hmmemit: 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/hmmemit - from package: hmmer

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

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