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awk '{while (match($0, /)[0-9].[0-9][0-9][0-9]:/)) {s=substr($0, RSTART+1, RLENGTH-2); r=int(100*s); if (r>100) r="error"; gsub(")" s ":", ")" r ":")}} 1' infile

awk '
NR==FNR{a[$1]=0;next}
{for (i in a) {s=match($0,i);if (s>0) a[i]++}}
END {for (i in a) print i,a[i]}
' name_list input.txt

SALINISPORA 2
PROPIONIBACTERIUM 1
RHODOCOCCUS 1
AZORHIZOBIUM...

Maybe it's also safer to include underscore:
awk 'NR==FNR{a[$1 "_"]=$2 "_";next}{ for (i in a) gsub(i,a[i])}1' template.txt input.txt
Although the 1st and 3rd parts are in different forms: AAAA0 to...

If the template file (replacement table) has 100 lines, above sed or perl commands will be long to fill the whole web pages.:)

$ cat template.txt
ACICJ ACIDIPHILIUM
ACIF2 ACIDITHIOBACILLUS...