#!/usr/bin/perl
use strict;
use warnings;

my %lista2 = (
1    =>    "CAT00.3",
2    =>    "CAT43.1",
3    =>    "CAT40.3"
);

# open filehandle for reading (check that open was successful or die)
open my $AL, '<', 'file.txt' or die $!;

# open filehandle for writing (check that open was successful or die)
open my $OA, '>', 'file2.txt' or die $!;

while (my $line = <$AL>) {
    if ($line =~ /^>(\d+)$/) {
        my $key = $1;
        
        if (exists $lista2{$key}) {
            $line =~ s/$key/$lista2{$key}/; 
        }
    }
    print $OA $line;
}
close $AL or die $!;
close $OA or die $!;