I am not quite sure what the poster is trying to do, in particular the question “is there a way to calculate the score between different disulfide bridges?”. Clearly, if different bridges are completely conserved between species in two different proteins or within the same protein, that’s it. (Sort of the converse of ‘slightly pregnant’.)
Nevertheless this answer discusses ‘scoring’ multiple sequence alignments (MSA) and describing the results, so it can be updated in response to any clarification the poster makes.
The Clustal MSA program already scores positions in an alignment
I do not know what MSA program the poster is using, but the output from Clustal X (at least standalone v. 2.1 for the Mac) already presents scores of a sort. This can be seen in a sample output, below:
The height of the individual bars in the bar graph below the alignment ranges from a maximum (where all five sequences in this set align) to what I assume is the zero baseline (where one of the sequences introduces a gap).
Closer examination, however, shows that the scoring system used is not a simple percentage identity: 0, 20, 40, 60, 80, 100%.
In the detail it can be seen that (4xK + 1xN) scores higher than (4xV + 1xK), and also gets a ‘:’ comment (see below). This is presumably because it is using the same PAM or BLOSUM amino acid comparison matrix used in the alignment to compute the height of the bars. (I leave the interested reader to plough through the literature to see if this is documented.)
What can one say?
The question seems to wish to transform the numerical score into a descriptive statement. The following assumes that one is taking one sequence as reference — here 1qjo.
• The simplest possibility would be a statement of the type:
“P at position 8 in the reference sequence is completely (100%)
conserved in the data set, whereas at position 49 the conservation is
only 80%, and at position 51 only 60%”.
This could be converted to descriptions using the percentage scale in a subjective and arbitrary manner which one would have to define, e.g. >75% but <100% = ‘highly conserved’, >50% but <75% = ‘moderately conserved’
• An alternative would be to use the descriptive categories — * : . — and convert them to descriptive terms ‘completely’, ‘highly’ and ‘moderately’. This result of this would be different from using percentages. What one would really be describing here is not the conservation of a particular amino acid, but the conservation of amino type at a particular position. So the statement would be something like (choosing a different example):
“As regards the eight positions in the reference sequence where E was
found in the data set, only position 40 was highly conserved and
position 58 moderately conserved.”
My example statements above all refer to “the data set”, emphasizing that any numbers or descriptions cannot be absolute, and their significance depends on the extent of the data set and whether it is biased towards sequences of a particular origin. The most obvious cause of bias is species e.g. a data set with 20 mammalian species and two insects. Not only species range is important, but it can happen that a problem is complicated by different forms of a protein in the same species, and that these forms may be more similar between species. A way of approaching the latter problem is to consult SCOPe, and if necessary construct a data set containing a range of SCOPe subcategories.
Other approaches to the disulphide bond problem
I am not quite clear whether any of the members of the family of proteins of interest to the poster lack cysteine at the position of the disulphide-bond forming cysteines of the references. If they do I would be tempted to use alphaFold to obtain predicted structures of these exceptional members and see if the positions at which the cysteines in the reference sequence occur are predicted also to be in close proximity in the exception.