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Table 1 PFAM domains most frequently present in the genomic neighborhood of GmrSD proteins

From: Phylogenomics and sequence-structure-function relationships in the GmrSD family of Type IV restriction enzymes

Domains Description
Methylase_S, N6_Mtase, HsdM_N, HSDR_N Elements of Type I RM systems
Helicase_C Present in a wide variety of helicases and helicase-related proteins. In the GmrSD genomic neighborhood this domain most frequently cooccurs with domains of restriction endonucleases: ResIII and HSDR_N, and with DUF3387. A domain similar to DUF3387, the putative inner membrane protein DUF1819, was found among overrepresented gene families in the genomic neighborhoods of the Pgl defense system [9].
ResIII Restriction endonuclease domain from the Type III RM systems
Tetratricopeptide repeat (TPR_15) A structural motif responsible for protein-protein interactions identified in a wide variety of proteins [75].
DUF262 The domain which we identified to be present in the GmrS protein.
SMC_N Found in the N terminus of structural maintenance of chromosomes (SMC) proteins and in RecF and RecN proteins, which are involved in the DNA metabolism and recombination. Proteins from the GmrSD genomic neighborhood that contain this domain most often have only this domain, which suggests that they are homologs of the DNA replication and repair protein RecF, or they also possess the AAA_23 domain, which is characteristic for the DNA repair protein RecN.
Phage_int_SAM_4 (Phage integrase, N-terminal SAM-like domain) Found in site-specific tyrosine recombinases characteristic for integrons – genetic elements able to acquire and rearrange open reading frames (ORFs) embedded in gene cassette units and convert them to functional genes by ensuring their correct expression [76].
HTH_19 DNA binding domain. In proteins from the GmrSD neighborhood it is most often a part of transcription regulators.