If I'm understanding you correctly, and you have protein sequences like this:

>prtn1
DTENKRK
KDFLTSE
NSLPRIS

and you want

>prtn1
DTENKRKKDFLTSENSLPRISS

you could use something like this

awk 'BEGIN {ORS=""}{if ($1 ~ /^>/) print "\n"$1"\n"; else print}END{print "\n"}' <protein file>

ORS="" removes the end of line when awk prints, so the protein sequence is concatenated into one line. Checking for a line starting with ">" means the ID can be printed on its own line, by including "\n" newline characters. This can handle multiple sequences, but ends up starting with a blank line, so if your file only has one sequence you might want to replace "\n"$1"\n" with $1"\n".