Table 1.
Positively selected genes in UPEC strains
| Name (Systematic) | P value | dn/ds | COG | Annotation |
|---|---|---|---|---|
| cedA (UTI89_C1924) | 1.75E-04 | 795.84 | — | Cell division regulatory protein |
| yhgA (UTI89_C3912) | 1.41E-06 | 323.80 | — | Hypothetical protein |
| yidQ (UTI89_C4239) | 1.58E-05 | 999.00 | — | Hypothetical protein |
| (UTI89_C4862) | 1.13E-09 | 822.62 | — | Hypothetical protein |
| fdnG (UTI89_C1689) | 2.24E-04 | 999.00 | C | α subunit of formate dehydrogenase N |
| ygcR (UTI89_C3134) | 1.55E-04 | 999.00 | C | Putative transport protein |
| cycA (UTI89_C4817) | 5.44E-05 | 275.05 | E | Serine/alanine/glycine APC transporter |
| argl (UTI89_C4860) | 1.09E-05 | 450.08 | E | Ornithine carbamoyltransferase chain I |
| yjjN (UTI89_C5064) | 2.22E-05 | 570.01 | E | Hypothetical zinc-type alcohol dehydrogenase-like protein |
| fruA (UTI89_C2442) | 1.69E-06 | 202.74 | G | PTS system, fructose-specific IIBC component |
| agal (UTI89_C3572) | 2.33E-04 | 999.00 | G | Putative galactosamine-6-phosphate isomerase |
| yicM (UTI89_C4218) | 6.60E-05 | 397.37 | G | Putative transport protein |
| yjiL (UTI89_C5044) | 2.37E-05 | 999.00 | I | Hypothetical protein |
| yjbN (UTI89_C4617) | 7.27E-09 | 191.93 | J | Hypothetical protein |
| topB (UTI89_C1958) | 1.17E-26 | 106.44 | L | DNA topoisomerase III |
| xseA (UTI89_C2827) | 1.22E-08 | 218.52 | L | Exodeoxyribonuclease VII large subunit |
| recC (UTI89_C3223) | 1.11E-04 | 316.28 | L | Exodeoxyribonuclease V γ chain |
| fepE (UTI89_C0589) | 1.65E-04 | 123.61 | M | Ferric enterobactin transport protein |
| cutE (UTI89_C0655) | 9.50E-08 | 999.00 | M | Apolipoprotein N-acyltransferase |
| ompF (UTI89_C1001) | 8.26E-05 | 999.00 | M | Outer membrane protein F |
| ompC (UTI89_C2497) | 2.42E-11 | 999.00 | M | Outer membrane protein 1b (1b;c) |
| yfaL (UTI89_C2514) | 1.04E-10 | 387.75 | M | Hypothetical protein |
| amiA (UTI89_C2768) | 9.89E-06 | 999.00 | M | Probable N-acetylmuramoyl-l-alanine amidase |
| fhuA (UTI89_C0166) | 6.68E-16 | 998.92 | P | Ferrichrome-iron receptor |
| entD (UTI89_C0583) | 4.68E-06 | 360.74 | Q | 4′-phosphopantetheinyl transferase |
| entF (UTI89_C0588) | 1.90E-11 | 999.00 | Q | Enterobactin synthetase component F |
| yoji (UTI89_C2491) | 2.18E-04 | 999.00 | Q | Hypothetical ABC transporter ATP-binding protein |
| ycdT (UTI89_C1088) | 4.77E-07 | 223.42 | T | Hypothetical protein |
| yegO (UTI89_C2351) | 2.33E-07 | 578.56 | V | Hypothetical protein |
The P value shown is the smallest P value for a test of selection in any UPEC foreground branch (see Fig. 1 B and C). Ratio of nonsynonymous to synonomous mutation rate (dn/ds) measures the strength of selection, where values >1 indicate positive selection, and larger values indicate stronger selection. COG category abbreviations are used; full category names are given in Fig. 3. “−” indicates that no COG category was assigned. Boldface highlights members of COG categories that are significantly enriched in the positively selected genes (see Fig. 3).