TABLE 1.
PCR primers used in this studya
| Primer name | ORF name | ORF product | Primer sequence | Primer location (nt position) |
|---|---|---|---|---|
| Z0953 Fwd | Z0953 | Hypothetical protein | GGCTTTAACGTGCGCTAACT | 897927-897946 |
| Z0953 Rev | TCATCTTTTTCCTCGTGCATC | 898046-898026 | ||
| Z0958 Fwd | Z0958 | Unknown protein encoded by CP-933K | ATGGATTTCACCAGCAGGAT | 902731-902750 |
| Z0958 Rev | ATTCATTCTGTTCTTTCATCATCG | 902830-902807 | ||
| Z0989 Fwd | Z0989 | Unknown protein encoded by prophage CP-933K | AGAAACCTGACTTCGCCTGA | 929184-929203 |
| Z0989 Rev | CTTTTGTTGCATCCTCAGCA | 929601-929582 | ||
| Z1142 Fwd | Z1142 | Urease-associated protein UreD | TGTCGGTCTGCTCACTGTTC | 1078712-1078731 |
| Z1142 Rev | TCTCCAGACGGTTAGCGAGT | 1079115-1079096 | ||
| Z1154 Fwd | Z1154 | Putative colicin immunity protein | TCCAGTTTCTGGTGATGTTTTG | 1085954-1085975 |
| Z1154 Rev | TGGCCCTTCCTTGTTCAATA | 1086158-1086139 | ||
| Z1174 Fwd | Z1174 | Putative tellurium resistance protein TerC | TAATGTTCGCGTTTGACTCG | 1103602-1103621 |
| Z1174 Rev | CGATGCTGTAACCATGATGC | 1103838-1103819 | ||
| Z1214 Fwd | Z1214 | Hypothetical protein | CCAGTGAACATATTTCCGGC | 1139766-113978 |
| Z1214 Rev | TGGGTGAAATGAATGAGGTTT | 1139897-1139877 | ||
| Z1348 Fwd | Z1348 | Hypothetical protein | TAAAACTGCGTCTGGCTGTG | 1267374-1267393 |
| Z1348 Rev | TTCTTTTTATCACCGGCCAC | 1267514-1267495 | ||
| Z1368 Fwd | Z1368 | Hypothetical protein | AGAAGAAGTGGTGTCACGGG | 1282029-1282048 |
| Z1368 Rev | GTTATCCGCCTTCATGGTGT | 1282191-1282172 | ||
| Z1385 Fwd | Z1385 | Putative secreted protein encoded by cryptic prophage CP-933 M | TTAGGTGCCGGAGGAATATG | 1294045-1294064 |
| Z1385 Rev | AAGACCTTTGCCTGATGTGG | 1294428-1294409 | ||
| Z1611 Fwd | Z1611 | putative phage inhibition, colicin resistance and tellurite resistance protein | TGGTGTTTTATGGTCAGCCA | 1496984-1497003 |
| Z1611 Rev | TATGCTTCCATTCACGTCCA | 1497736-1497717 | ||
| Z1780 Fwd | Z1780 | Hypothetical protein | CGTGAGGCAGCACAAAACTA | 1634608-1634627 |
| Z1780 Rev | GACGCGTAATGCGTGTTCTA | 1634991-1634972 | ||
| Z1914 Fwd | Z1914 | Putative minor tail fiber protein CP-933X | TTTTGAGATGAACGGGAAGG | 1736664-1736683 |
| Z1914 Rev | TAATCTTTGTCTGTCCCCGC | 1736906-1736887 | ||
| Z2053 Fwd | adfO | Putative intestinal colonization factor | TGG TGG CCC GCA TAC AGC | 1860232-1860249 |
| Z2053 Rev | TGC CCA GTC AGC CCA GGT TA | 1860733-1860714 | ||
| Z2054 Fwd | ckf | Putative killer protein | ATG CTC GTC ACA TAT AGA TTG | 1861195-1861215 |
| Z2054 Rev | GTT CGT AAG CTG TGA AGA CA | 1861396-1861377 | ||
| Z2066 Fwd | Z2066 | Unknown protein encoded by prophage CP-933O | TAAGGCACCGGAAATCAAAC | 1867809-1867828 |
| Z2066 Rev | TGCATCAGATTCACTCTGCC | 1868228-1868209 | ||
| Z2096 Fwd | Z2096 | Unknown protein encoded within prophage CP-933O | TTCTTTGCATGCCTCTCTGA | 1886847-1886828 |
| Z2096 Rev | CGGGAACGATGAAGGTAAAA | 1886665-1886684 | ||
