sort both files on the 2nd column and join on the 2nd column (replace '\t' with a tab )..

join -t '\t' -1 2 -2 2 <(sort -t '\t' -k2,2 output1.tsv) <(sort -t '\t' -k2,2 output2.tsv)

Let's do this in R:

table1 = data.frame(read.table("~/tmp/test1.out", header=F))
table2 = data.frame(read.table("~/tmp/test2.out", header=F))
names(table1) = c("gene","hit")
names(table2) = names(table1)
merge(table1, table2, by="hit")

output:

> merge(table1, table2, by="hit")
    hit gene.x gene.y
1 Hsp90   PFD1   GHT3

Did this using Perl.

cat o1.txt o2.txt >o3.txt  ## combined both outputs

SCRIPT

open FH,"o3.txt";
%HoA=();
print "_______INPUT_DATA_________\n";
while(<FH>)
{
print "$_";
    @array=split;
    for($i=1;$i<=$#array;$i++)
    {
    push @{ $HoA{$array[$i]} }, "$array[0]";
    }
}
print "___________RESULT_________\n";
foreach $k (sort keys %HoA)
{
    print "$k\t@{$HoA{$k}}\n";
}

OUTPUT:

________INPUT_DATA_________
PFD1 Hsp90
PFD2 Gan80
PFD5 Kan38
GHT1 Lsg70
GHT2 Jkl78
GHT3 Hsp90
GHT6 Odf45
___________RESULT_________
Gan80    PFD2
Hsp90    PFD1 GHT3
Jkl78    GHT2
Kan38    PFD5
Lsg70    GHT1
Odf45    GHT6