makeprotseq: command not found

Have You tried accessing the binary with the full path?

Maybe Your $PATH variable doesn't contain the default paths? echo $PATH should give something like:

[root@server ~]# echo $PATH

If it's empty, You may set the PATH variable with this command

export PATH="/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin"

On Debian possible default full paths are:

/usr/bin/makeprotseq - from package: emboss

You may install the required package with command apt-get install {package}
Error in other languages:
makeprotseq: bevel nie gevind nie
makeprotseq: comandă negăsită
makeprotseq: comando não encontrado
makeprotseq: commande introuvable
makeprotseq: command not found
makeprotseq: käsku ei ole
makeprotseq: không tìm thấy lệnh
makeprotseq: komanda nerasta
makeprotseq: Kommando nicht gefunden.
makeprotseq: kommandot finns inte
makeprotseq: komut yok
makeprotseq: nie znaleziono polecenia
makeprotseq: níor aimsíodh an t-ordú
makeprotseq: no se encontró la orden
makeprotseq: no s'ha trobat l'ordre
makeprotseq: opdracht niet gevonden
makeprotseq: parancs nem található
makeprotseq: perintah tidak ditemukan
makeprotseq: príkaz nenájdený
makeprotseq: příkaz nenalezen
makeprotseq: команда не найдена
makeprotseq: командата не е открита
makeprotseq: 命令找不到
makeprotseq: コマンドが見つかりません