For a visualization of the results, a program is provided that creates graphical overviews of the proteins and the detected domains based on the database content. Code and data availability All python and C programs (Methods S6) that were created for this study are open source and available under the ISC license (http://www.opensource.org/licenses/isc-license.txt). The data base files and all other files are free availability under the Creative Commons Attribution License (http://creativecommons.org/li- censes/by/3.0/). The generated detailed results are available in the supplemen- tary material. This includes the resulting sequences of the HMM searches (Methods S7), the alignments (Methods S7), the trees in Newick format (Methods S7), visualization of the trees (Methods S1 and S2) as well as the database that hold the integrated data (Methods S5). Also a text file of selected parts of the database is included (Methods S5). The created Hidden-Markov-Models are incorporate into domain search web service SMART [37]. Supporting Information Methods S1 Maximum likelihood trees of the AT, DH, ER, and KR domains Found at: doi:10.1371/journal.pone.0003515.s001 (7.24 MB ZIP) Methods S2 Maximum likelihood trees of the KS, PP, MT and TE domains Found at: doi:10.1371/journal.pone.0003515.s002 (4.38 MB ZIP) Methods S3 Box plots of bit score and Robison-Foulds distances distributions Found at: doi:10.1371/journal.pone.0003515.s003 (0.04 MB ZIP) Methods S4 Supplementary Information Found at: doi:10.1371/journal.pone.0003515.s004 (0.46 MB PDF) Methods S5 SQLite data base of the integrated information and tables of selected columns in CSV-format. Found at: doi:10.1371/journal.pone.0003515.s005 (4.39 MB ZIP) Source code of programs (C and Python) and Methods S6 patches. References 1. Pace NR (1997) A molecular view of microbial diversity and the biosphere. Science 276: 734–740. 2. Yun J, Ryu S (2005) Screening for novel enzymes from metagenome and SIGEX, as a way to improve it. Microb Cell Fact 4: 8. 3. Beja O, Aravind L, Koonin E, Suzuki M, Hadd A, et al. (2000) Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science 289: 1902–6. 4. Kannan N, Taylor SS, Zhai Y, Venter JC, Manning G (2007) Structural and Functional Diversity of the Microbial Kinome. PLoS Biol 5: e17. 5. Podar M, Eads J, Richardson T (2005) Evolution of a microbial nitrilase gene family: a comparative and environmental genomics study. BMC Evol Biol 5: 42. 6. Raes J, Foerstner KU, Bork P (2007) Get the most out of your metagenome: computational analysis of environmental sequence data. Curr Opin Microbiol 10: 490–498. 7. Staunton J, Weissman KJ (2001) Polyketide biosynthesis: a millennium review. Nat Prod Rep 18: 380–416. 8. Zucko J, Skunca N, Curk T, Zupan B, Long PF, et al. (2007) Polyketide synthase genes and the natural products potential of Dictyostelium discoideum. Bioinformatics 23: 2543–2549. 9. Zhu G, LaGier MJ, Stejskal F, Millership JJ, Cai X, et al. (2002) Cryptosporidium parvum: the first protist known to encode a putative polyketide synthase. Gene 298: 79–89. 10. Castoe TA, Stephens T, Noonan BP, Calestani C (2007) A novel group of type I polyketide synthases (PKS) in animals and the complex phylogenomics of PKSs. Gene 392: 47–58. 11. Calestani C, Rast JP, Davidson EH (2003) Isolation of pigment cell specific genes in the sea urchin embryo by differential macroarray screening. Development 130: 4587–4596. PKS I Screen in Metagenomes Found at: doi:10.1371/journal.pone.0003515.s006 (0.06 MB ZIP) Methods S7 Sequences, alignment and tree files of the different domains. Found at: doi:10.1371/journal.pone.0003515.s007 (6.92 MB ZIP) Figure S1 Bit score distributions of the hits of HMM searches for all eight domains. Found at: doi:10.1371/journal.pone.0003515.s008 (9.61 MB TIF) Figure S2 Robison-Foulds distances distributions Found at: doi:10.1371/journal.pone.0003515.s009 (2.88 MB TIF) Table S1 Number of HMM search result sequences of different annotation classes Found at: doi:10.1371/journal.pone.0003515.s010 (0.11 MB DOC) Table S2 Domain sequences marked as PKS I per taxonomic group Found at: doi:10.1371/journal.pone.0003515.s011 (0.10 MB DOC) Table S3 Number of common taxa and Robison-Fould distances of the test and reference tress Found at: doi:10.1371/journal.pone.0003515.s012 (0.10 MB DOC) Table S4 BLAST hits per domain in UniRef Found at: doi:10.1371/journal.pone.0003515.s013 (0.10 MB DOC) Table S5 Counting of the group members of the multi hit proteins Found at: doi:10.1371/journal.pone.0003515.s014 (0.10 MB DOC) Table S6 Counting of the group members of the single hit proteins Found at: doi:10.1371/journal.pone.0003515.s015 (0.10 MB DOC) Acknowledgments We would like to thank all members of our group for support and feedback, especially Jeroen Reas, and the reviewers for their constructive and stimulating comments. 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(2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 66–74. PLoS ONE | www.plosone.org 7 October 2008 | Volume 3 | Issue 10 | e3515