you can simply substitute a number into the hash-value s/^>(\d+)/$lista2{$1}/

the following demonstration is safer because it is also catching missing hash entries

use strict;
use warnings;


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

while (<DATA>) {
    s/^>(\d+)/$lista2{$1} || die "unknown number $1"/e;
    print 
}


__DATA__
>1
AACTCTGGGACAATGGCACACGGGAAACAGATAATGAACGATCAGCACAGGGAACTAGCG
>2
AACTCTGGGACAATGGCACACGGGAAACAGATAATGAACGATCAGCACAGGGAACTAGCG
>3
AACTCTGGGACAATGGCACACGGGAAACAGATAATGAACGATCAGCACAGGGAACTAGCG
>4
[download]

unknown number 4 at d:/Users/lanx/pm/hash_regex.pl line 14, <DATA> lin
+e 7.
CAT00.3
AACTCTGGGACAATGGCACACGGGAAACAGATAATGAACGATCAGCACAGGGAACTAGCG
CAT43.1
AACTCTGGGACAATGGCACACGGGAAACAGATAATGAACGATCAGCACAGGGAACTAGCG
CAT40.3
AACTCTGGGACAATGGCACACGGGAAACAGATAATGAACGATCAGCACAGGGAACTAGCG

Compilation exited abnormally with code 255 at Sat Apr 28 00:16:17
[download]

update

just noticed, the s/^>(\d+)/$lista2{$1}/ variant will already warn you.

Use of uninitialized value within %lista2 in substitution iterator at hash_regex.pl line 14, <DATA> line 7.