hmm2index: 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/hmm2index - from package: hmmer2

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

Error in other languages:
hmm2index: bevel nie gevind nie
hmm2index: comandă negăsită
hmm2index: comando não encontrado
hmm2index: commande introuvable
hmm2index: command not found
hmm2index: käsku ei ole
hmm2index: không tìm thấy lệnh
hmm2index: komanda nerasta
hmm2index: Kommando nicht gefunden.
hmm2index: kommandot finns inte
hmm2index: komut yok
hmm2index: nie znaleziono polecenia
hmm2index: níor aimsíodh an t-ordú
hmm2index: no se encontró la orden
hmm2index: no s'ha trobat l'ordre
hmm2index: opdracht niet gevonden
hmm2index: parancs nem található
hmm2index: perintah tidak ditemukan
hmm2index: príkaz nenájdený
hmm2index: příkaz nenalezen
hmm2index: команда не найдена
hmm2index: командата не е открита
hmm2index: 命令找不到
hmm2index: コマンドが見つかりません