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Results: 3

1.
Fig 3.

Fig 3. From: Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli.

Locations and sizes of CFT073 and EDL933 islands. Island size, vertical axis; position in colinear backbone, horizontal axis. All islands >4 kb are shown. Islands located at tRNAs are indicated by tRNA labels. One tmRNA (ssrA) is also an insertion target. *, CFT073 and EDL933 islands in the same backbone location but not near tRNAs.

R. A. Welch, et al. Proc Natl Acad Sci U S A. 2002 December 24;99(26):17020-17024.
2.
Fig 2.

Fig 2. From: Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli.

Shared E. coli proteins. Comparison of the predicted proteins of the three E. coli strains shows the number of orthologs in each shared category and numbers of strain-specific proteins. Hypervariable proteins and proteins spanning island–backbone junctions were excluded from the analysis. Number of proteins counted: K-12, 4,288; CFT073, 5,016; EDL933, 5,063. In the totals for the three strains, orthologous proteins are counted only once. Orthologous proteins meet the same match criteria used for designation of backbone (see Materials and Methods).

R. A. Welch, et al. Proc Natl Acad Sci U S A. 2002 December 24;99(26):17020-17024.
3.
Fig 1.

Fig 1. From: Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli.

Map of the CFT073 genome and comparison with K-12 strain MG1655. The outer circle shows ORFs, colored according to the K-12 comparison in the second circle, where DNA regions are shown: blue, backbone, i.e., E. coli near match to MG1655; red, CFT073 islands (insertions); orange, islands (substitutions replacing K-12 segments); violet, K-12 islands. ORFs in the outer ring that span island–backbone junctions are pink. Third circle, RNAs: green, rRNA operons; blue, tRNAs; gold, miscellaneous RNAs. Fourth circle, scale in bp. Fifth circle, GC skew calculated for each ORF >100 aa, colored according to the same scheme of the ORF circle and plotted around the mean. Sixth circle, GC skew calculated over the whole sequence (window, 10 kb) plotted around the mean. Seventh circle, codon-adaptation index CAI (inverse, 1-CAI is plotted); pink rays indicate CAI values <0.2; purple rays, values >0.2. The pink rays can be seen to correspond with islands. A detailed linear map with ORF annotations is available at www.genome.wisc.edu. Maps were created by GENVISION from DNASTAR.

R. A. Welch, et al. Proc Natl Acad Sci U S A. 2002 December 24;99(26):17020-17024.

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