#warning windows double quotes
perl -lanE "print $F[0],qq(\t)x($F[3]=~/Pro/?1:$F[3]=~/Bact/?2:3),$F[4]" genetable.txt

ENSG00000088992 0.31
ENSG00000105374 0.37
ENSG00000005810         0.29
ENSG00000088992         0.27
ENSG00000109016         -0.37
ENSG00000069248         0.32
ENSG00000005810                 -0.29
ENSG00000105374                 -0.27
ENSG00000105374                 -0.27
ENSG00000105374                 -0.30
ENSG00000133107         0.35

##</code><code>##

perl -lanE "BEGIN{@h=qw(Gene Prot_Ente Bact_Bact Firm_Lach);print join qq(\t),@h}
            print $F[0],qq(\t)x($F[3]=~/$h[1]/?1:$F[3]=~/$h[2]/?2:3),$F[4]" genetable.txt

Gene    Prot_Ente       Bact_Bact       Firm_Lach
ENSG00000088992 0.31
ENSG00000105374 0.37
ENSG00000005810         0.29
ENSG00000088992         0.27
ENSG00000109016         -0.37
ENSG00000069248         0.32
ENSG00000005810                 -0.29
ENSG00000105374                 -0.27
ENSG00000105374                 -0.27
ENSG00000105374                 -0.30
ENSG00000133107         0.35