PKS I Screen in Metagenomes Figure 1. Maximum likelihood-tree of the AT domain. doi:10.1371/journal.pone.0003515.g001 Taken together, these quality measurements indicate that the tree approach can properly classify the candidate sequences retrieved by HMMs into PKS and non-PKS I members. PKS I domain densities in various environments The number of domains that fall in branches which are classified as type I PKS members as they contain known PKS I sequences are visualized in Fig 3. In nearly all seven data sets the KS domain is found most frequently (with the exception of enhanced biological phosphorus removal sludge data sets) followed by the AT, PP or KR domains. ER and TE sequences occur generally in much lower counts. In agreement with previous studies the MT domain appears very rarely and could only be found in UniRef, the Minnesota farm soil sample and the phosphorus removal sludge. The discrepancy between the AT and KS domain occurrences might indicate different, domain specific HMM sensitivities as they tend to occur at equal copies, but it could have also biological reasons as the number of AT domains in PKS I proteins might differ from the number of KS domains if a trans-acting AT domain is involved [30]. The density of PKS I domains has the highest value in UniRef when the number of tree-refined PKS I sequences is normalized by the total number of proteins in each of the data sets (Fig 4A). It is around three times higher than that of Minnesota farm soil sample which has the highest in all environments. PLoS ONE | www.plosone.org 3 October 2008 | Volume 3 | Issue 10 | e3515