Most conserved is the primary sequence of the amino acyl acceptor stem. This portion of the molecule has an invariable A residue in the discriminator position and a G-U pair at position 3 (except in S"eculamonas ecuadoriensis", which has a G-C pair); this position is the recognition site for alanyl tRNA synthase. P2 is a helix of variable length (3 to 10 base pairs) and corresponds to the anticodon stem of tRNAs, yet without an anticodon loop (as not required for tmRNA function). P2 stabilizes the tRNA-like structure, but four nucleotides invariant across oomycetes and jakobids suggest an additional, currently unidentified function. P3 has five base pairs and corresponds to the T-arm of tRNAs, yet with different consensus nucleotides both in the paired region and the loop. The T-loop sequence is conserved across oomycetes and jakobid, with only few deviations (e.g., "Saprolegnia ferax"). Finally, instead of the tRNA-like D-stem with a shortened three-nucleotide D-loop characteristic for bacterial tmRNAs, mitochondrial counterparts have a highly variable 5 to 14-nt long loop.