The SecY protein is the main transmembrane subunit of the bacterial Sec export pathway and of a protein-secreting ATPase complex, also known as a SecYEG translocon.

[2] Secretion of some proteins carrying a signal-peptide across the inner membrane in Gram-negative bacteria occurs via the preprotein translocase pathway.

Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component within the membrane.

SecB maintains preproteins in an unfolded state after translation and targets these to the peripheral membrane protein ATPase SecA for secretion.

[6] SecY is also encoded in the chloroplast genome of some algae where it could be involved in a prokaryotic-like protein export system across the two membranes of the chloroplast endoplasmic reticulum (CER) which is present in chromophyte and cryptophyte algae.