Supplement

Computational Prediction of Conserved Operons and Phylogenetic Footprinting of Transcription Regulatory Elements in the Metal-Reducing Bacterial Family Geobacteraceae

Bin Yan^a, Barbara Methe^b, Derek Lovley^c, and Julia Krushkal^a

^a Center of Genomics and Bioinformatics and Department of Preventive Medicine, University of Tennesee Health Science Center, 66 N. Pauline St., Ste. 633, Memphis, TN 38163, USA.

Tel.: +1 (901) 448-1361; fax: +1 (901) 448-7041.

e-mail: jkrushka@utmem.edu

^b The Institute for Genomic Research, Rockville, MD, USA

^c Department of Microbiology, Morrill Science Center IV North, University of Massachusetts, 639 North Pleasant Str., Amherst, MA 01003, USA.

Tel. : +1 (413)545-2051; fax: +1 (413)545-1578

e-mail: dlovley@microbio.umass.edu

A. Overall information about the 26 conserved Geobacteraceae operons

List of orthologous genes and their locations in 26 conserved operons

Provides detailed information about the sequence data for 26 operons used in analysis, including the location of the predicted non-coding regions in each species, and the links to operon sequences.

List of files with sequence data for 26 operons

Provides the sequence data files, input and output files for AlignACE

Help file describing the names and format of AlignACE input and output files

B. Motifs predicted by comparative genomic analysis of the noncoding regions of the 26 operons

Expanded versions of Tables 1-3 that include motif sequence information

The tables below list motifs that satisfy various criteria of potential biological importance. An asterisk (*) indicates an expanded version of the table that contains motif sequence data.

Table 1*. Motifs identified by AlignACE most similar to E. coli transcription factor binding sites (CompareACE similarity score of 0.7 or higher).

Table 2*. Top palindromic motifs identified by AlignACE (CompareACE similarity score of a motif to its reverse complement of 0.7 or higher).

Table 3*. Top motifs identified by AlignACE highly similar to conserved motifs in other bacterial species (CompareACE score of 0.8 or higher). These are highly significant motif hits with CompareACE score of 0.8 or higher. To view the explanded list of motifs satisfying weaker similarity criteria to conserved motifs in other prokaryotic species, follow the link to Geobacteraceae motifs similar to motifs conserved in other bacteria (CompareACE score of 0.7 or higher).

Overlap between ribosome-binding sites predicted by RBSfinder and motifs predicted by AlignACE in the noncoding regions of the 26 operons

Predicted RBS sites and motifs that overlap with them by at least 4 out of 5 bp

D. Motifs predicted by the AlignACE software that overlapped with predictions of the NNPP program

Motifs predicted by the AlignACE software in the noncoding regions of 26 operons that overlapped with predictions provided by the NNPP program