Perhaps the title of my post is misleading, but for instance consider this "Period-like" protein. According to this link:
Proteins of unknown function which exhibit significant sequence similarity to a defined protein family have been named in accordance with other members of that family.., e.g. "Holliday junction resolvase family endonuclease".
It is also possible to use "-like" in the name. Bear in mind that this should only be used for cases that are outliers to a tight homomorphic family, e.g. "Holliday junction resolvase-like protein".
So I could presume that the "Period-like" protein was named so because it exhibited "significant" similarity to the Period protein family, but its function was not/has not been (experimentally?) confirmed.
However, this reductase here was also probably assigned a name based on sequence similarity. UniProt indicates it was also "predicted" just like the Period-like protein; as evidenced by the
Status line on the UniProt webpage. It is probable that this particular protein does not have any additional evidence backing its identification either. So why wasn't this named "NADH:ubiquinone reductase-like" instead?
In general I would like to know under what circumstances a protein gets suffixed with the "-like" moniker (and when it wouldn't). Additionally, when one encounters a "X-like" protein, which properties of the protein can one presume to be related to the family that protein is purported to belong to? (Fold? Function?)
(I apologize if this is something that is supposed to be obvious and/or trivial.)
Edit: this NCBI link here does explain the usage of the "-like" suffix in the context of equivalog-type HMMs but the first and last points under that section appear to contradict one another somewhat? (First point states equivalogs are homologs that share a specific function but whose evolutionary relationship is unknown, but the last point claims despite obvious sequence similarity to XXX, it may or may not have the same role and function as XXX.)
I could be wrong, but in my experience annotation with "-like" doesn't appear to follow an overly systematic/objective process. I don't think there are obvious criteria such as "ABC-like proteins must be 30-50% identical to ABC proteins, and lack experimental evidence". I think its a slightly more holistic way of 'organising' the information.
That is a good assumption. It is a place-holder an annotator placed on the name when they can't be reasonably certain that the protein is what they think it is. All indications point the new protein having that function/characteristics/fold but it remains a hypothesis, until someone experimentally proves it to be so.