TABLE 2.
ORFs shared by the EPEC and EHEC LEEs
| EDL933 ORF (product length [aa]) | E2348/69 ORF (product length [aa]) | Gene name (former name) | Protein description | Comparison of EDL933 and E2348/69 coding regionsa
|
||||
|---|---|---|---|---|---|---|---|---|
| % Identity | No. of variable sites | No. of gaps (length) | dS ± SE | dN ± SE | ||||
| L 0016 (248) | orf30 (206) | Unknown | 93.40 | 41 | 1 (126) | 0.1233 ± 0.0289 | 0.0505 ± 0.0109 | |
| L 0017 (92) | orf29 (92) | Unknown | 97.85 | 6 | 0 | 0.0174 ± 0.0175 | 0.0233 ± 0.0105 | |
| L 0018 (73) | orf28 (73) | escF | Type III secretion apparatus | 100.00 | 0 | 0 | 0.0000 ± 0.0000 | 0.0000 ± 0.0000 |
| L 0019 (135) | orf27 (135) | Unknown | 99.02 | 4 | 0 | 0.0357 ± 0.0208 | 0.0031 ± 0.0031 | |
| L 0020 (312) | orf26 (321) | espB (eaeB) | Secreted protein | 74.01 | 261 | 8 (27)b | 1.0843 ± 0.1432 | 0.2084 ± 0.0198 |
| L 0021 (374) | orf25 (380) | espD | Secreted protein | 80.36 | 222 | 1 (18)b | 0.5402 ± 0.0602 | 0.1503 ± 0.0144 |
| L 0022 (192) | orf24 (192) | espA | Secreted protein | 84.63 | 89 | 0 | 0.4329 ± 0.0731 | 0.1110 ± 0.0167 |
| L 0023 (351) | orf23 (351) | Unknown | 94.32 | 60 | 0 | 0.1943 ± 0.0327 | 0.0268 ± 0.0058 | |
| L 0024 (406) | rorf12 (406) | escD | Type III secretion apparatus | 98.28 | 21 | 2 (4)b | 0.0524 ± 0.0141 | 0.0075 ± 0.0029 |
| L 0025 (934) | orf22 (939) | eae | Intimin | 87.23 | 360 | 6 (33)b | 0.2850 ± 0.0243 | 0.1023 ± 0.0073 |
| L 0026 (156) | orf21 (156) | orfU | Putative chaperone | 95.33 | 22 | 0 | 0.1885 ± 0.0474 | 0.0138 ± 0.0062 |
| L 0027 (558) | orf20 (550) | tir | Translocated intimin receptor | 66.48 | 549 | 9 (54) | 1.0697 ± 0.1023 | 0.3168 ± 0.0191 |
| L 0028 (203) | orf19 (203) | Similar to Shigella IpgB (27%) | 82.52 | 107 | 0 | 0.4905 ± 0.0807 | 0.1369 ± 0.0182 | |
| L 0029 (127) | rorf10 (120) | Unknown | 78.06 | 79 | 1 (21)b | 1.4865 ± 0.4083 | 0.1231 ± 0.0221 | |
| L 0030 (168) | orf18 (176) | Unknown | 74.70 | 127 | 4 (42) | 0.9421 ± 0.1614 | 0.1883 ± 0.0247 | |
| L 0031 (305) | orf17 (305) | sepQ | Type III secretion apparatus | 95.32 | 43 | 0 | 0.1145 ± 0.0252 | 0.0308 ± 0.0067 |
| L 0032 (91) | orf16 (91) | Unknown | 98.91 | 3 | 0 | 0.0000 ± 0.0000 | 0.0142 ± 0.0082 | |
| L 0033 (125) | orf15 (125) | Unknown | 99.74 | 1 | 0 | 0.0126 ± 0.0126 | 0.0000 ± 0.0000 | |
| L 0034 (446) | orf14 (446) | escN (sepB) | Type III secretion apparatus | 99.40 | 8 | 0 | 0.0188 ± 0.0077 | 0.0020 ± 0.0014 |
| L 0035 (675) | orf13 (675) | escV (sepA) | Type III secretion apparatus | 99.61 | 8 | 0 | 0.0107 ± 0.0048 | 0.0019 ± 0.0011 |
