This is definitely not my field, hence my low confidence level, but 'domain' seems to be the word you need.
There is a mechanism for the formation and shuffling of said domains, this is the modularization hypothesis. This mechanism is divided into three stages. The first stage is the insertion of introns at positions that correspond to the boundaries of a protein domain. The second stage is when the "protomodule" undergoes tandem duplications by recombination within the inserted introns. The third stage is when one or more protomodules are transferred to a different nonhomologous gene by intronic recombination. All states of modularization have been observed in different domains such as those of hemostatic proteins.
The principle of exon shuffling is different from that of gene duplication: new genes are created by recombining previously existing protein-coding domains, which leads to the origin of mosaic proteins [Gilbert, 1978; ; Kaessmann et al., 2002; Long et al., 2003]. The first evidence for exon shuffling was obtained from studies on proteases of blood coagulation and fibrinolysis, followed by the discovery of a variety of multidomain proteins in animals (reviewed in [Patthy, 2003]). The correlation between exon-intron organization of the gene and the domain organization of the corresponding protein is most evident in the case of young vertebrate genes, e.g. genes coding for proteases of blood coagulation, fibrinolytic and complement cascades, selectins, cartilage link proteins, fibronectin, factor H, tenascins, etc. [Patthy, 2003].
Note added at 34 mins (2017-02-21 23:02:34 GMT)
Domains are evolutionarily conserved regions of proteins with generally independent structural and functional properties. Although only a fairly limited set of domains has been created during evolution, combining these domains in different ways has led to the huge number of observed protein domain architectures. These multidomain proteins have diverse functions that rely on the collective properties of their component domains. Therefore, a key to understanding the evolution of proteins is to understand how multidomain proteins gain, lose and rearrange domains.
The domain shuffling theory is similar to the exon shuffling theory, but in sharp contrast, maintains that the unit of shuffling during evolution is a functional protein domain, not an exon. The functional domain does not necessarily correspond to the exon. Although there are some cases where it does, most functional domains consist of more than one exon or occupy only part of a large exon. For example, the Kringle domain is known to have been shuffled as a unit during evolution. The Kringle domain is a characteristic supersecondary structure frequently found in the serine proteinases involved in the blood clotting system. Even though the Kringle domain is, in most cases, split into three exons by two introns, those found in various proteins are almost always complete forms and never found as parts corresponding to the exons. At present, however, there is no known genetic mechanism for facilitating domain shuffling, and domain shuffling seems to have taken place in prokaryotes as well (3).
| Helena Chavarria|
Local time: 02:15
Native speaker of: English
PRO pts in category: 4