hmm2search: 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/hmm2search - from package: hmmer2

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

Error in other languages:
hmm2search: bevel nie gevind nie
hmm2search: comandă negăsită
hmm2search: comando não encontrado
hmm2search: commande introuvable
hmm2search: command not found
hmm2search: käsku ei ole
hmm2search: không tìm thấy lệnh
hmm2search: komanda nerasta
hmm2search: Kommando nicht gefunden.
hmm2search: kommandot finns inte
hmm2search: komut yok
hmm2search: nie znaleziono polecenia
hmm2search: níor aimsíodh an t-ordú
hmm2search: no se encontró la orden
hmm2search: no s'ha trobat l'ordre
hmm2search: opdracht niet gevonden
hmm2search: parancs nem található
hmm2search: perintah tidak ditemukan
hmm2search: príkaz nenájdený
hmm2search: příkaz nenalezen
hmm2search: команда не найдена
hmm2search: командата не е открита
hmm2search: 命令找不到
hmm2search: コマンドが見つかりません