Supplementary data files for exploring a diverse world of effector domains and amyloid signaling motifs in fungal NLR proteins

This dataset includes 20 supplementary data files for manuscript Exploring a diverse world of effector domains and amyloid signaling motifs in fungal NLR proteins by Jakub W. Wojciechowski, Emirhan Tekoglu, Marlena Gąsior-Głogowska, Virginie Coustou, Natalia Szulc, Monika Szefczyk, Marta Kopaczyńska, Sven J. Saupe, and Witold Dyrka (under revision). 

• SF2. Profile HMMs of NLR effector domains. The file includes previously unpublished models.
• SF3. Multiple sequence alignments of N-termini clusters. 
• SF4. Tabularized results of N-termini annotation.
• SF5. Structure prediction of HeLo-/Goodbye-/MLKL-like domains. Full AlphaFold2/ColabFold outputs.
• SF6. Structure prediction of previously unannotated domains. Full AlphaFold2/ColabFold outputs.
• SF7. PCFGs for BASS. The file includes previously unpublished grammars and a sample scanning configuration.
• SF8. Candidate short NLR N-termini with ASMs. The FASTA file includes sequences from clusters with high content of ASM-like  sequences, according to the BASS PCFGs (SF7).
• SF9. Profile HMMs of ASMs found in short NLR N-termini.
• SF10. Profile HMM of HeLo-related HRAMs.
• SF11. Genomic neighbors of candidate short N-termini NLRs with ASMs The list includes accessions of proteins  encoded by genes within the neighborhood of 20kbp of genes encoding the query proteins (SF8).
• SF12. Short C-termini of 200–400 aa long proteins genomically neighboring candidate short NLR N-termini with ASMs. The FASTA file concerns target proteins listed in SF11.
• SF13. Pairwise hits of the same ASMs in N-termini of NLRs and C-termini of genomically neighboring proteins. The table is based on SF8–9 and SF11–12. 
• SF14. Lists of HMMER domain hits of effector domain profiles. The lists were obtained through iterative searches in NCBI “nr” starting from Pfam profiles of known NLR effector domains.
• SF15. Short C-termini of effector proteins. The FASTA file concerns target proteins listed in SF14.
• SF16. Short N-termini of Pfam NACHT and NB-ARC proteins. The FASTA file concerns proteins from NCBI “nr” associated with the two families in the Pfam database.
• SF17. Profile HMMs of ASMs found both in effector C-termini and NLR N-termini of genomically neighboring proteins.
• SF18. Genomic neighbors of candidate short N-termini Pfam NACHT and NB-ARC proteins. The list includes accessions of proteins encoded by genes within the neighborhood of 20kbp of genes encoding the query proteins (SF16).
• SF19. Pairwise hits of the same ASMs in N-termini of NACHT/NB-ARC NLRs and C-termini of genomically neighboring effector proteins. The table is based on SF15–18. 
• SF20. Pairwise hits of the same ASMs in N-termini of NLRs and C-termini of genomically co-occurring effector proteins. The table is based on SF8–9 and SF15. 
• SF21. BaMLKL homologs identified with hmmsearch in Basidiomycota. A FASTA file.