hmmsim: 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/hmmsim - from package: hmmer

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

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