Table 3 Counts of each family in selected genomes

Rossmann fold methyltransferase (MTase) makes the list of 10 most commonly used sequence and structure families [15]. In analyzed genomes, 4.6% of Rossmann fold MTase does not have motif-I (Gly-rich) and may lack MTase activity. Fold: Rossmann-fold.

Present in many bacteria and metazoan. Fold: Met synthase activation domain-like.

Human genome encodes protein similar to diphthine synthase but not other Class-III MTases (i.e. from tetrapyrrole biosynthesis pathway) identified in analyzed genomes. Fold: Tetrapyrrole-methyltransferase.

Every analyzed here genome has at least one putative SPOUT rRNA MTase, in archaea the same base of tRNA is methylated by Rossmann-fold instead of SPOUT MTase. Fold: α/β knot.

Present in all Eukaryota with sporadic lateral transfer to bacteria and archaea (but not identified in prokaryotic genomes analyzed here). In S. cerevisiae all selected sequences similar to SET-domain MTases are conserved within smart00317 domain (in contrast to SET-domain proteins other then MTases). Fold: β-clip.

This enzyme performs cyclopropane fatty acid synthesis and is important for Mycobacterium survival. Fold: Rossmann-fold.

This is plant enzyme has similarity to proteins with unknown function infrequently distributed in bacteria, archaea and fungi (discussed earlier). Fold: Rossmann-fold (predicted).

The mammalian enzyme is highly specific but the bacterial enzyme can use other acceptors then SAM and can synthesize spermine. Spermidine synthase but not spermine synthase is essential for survival of Arabidopsis and S. cerevisiae [142-144]. Fold: Rossmann-fold.

Was found in Streptomyces purpurascens only. Fold: Rossmann-fold.

ICMT enzymes are present in all eukaryotic organisms [145]. Fold: unknown (predicted: all-α).

Gene encoding fluorinating enzyme was identified in Streptomyces cattleya but not yet in plants synthesizing fluorinated metabolites. Fold: Rossmann-like and β-barrel.

QueA (tRNA ribosyltransferase – isomerase) homologs are found only in bacteria. Fold: QueA-like (TIM-barrel and β-barrel).

SAM decarboxylase activity has been purified from all three domains of Life. However M. tuberculosis and H. pylori lack clearly identifiable homologue of this enzyme. Fold: SAM-decarboxylase.

SAM synthases from bacteria and eukaryotes are closely related at the sequence level and have very similar structures [73]. SAM synthase is involved in development and abiotic stress tolerance in plants and have complex expression pattern [146, 147]. Fold: SAM-synthetase.

ACC is the precursor of important plant hormone – ethylene. Human homologs have different function. Fold: PLP-dependent transferases.

Found in some bacteria only. Fold: GNAT.

Found in some enterobacteria and gamma proteobacteria only. Fold: ribbon-helix-helix.

Numbers of SAM-binding CBS domains presented here are approximate because of strong similarity to CBS domains binding other adenosine derivatives. Fold: CBS-domain.

Biotin biosynthesis is unique to plants, some fungi and most bacteria. Fold: PLP-dependent transferases.

Human lacks SAM-dependent radical enzyme from biotin and thiamine biosynthetic pathways. Those enzymes generate highly oxidizing 5'-deoxyadenosyl radical in an anaerobic reducing environment, and utilize this radical as catalytic and stoichiometric oxidant in many different enzymatic reactions [148]. Those enzymes are essential for anaerobic growth. Fold: TIM-barrel.