About FAM / Family with Sequence Similarity:
When analyzing proteins, they get classified into family groups. Currently, it is proteins that are assigned to different family groupings, based upon the presence of a specific family pattern, domain, or physical structure. Proteins that belong to the same family will generally have physical similarities between one and the other, whilst there aren’t necessarily as many similarities between different families. Where some families will have a short well-defined structure, others can contain longer less defined motifs. By using this visualization method, it can be clear to identify simple differences within family bandings together.
It can be difficult to obtain evidence around individual proteins and their family characteristics. Genome projects are able to process and generate sequence data quickly. Their goal is to determine the function of proteins predicted by this sequencing project. It works on an assumptive basis that the shared features can classify proteins into families. With a further underlying assumption being that proteins within the same family may possess similar or identical biochemical functions. The concept being that functions from well-known and characterized proteins can be applied to other members where their individual proteins are less well understood or known.
By using this method to quantify similarities can have flaws. By assuming these similarities there is the chance that there is a chance that other features such as the detection of a multidomain structure which many protein families have. The ideal outcome would be where proteins are only classified into a family subject to them demonstrating a highly similar architectural construction.