Table 2.
Primers used for the investigation of P2-like regions
| Primer name | Target gene(s) | Sequence 5′ to 3′ | Position (bp)a | Reference |
|---|---|---|---|---|
| FI_fw | Tail sheath monomer FI gene | TGCGTGTGGAAGACGGCACC | 24612–24631 | This study |
| FI_rev | CGGCCTTGAGGGTTTCCGCAT | 25413–25433 | This study | |
| Latecontrol_D_fw | Late control protein D gene | TTCGTGGCGCTGTCCTGACG | 29694–29713 | This study |
| Latecontrol_D_rev | TGGAGAACTCCGCAACGCCC | 30448–30467 | This study | |
| Terminase_fw | Terminase gene | GGGAGCCGAACGGATTGGCG | 10561–10580 | This study |
| Terminase_rev | CTTGAGCACCGCATCCGCGA | 11298–11317 | This study | |
| Capsid_fw | Capsid gene | CCGTCGGTCACCCAGACCCT | 12975–12994 | This study |
| Capsid_rev | AGCGGCCAGCATTTCGCTGT | 13655–13636 | This study | |
| Lysin_fw | Lysin gene | ATGCTGGCCGTGTCCGAAGG | 15834–15853 | This study |
| Lysin_rev | CTGACCGTAACCGGCACCCG | 16204–16223 | This study | |
| Tail_protein_fw | Phage tail gene | AGGGCGCTGACTGATGCCGT | 17271–17290 | This study |
| Tail_protein_rev | AGCTCCATCGGGCGGGTGAC | 17655–17674 | This study | |
| Baseplate_J_fw | Baseplate gene J | GGTTGCCCGTACCCTGACGC | 19335–19354 | This study |
| Baseplate_J_rev | GACAGACGGATGTCGCGCCC | 19960–19979 | This study | |
| L413C_specific_fw | C (repressor) | AGGATCCAGCCCTTTCTAAA | 1632–1651 | This study |
| L413C_specific_rev | AATCCTTTTCGCGGAGTGG | 1243–1261 | This study | |
| gpO_fw | Capsid scaffolding protein O gene | TTTCGTATCGGCGTTGAGG | 11984–12002 | This study |
| gpO_rev | TGTTTTTCAGGCGGGTGAA | 12710–12728 | This study | |
| cpxP2_fw | cpxP integrase gene | AGCCATATGTTCGACGGCAT | 4327924–4327943* | This study |
| integrase_rev | AGGCCAGCGCCAAATTATTC | 439–458 | This study | |
| P2_cdta_up_novel_fw | Spacer region gene | CCAAGAGCACGCCAGCACTGA | 8727–8747 | This study |
| P2_cdta_up_novel_rev | TGGCAAATCTCCTTTGGGCTAGTG | 8261–8284 | This study | |
| Cdta_up_novel_overlap_fw | cdtA spacer gene | TCAATCGCGTTTTGCACTCACGG | 8500–8522 | This study |
| Cdta_up_novel_overlap_rev | AGGTCCAGCCCCGGGTAATGG | 8018–8038 | This study | |
| P2_novel_overlap_fw | Capsid packaging protein Q spacer gene | ACAAGGGAAAGCCGACGGCAT | 9259–9279 | This study |
| P2_novel_overlap_rev | TCAGTTATCGTCAGTGCTGGCGTGC | 8717–8741 | This study | |
| Cdtc_P2_overlap_fw | cdtC replication gene A | CATACCTTCAACAACAGGTGCGGT | 6227–6250 | This study |
| Cdtc_P2_overlap_rev | TACCGGTTCCCACGCCTTCTG | 5591–5611 | This study | |
| P2_short_orfs_fw | Short ORFs | CGCCGTCAGGTTGGCGCAA | 2367–2385 | This study |
| P2_short_orfs_rev | AACCAGCGCAGAAGCACCGC | 3281–3300 | This study | |
| ogr_fw | ogr-fieF | ACGTGAATTGCAGCGCCACG | 30840–30859 | This study |
| fieF_rev | CCAGCGCCAGCAGAATTGCG | 4361610–4361629* | This study | |
| P2_PQ_fw | Capsid packaging protein Q gene | AACACCGCAACCTGCGGCAA | 9974–9993 | This study |
| P2_PQ_rev | CCACCAGTAAACATCCTCT | 9579–9597 | This study | |
| P2_P_fw | Terminase protein P gene | AACCTGTTCATGTGTGAA | 10676–10693 | This study |
| P2_P_rev | AACGAGCTGGTGATGTCGG | 10191–10209 | This study | |
| P2_repA_fw | Replication gene A | TTTCGATAATCTGGTTACG | 4915–4933 | This study |
| P2_repA_rev | TATGGTCATGTTGCTGGCGC | 4213–4232 | This study | |
| P2_repA_ext_fw | Replication gene A distant region | TTGCTTCAAAGACTGACTG | 3376–3394 | This study |
| P2_repA_ext_rev | GAAATGAACGACGTCGAACGT | 2298–2318 | This study | |
| CDT-IIIs | cdt-VB | GAAAGTAAATGGAATATAAATGTCCG | 7291–7316 | 11 |
| CDT-IIIas | TTTGTGTCGGTGCAGCAGGGAAAA | 6761–6784 | 11 |
a
The reference sequence for the primers indicated with an asterisk is CP002967 (whole genome of Escherichia coli strain W). Positions are given in reference to GenBank accession number KC618326.1, except where indicated otherwise.