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It is suggested that Membrane Transporter functionality is based on low energy paths between proteins of different conformations.
Experience to date is encouraging and the data available reveal that this method is able to distinguish between proteins of different allergenic potential.
We are therefore interested in seeing to what extent such features are shared between proteins of different compartments.
Amino acid composition and subtle sequence similarities between proteins of different compartments are also potential indicators of functional similarity.
The one is there exist many-to-many mappings between proteins of different species, which is the result of biological evolution, such as gene duplication [ 10].
Interactions between proteins of the same functional class are more likely to be conserved across species than interactions between proteins of different functions, which may indicate a lower rate of evolution of interactions related to function.
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ISORank [ 11] adopts similar strategy to obtain potential mappings between proteins of two different PPI networks and computes their global network alignment.
This is in sharp contrast to the comparison between proteins of vastly different sizes such as untagged CENP-A (140 amino acids; ∼16 kDa) and tagged CENP-A-GFP or -YFP (385 amino acids, ∼43 kDa).
The reason for this strikingly different behavior of HEF proteins is unknown, but either subtle amino acid differences between HEF proteins of different virus strains or between the cloned HEF-gene and the gene present in virus particles of C/JHB/1/66 have been discussed (Pekosz and Lamb, 1999).
Given that signal sequences between secreted proteins of different species can be interchanged, it is reasonable to expect that both mammalian and yeast signal sequence trapping (SST) systems would secrete Haemonchus contortus proteins with similar efficiency and quality.
The basis for deriving orthology between related proteins of different plant species is their degree in similarity.
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