my ( %merged, %evalues, %lowest );
while ( <DATA> ) {
    chomp;
    my ( $evalue ) = m/\s(\S+)$/;
    my ( $k, $v ) = split /\s+/, $_, 2;
    $merged{$k} = $merged{$k}
                ? "$merged{$k}\t$v"
                : $v;
    if ( ! exists $evalues{$k} ||  $evalue < $evalues{$k} ) {
        $evalues{$k} = $evalue;
        $lowest{$k} = $_;
    }
}

open my $f1, ">", "file1~" or die $!;
print $f1 "$_\t$merged{$_}\n" for sort keys %merged;

open my $f2, ">", "file2~" or die $!;
print $f2 "$lowest{$_}\n" for sort keys %lowest;

__DATA__
Q3KIL4_PSEPF    ONE    134    380    1    252    216.3    6.3e-64
Q3M236_ANAVT    TWO    107    563    1    468    203.2    5.3e-60
Q3M236_ANAVT    THREE    250    494    1    277    219.1    8.6e-65
Q3M5F5_ANAVT    FOUR    296    608    1    355    166.2    7.4e-49
Q3M5F5_ANAVT    FIVE    299    584    1    304    188.2    1.7e-55
Q3M7Z1_ANAVT    SIX    51    181    1    140    99.0    1.2e-28
Q3MAD2_ANAVT    SEVEN    107    508    1    468    350.1    3.3e-104
Q3MAD2_ANAVT    EIGHT    230    457    1    277    201.1    2.3e-59
Q3MBT3_ANAVT    NINE    203    606    1    468    102.5    1.1e-29
Q3MBT3_ANAVT    TEN    326    559    1    277    221.6    1.6e-65
Q3MBT3_ANAVT    ELEVEN    134    333    1    234    -334.1    2.7e-44
Q3MD63_ANAVT    TWELVE    173    491    1    355    248.5    1.2e-73