hmmconvert: 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/hmmconvert - from package: hmmer

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