exonerate: command not found

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

[root@server ~]# echo $PATH
/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin

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 CentOS possible default full paths are:

/usr/bin/exonerate - from package: exonerate

You may install the required package with command yum install {package}

On Debian possible default full paths are:

/usr/bin/exonerate - from package: exonerate

You may install the required package with command apt-get install {package}

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