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 The file includes previously unpublished models.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 The file includes previously unpublished grammars and a sample scanning configuration.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.