| Z2097 Fwd | Z2097 | Unknown protein encoded within prophage CP-933O | TTCTTTGCATGCCTCTCTGA | 1886847-1886828 |
| Z2097 Rev | CGGGAACGATGAAGGTAAAA | 1886665-1886684 | ||
| Z2098 Fwd | Z2098 | Unknown protein encoded within prophage CP-933O | GCTGAATGATTCCCATGTCA | 1887762-1887743 |
| Z2098 Rev | ACCCACGAAAGAGCAGAACA | 1887608-1887627 | ||
| Z2104 Fwd | Z2104 | Putative ARAC-type regulatory protein | CATGGTTTGCTCCCCAATTA | 1892233-1892252 |
| Z2104 Rev | CGGAATGTCAGTCAGACGAG | 1892440-1892421 | ||
| Z2105 Fwd | Z2105 | Unknown protein encoded within prophage CP-933O | CTTCAAAAAGAAAACCCGCA | 1893385-1893404 |
| Z2105 Rev | GATCTTCGCTTTCTCGGATG | 1893523-1893504 | ||
| Z2121 Fwd | Z2121 | Unknown protein encoded within prophage CP-933O | CAAGCAGCATTCTTGCAGAC | 1904821-1904840 |
| Z2121 Rev | GCTGACATGCGTAACGAGAA | 1904991-1904972 | ||
| Z2148 Fwd | Z2148 | Unknown protein encoded within prophage CP-933O | AATATTTTCCCACGTCCCGT | 1927623-1927604 |
| Z2148 Rev | GACAGGGTAATCACGCAGGT | 1927516-1927535 | ||
| Z2149 Fwd | Z2149 | Hypothetical protein | CTTTCGGACTCAGGTGAAGC | 1927995-1928014 |
| Z2149 Rev | GGTAAGCCTTCACCAACCAA | 1928224-1928205 | ||
| Z2150 Fwd | Z2150 | Unknown protein encoded by prophage CP-933R | ACCCCAGTCTCAGGTGTGTC | 2117258-2117277 |
| Z2150 Rev | CGGTGAGAGGAGGCTTACTG | 2117540-2117521 | ||
| Z2366 Fwd | Z2366 | Unknown protein encoded within prophage CP-933R | GAAGAACAGAACCCGCAGAA | 2138525-2138544 |
| Z2366 Rev | TGTCTGAACAGGTGCTCTGG | 2138730-2138711 | ||
| Z2979 Fwd | Z2979 | Putative stability/partitioning protein encoded within prophage CP-933T | CACACCACAGGAAGTGGATG | 2677781-2677800 |
| Z2979 Rev | TCCTTTTCACGAATAACCGC | 2678275-2678256 | ||
| Z3931 Fwd | Z3931 | Unknown protein encoded by prophage CP-933Y | CCGGCACAAACAATAATTCC | 3554499-3554518 |
| Z3931 Rev | AGGTGTTGATGATGTTGCCA | 3554671-3554652 | ||
| Z3933 Fwd | Z3933 | Serine/threonine protein phosphatase | GGCAAGAGCTTTAGCCAGAA | 3556023-3556042 |
| Z3933 Rev | AATCACATTCCCCTGGTTCA | 3556182-3556163 | ||
| Z4315 Fwd | Z4315 | Hypothetical protein | TGCTTCCGTTCTTATTTGCC | 3921831-3921850 |
| Z4315 Rev | GCATAAAGGATGGCGTCAAG | 3922024-3922005 | ||
| Z4325 Fwd | Z4325 | Putative enterotoxin | TATCAGGCCCTTCAAAATGG | 3929618-3929637 |
| Z4325 Rev | TATTGCCAAGTACGCCACAA | 3929831-3929812 | ||
| Z6020 Fwd | Z6020 | Hypothetical protein | CTTCCACGAGGCATTTCATT | 2281021-2281040 |
| Z6020 Rev | ACTGATGAGGTTGTCGGAGC | 2281237-228121 | ||
| Z6021 Fwd | Z6021 | Putative flagellar L-ring protein precursor | AGAAACCTGACTTCGCCTGA | 2282433-2282414 |
| Z6021 Rev | CCAGCTTTCCTCCGTGATAA | 2281605-2281624 | ||
| Z6044 Fwd | Z6044 | Putative major head protein/prohead proteinase | CTTCGCATGACTGAAGGTGA | 2304946-2304965 |
| Z6044 Rev | CTGGGAACTGATGGAGGTGT | 2305822-2305803 |
a
Primer locations and nomenclature of the ORFs refer to nucleotides in the sequence of STEC O157 strain EDL933 (GenBank accession no. AE005174); nt, nucleotide.