Ahmad - please clarify what you mean by it doesn't seem to work. Are you observing an error or are you not getting the correct/desired results?
If I look at the documentation for getgenpept, one of the examples is
Seq = getgenpept('AAA59174')
and it produces some result. You have even shown that something like
human = getgenpept('AAA69808','SequenceOnly',true);
chicken = getgenpept('NP_989750','SequenceOnly',true);
works too. So what is different between the above two statements and your code that gets the input from the user? Note what you are doing
protein1=input('NCBI accession number of the first protein: ', 's');
protein2=input('NCBI accession number of the second protein: ', 's');
protein1 and protein2 are variables of data type char (so are string variables). With your input example this means that
protein1 == 'AAA69808'
protein2 == 'NP_989750'
Now since these are string variables and the first input to the getgenpept is a string variable, there is no need to wrap these variables in quotes like
seq1 = getgenpept('protein1','SequenceOnly',true);
seq2 = getgenpept('protein2','SequenceOnly',true);
because if you do, then what you are really passing this function are strings representing the variable name of protein1 or protein2 and not the value of the variable.
Remove the single quotes and change these two lines to
seq1 = getgenpept(protein1,'SequenceOnly',true);
seq2 = getgenpept(protein2,'SequenceOnly',true);