The Complete Genome Sequence of Escherichia coli K-12 by Frederick R. Blattner, Guy Plunkett, Craig A. Bloch, Nicole T. Perna, Valerie Burland, Monica Riley, Julio Collado-Vides, Jeremy D. Glasner, Christopher K. Rode, George F. Mayhew, Jason Gregor, Nelson Wayne Davis, Heather A. Kirkpatrick, Michael A. Goeden, Debra J. Rose, Bob Mau, and Ying Shao Science Volume 277(5331):1453-1462 September 5, 1997 Published by AAAS

Figure 1 The overall structure of theE. coli genome. The overall structure of theE. coli genome. The origin and terminus of replication are shown as green lines, with blue arrows indicating replichores 1 and 2. A scale indicates the coordinates both in base pairs and in minutes (actually centisomes, or 100 equal intervals of the DNA). The distribution of genes is depicted on two outer rings: The orange boxes are genes located on the presented strand, and the yellow boxes are genes on the opposite strand. Red arrows show the location and direction of transcription of rRNA genes, and tRNA genes are shown as green arrows. The next circle illustrates the positions of REP sequences around the genome as radial tick marks. The central orange sunburst is a histogram of inverse CAI (1 – CAI), in which long yellow rays represent clusters of low (<0.25) CAI. The CAI plot is enclosed by a ring indicating similarities between previously described bacteriophage proteins and the proteins encoded by the complete E. coli genome; the similarity is plotted as described in Fig. 3 for the complete genome comparisons. Frederick R. Blattner et al. Science 1997;277:1453-1462 Published by AAAS

Figure 2 Base composition is not randomly distributed in the genome. Base composition is not randomly distributed in the genome. G-C skew [(G – C)/(G + C)] is plotted as a 10-kb window average for one strand of the entire E. coligenome. Skew plots for the three codon positions are presented separately; leftward genes, rightward genes, and non–protein-coding regions are shown in lines 5, 6, and 7. The two horizontal lines below the skew plots show the distribution of two highly skewed octamer sequences, GCTGGTGG (Chi) and GCAGGGCG (8-mer). Tick marks indicate the position of each copy of a sequence in the complete genome and are vertically offset to indicate the strand containing the sequence. The next 18 horizontal lines correspond to distinct classes of repetitive elements. The penultimate line contains a histogram showing the similarity (the product of the percent of each protein in the pairwise alignment and the percent amino acid identity across the aligned region) of known phage proteins to the proteins encoded by the complete E. coli genome. The last line indicates the position and orientation of the EcoK restriction-modification site AACNNNNNNGTGC (N, any nucleotide). Two vertical lines through the plots show the location of the origin and terminus of replication. Frederick R. Blattner et al. Science 1997;277:1453-1462 Published by AAAS