use strict;
use warnings;

my %smallest =
   map  {
            $_->[0] => {
               org => $_->[1],
               val => $_->[2] }
        }
   sort { $b->[2] <=> $a->[2] }
   map  { chomp; [ split m{\t} ] }
   <DATA>;

my @sorted = ();
foreach my $protein ( sort keys %smallest )
{
    push @sorted, [
       $protein,
       $smallest{$protein}->{org},
       $smallest{$protein}->{val} ];
}

print Data::Dumper->Dump([\@sorted], [qw{*sorted}]);

__END__
protein1	organism1	0.843534
protein2	organism2	2.45
protein3	organism3	9.5322
protein4	organism4	0.3475474
protein1	organism6	9.4534
protein2	organism7	0.43534
protein2	organism8	1.2434
protein3	organism9	0.000003
protein3	orgnanism10	1.23325

##</code><code>##

@sorted = (
            [
              'protein1',
              'organism1',
              '0.843534'
            ],
            [
              'protein2',
              'organism7',
              '0.43534'
            ],
            [
              'protein3',
              'organism9',
              '0.000003'
            ],
            [
              'protein4',
              'organism4',
              '0.3475474'
            ]
          );