jackhmmer: 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 Debian possible default full paths are:

/usr/bin/jackhmmer - from package: hmmer

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

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