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while ($line=<FILE>){

...
        $hit2= $line=~ /^(>data_\d+\s+PROTID_\d+.*\n.*)/s;
        print OUT2 "$hit2\n";
}

    $str = "text with some pattern in it";
    $c = $str =~ / (some pattern) /;  # sets $c to the numeric value "
+1"
    @m = $str =~ / (some pattern) /;  # assigns "some pattern" as sole
+ element of @m
    ( $m ) = $str =~ / (some pattern) /; # sets $m to "some pattern"