aimed at the exploration of the complex sequence landscape of this class of plant proteins. Each entry gathers sequence information, domain and motif annotations from multiple third-party sources but also in-house advanced annotations aimed at addressing caveats of the existing broad-based annotations. NLRscape provides a top-down perspective of the NLR sequence landscape but also services for assisting a bottom-up approach starting from a given input sequence. Sequences are clustered by their domain organization layout, global homology and taxonomic spread-in order to allow analysis of how particular traits of an NLR family are scattered within the plant kingdom. Tools are provided for users to locate their own protein of interest in the overall NLR landscape, generate custom clusters centered around it and perform a large number of sequence and structural analyses using included interactive online instruments. Amongst these, we mention: taxonomy distribution plots, homology cluster graphs, identity matrices and interactive MSA synchronizing secondary structure and motif predictions. NLRscape can be found at: https://nlrscape.biochim.ro/.

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Figures

Figure 1.
Figure 1.
NLRscape atlas—a brief overview of the main features.
Figure 2.
Figure 2.
Tools for cluster analysis.
Figure 3.
Figure 3.
Overview of the main NLR classes and their domain organisation in NLRscape.
Figure 4.
Figure 4.
(A) Clustering by homology workflow alongside cluster member histograms for each identity cutoff. (B) Description of the cluster naming system.
Figure 5.
Figure 5.
Taxonomic distribution of the main NLR classes. Included are sequences showing the complete canonical organisation with/without marginal domains. To ease comparison also provided is the baseline distribution computed on the entire UniProtKB database.
Figure 6.
Figure 6.
The taxonomic spread (A) and NLR class distribution (B) of the homology clusters at 30% identity. The 2D graph embedding represents clusters as nodes with a radius proportional to the number of constituents, coloured accordingly to the histogram, while edges illustrate inter-cluster homology relations. Displayed are only clusters with more than 10 members.
See this image and copyright information in PMC

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