hmm2emit: 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/hmm2emit - from package: hmmer2

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

Error in other languages:
hmm2emit: bevel nie gevind nie
hmm2emit: comandă negăsită
hmm2emit: comando não encontrado
hmm2emit: commande introuvable
hmm2emit: command not found
hmm2emit: käsku ei ole
hmm2emit: không tìm thấy lệnh
hmm2emit: komanda nerasta
hmm2emit: Kommando nicht gefunden.
hmm2emit: kommandot finns inte
hmm2emit: komut yok
hmm2emit: nie znaleziono polecenia
hmm2emit: níor aimsíodh an t-ordú
hmm2emit: no se encontró la orden
hmm2emit: no s'ha trobat l'ordre
hmm2emit: opdracht niet gevonden
hmm2emit: parancs nem található
hmm2emit: perintah tidak ditemukan
hmm2emit: príkaz nenájdený
hmm2emit: příkaz nenalezen
hmm2emit: команда не найдена
hmm2emit: командата не е открита
hmm2emit: 命令找不到
hmm2emit: コマンドが見つかりません