| L 0036 (117) | orf12 (117) | Unknown | 99.44 | 2 | 0 | 0.0290 ± 0.0206 | 0.0000 ± 0.0000 | |
| L 0037 (99) | rorf9 (98) | sepZ | Type III secretion apparatus | 70.71 | 87 | 1 (3) | 0.6527 ± 0.1324 | 0.2947 ± 0.0435 |
| L 0038 (142) | rorf8 (142) | Unknown | 93.01 | 30 | 0 | 0.2223 ± 0.0534 | 0.0344 ± 0.0104 | |
| L 0039 (190) | rorf7 (190) | escJ (sepD) | Type III secretion apparatus | 99.13 | 5 | 0 | 0.0423 ± 0.0191 | 0.0000 ± 0.0000 |
| L 0040 (151) | rorf6 (151) | Unknown | 98.46 | 7 | 0 | 0.0433 ± 0.0218 | 0.0084 ± 0.0049 | |
| L 0041 (512) | rorf5 (512) | escC (sepC) | Type III secretion apparatus | 99.42 | 9 | 0 | 0.0143 ± 0.0064 | 0.0034 ± 0.0017 |
| L 0042 (151) | rorf4 (151) | cesD (sepE) | Chaperone of espD | 99.56 | 2 | 0 | 0.0200 ± 0.0142 | 0.0000 ± 0.0000 |
| L 0043 (137) | orf11 (137) | Unknown | 99.52 | 2 | 0 | 0.0000 ± 0.0000 | 0.0063 ± 0.0045 | |
| L 0044 (123) | orf10 (123) | Unknown | 99.19 | 3 | 0 | 0.0126 ± 0.0126 | 0.0070 ± 0.0049 | |
| L 0045 (152) | rorf3 (152) | Similar to E. coli P19 (40%) | 98.91 | 5 | 0 | 0.0210 ± 0.0149 | 0.0084 ± 0.0049 | |
| L 0046 (345) | orf9 (345) | escU (sepF) | Type III secretion apparatus | 99.52 | 5 | 0 | 0.0172 ± 0.0086 | 0.0013 ± 0.0013 |
| L 0047 (258) | orf8 (258) | escT (sepG) | Type III secretion apparatus | 98.84 | 9 | 0 | 0.0459 ± 0.0164 | 0.0017 ± 0.0017 |
| L 0048 (89) | orf7 (89) | escS (sepH) | Type III secretion apparatus | 100.00 | 0 | 0 | 0.0000 ± 0.0000 | 0.0000 ± 0.0000 |
| L 0049 (217) | orf6 (217) | escR (sepI) | Type III secretion apparatus | 99.69 | 2 | 0 | 0.0069 ± 0.0069 | 0.0020 ± 0.0020 |
| L 0050 (231) | orf5 (231) | Unknown | 99.14 | 6 | 0 | 0.0072 ± 0.0072 | 0.0091 ± 0.0041 | |
| L 0051 (199) | orf4 (199) | Unknown | 99.33 | 4 | 0 | 0.0233 ± 0.0135 | 0.0021 ± 0.0021 | |
| L 0052 (107) | orf3 (107) | Unknown | 100.00 | 0 | 0 | 0.0000 ± 0.0000 | 0.0000 ± 0.0000 | |
| L 0053 (72) | orf2 (72) | Unknown | 99.54 | 1 | 0 | 0.0244 ± 0.0245 | 0.0000 ± 0.0000 | |
| L 0054 (129) | orf1 (129) | Similar to Bordetella bpH3 (43%, 37 aa) | 99.74 | 1 | 0 | 0.0000 ± 0.0000 | 0.0034 ± 0.0034 | |
| L 0055 (398) | rorf2 (398) | Similar to Shigella VirA (22%) | 98.50 | 18 | 0 | 0.0239 ± 0.0094 | 0.0126 ± 0.0037 | |
| L 0056 (272) | rorf1 (272) | Similar to E. coli YijK (36%) | 99.02 | 8 | 0 | 0.0262 ± 0.0122 | 0.0053 ± 0.0029 | |
a
dS, rate of synonymous substitution; dN, rate of nonsynonymous substitution.
b
One or more gap-containing regions were eliminated from the dS and dN analysis; all alignments are available upon request.