Figure 2. Box plots of the bit score distribution of HMM search result sequences for the AT domain classified as PKS I or as non-PKS I using the tree. doi:10.1371/journal.pone.0003515.g002 Figure 3. Number of sequences in the data sets that are annotated as type I PKS domains based on the maximum- likelihood tree. The intensity of the color is equivalent to the relative number of sequences inside a data set. The KS domain has in the larger data sets the highest number of hits and the ratio of the AT, KS and PP domain is mostly similar. doi:10.1371/journal.pone.0003515.g003 In UniRef, many different PKS I domains are found in the same protein while the metagenomic sequences mostly encode protein fragments with a single domain due to the shotgun approach taken during data generation. Assuming that each of these metagenomic domain sequences represent a full type I PKS protein we normalized the number of single and multi domain hit proteins PKS I Screen in Metagenomes Figure 4. A – PKS I classified sequences normalized by total number of screened proteins. B – PKS I classified sequences normalized proteins-wise (all domains of one protein are counted together as one entity) by total number of screened proteins. doi:10.1371/journal.pone.0003515.g004 by the number of screened proteins (Fig. 4B). We found that only the farm soil has a higher PKS I density than UniRef, and PKS I seem most rare in the gut sample where only a single domain occurrence could be detected. The identified PKS I proteins were also normalized by the number of genome equivalents for the Minnesota farm soil, Sargasso Sea, whale falls and acid drainage mine data sets as for these environments average effective genome sizes have been estimated [31]. With nearly seven type I PKS per genome equivalent, the farm soil has the highest density of these proteins (Fig. 5). This is in the range of fully sequenced genomes of organisms from soil habitats [12]. In UniRef, the largest proportion of potential PKS I proteins identified originated from Actinobacteria (5642 sequences), followed by Proteobacteria (3625 sequences). This is similar to statements of previous studies and may be biased by the number of sequenced genomes of these phylogenetic groups [12]. The counting of all taxonomic groups can be found in Table S2. We did not find potential type I PKS members in archaeal proteins. A possible reason for this is the lack of an FAS AT domain in archaea [12] and the low likelihood of horizontal transfer of PKS I genes. As the source organisms of proteins from environmental samples are unknown, a detailed analysis of the taxonomic distribution is currently impossible. As expected, the majority of the environmental sequences are located in clades dominated by bacterial PKS I domains, but there PLoS ONE | www.plosone.org 4 October 2008 | Volume 3 | Issue 10 | e3515