TABLE 1.
Potential IHF- and C1-binding sites and rho-independent terminators in P22 DNAa
| Location | Similarity score | Sequence | Potential function |
|---|---|---|---|
| Potential IHF-binding sites | |||
| 427–453 | 57.4 | TTCTTGATATTAACTGTTTATCTTCAA | |
| 2855–2829 | 50.1 | AGATAAAAACTATCAAATTATACATTA | |
| 3032–3006 | 52.4 | CCTTTTAAGTCAACAACATACCACGTC | |
| [3087–3113] | 61.7 | CCAGTTAAATCAAATACTTACGTATTA | |
| [11584–11558] | 53.3 | GCATATGAATCAACTGTTTAAGTGTCA | |
| 12711–12685 | 49.8 | AAGTAACGATAAAATATTTAAGTTTTC | |
| 19623–19597 | 53.5 | CAACTTTATTCAAAAAGTCAATATCAT | |
| 21186–21212 | 54.2 | CACTGAAATTTAACAAGTGACTTTCAG | |
| [21579–21605] | 52.6 | CCGAAAAAATCAATAACTTAGGGATTT | |
| 37218–37244 | 51.4 | TAGAAAAAAACAACCACGCAATCTGCA | |
| Lambda cro/cII | 61.5 | TGCATACATTCAATCAATTGTTATCTA | |
| Potential C1-binding sites | |||
| 2946–2959 | TTGCATCGGTTTGC | ||
| 2956–2969 | TTGCAAGGCTTTGC | ||
| 4647–4660 | TTGCGGGTGCTTGC | PaI | |
| 13809–13796 | TTGCGAGTGCTTGT | PRE | |
| 18448–18435 | TTGCCTAACCTTGC | ||
| 19237–19224 | TTGCGAGCACTTGC | ||
| 24346–24333 | TTGCCCGTATTTGT | ||
| 26998–26985 | TTGCCGGGTCTTGT | ||
| 27542–27529 | TTGCCGGGTCTTGT | ||
| 34184–34171 | TTGCTGCGGATTGT | ||
| 40808–40795 | TTGCGAGAGGTTGT | ||
| Rho-independent terminators | |||
| 2871–2900 | ATTGATCGTTGTTACCGATCAATTTTTATT | ||
| 5152–5179 | ACCGCCATCAGGCGGCTTGGTGTTCTTT | ||
| [5167–5144] | GCCGCCTGATGGCGGTTTTTTATT | ||
| 10157–10188 | AGCCGCACTCAGGCGGCTGTCGTTTCTTCTTT | ||
| [10174–10148] | AGCCGCCTGAGTGCGGCTTTTTCATAT | ||
| [10519–10490] | TTGCCGCTCTATATGGGCGGCATTCTTTTT | ||
| [18516–18488] | CTCGCTTTCACAGCGGCTTTCTCTTCGTT | ||
| 21218–21246 | TGCCTCGCAGATGCGGGGCGTTTTTGTAT | ||
| 22161–22187 | AGCCGCTTACTTAGCGGCTTGACGTTT | ||
| [22179–22154] | AGCCGCTAAGTAAGCGGCTTTTTTAT | ||
| 37691–37723 | AGCCGGAGTGACCCGGCTTGATTATTACTTTTT | ||
| [37708–37682] | AGCCGGGTCACTCCGGCTTTTTGATAT | ||
| 39487–39512 | ACCCAGCTTCGGCTGGGTTTTTTTAT | ||
| 39634–39660 | ACCGTAGCCATGCTGCGGCAATTCCTT | ||
| [39652–39623] | GCCGCAGCATGGCTACGGTGAATTTTTTGT | ||
| 40243–40265 | TCCCGCATTGCCGGGGTTTTTAT |
In the case of IHF-binding sites, we have included the similarity scores calculated by MacTargsearch (24). The bases which are identical to the consensus sequence are highlighted in boldface. For comparison, we have included a characterized IHF-binding site in coliphage λ. Putative C1-binding sites were determined by scanning the sequence for the consensus sequence (TTGCN6TTGY), while rho-independent terminators were determined using the Genetics Computer Group terminator program. Only those sites for which there was evidence of a stem-loop structure (boldface and underlined) followed by a region rich in thymine residues were included. The sites in brackets are those associated with the complementary strand.