Table 1.
Allele designations of chromosomal gene disruptions
| Mutation* | Template(s) | Homology extensions† | Priming sites‡ |
|---|---|---|---|
| DE(lacZYA)514 | pKD3, pKD4 | 36 nt; H1: 365662C; H2: 360842 | P0; P2 |
| DE(ompR-envZ)516 | pKD13 | 50 nt; H1: 3534269C; H2: 3532141 | P1; P4 |
| DE(torSTRCAD)517 | pKD13 | 50 nt; H1: 1052654; H2: 1061625C | P1; P4 |
| ΔarcB40 | pKD3 | 50 nt; H1: 3350706C; H2: 3348269 | P1; P2 |
| ΔcyaA1403 | pKD13 | 38 nt; H1: 3988674; H2: 3991330C | P1; P4 |
| ΔphnR171 | pKD4 | 36 nt; H1: 2242; H2: 3016C | P3; P2 |
| ΔpstB608 | pKD4 | 44 nt; H1: 3906010C; H2: 3905260 | P1; P2 |
| ΔpstCA607 | pKD4 | 44 nt; H1: 3908039C; H2: 3905991 | P1; P2 |
| ΔpstS605 | pKD3, pKD4 | 36 nt; H1: 3909143C; H2: 3908059 | P3; P2 |
| ΔpstSCAB-phoU606 | pKD13 | 36 nt; H1: 3909339C; H2: 3904418 | P1; P4 |
| ΔrecA635 | pKD13 | 50 nt; H1: 2821868C; H2: 2820743 | P1; P4 |
All except two were made in pKD20 transformants of BW25113. DE(lacZYA)514 mutants were made in the isogenic Lac+ strain BW25993; phnR was disrupted in three similar strains carrying the Salmonella typhimurium LT2 phosphonatase gene cluster (32) on the chromosome. Some were also made in MG1655 transformants.
Extension lengths are given first. Numerals identify the 3′ nucleotide of the extension in the E. coli genome sequence [(ref. 33; GenBank accession no. U00096) or the S. typhimurium phnR entry (GenBank accession no. U69493)]. C, complement; H1, homology 1; H2, homology 2.
One primer had the H1 extension and the 3′ sequence for priming site 0 (P0), 1 (P1), or 3 (P3). The other had the H2 extension and the 3′ sequence for the complement of priming site 2 (P2) or 4 (P4).