Fig. 6: Pfam–nucleic acids interactions.

a The interaction of Pfam HLH domain and double-stranded DNAs contains 22 of 39 entries with HLH domains in the PDB and 22 of 35 UniProts with 30 unique DNA sequences. HLH domains are aligned based on Pfam hidden Markov model positions by pair_fit in PyMOL. The coordinates and PyMOL script files can be downloaded from http://dunbrack2.fccc.edu/ProtCiD/Results/EntityPfamArchWithPfam.aspx?PfamId=HLH web page and are included in HLH_pdb.tar.gz with other ligands or http://dunbrack2.fccc.edu/ProtCiD/IPdbfam/PfamLigands.aspx?Ligand=DNA web page and are included in DNA.tar.gz with other DNA–interacting Pfams. b. The interaction of Pfam dsrm domains and double-stranded RNAs occurs in 33 of 91 entries with the (dsrm) Pfam, and 11 of 45 UniProts. c. The interaction of Pfam DEAD domains and single-stranded DNAs contains 19 entries and 6 UniProts. d The interaction of Pfam DEAD domains and single-stranded RNAs occurs in 61 entries and 24 UniProts, interacting with 34 distinct RNA sequences. The DEAD domains of D3TI84_ANAPL [https://www.uniprot.org/uniprot/D3TI84] (PDB: 4A36 [https://doi.org/10.2210/pdb4A36/pdb]) and DDX58_HUMAN [https://www.uniprot.org/uniprot/O95786] (9 entries) structures interact with dsRNA (not shown). Nucleic acids are colored in orange.