Unless mySQL and T-SQL (what's T-SQL?) are very different from Oracle, I think you mean this:

SELECT DISTINCT min(tmp.escore) as escore, tmp.org_id
FROM (
    SELECT id2, escore, org_id2
    FROM blast, protein
    WHERE id1 = id
    AND text_id = ?
    UNION
    SELECT id1, escore, org_id1
    FROM blast, protein
    WHERE id2 = id
    AND text_id = ? ) tmp
GROUP BY tmp.org_id
[download]

If I knew what columns belonged to which tables I might be able to offer more advice - without that information, I get a headache every time I try to visualize what's going on here...

---

Update
With the WHERE EXISTS, you end up selecting from the original blast and protein tables if the subselect returns any rows, when what you want to do is select from the subselect results.