TABLE 3.
Off-pathway mutations identified in CipR and StrepR isolates of F. novicida and LVS.
| Type | Locus | Protein | Nucleotide change | Amino acid change | Severity |
| Fn CipR | |||||
| Frameshift | AW25_RS00910 | Thiopurine S-methyltransferase | 346_358delCC TAAGATAGCAA | Pro116fs | High |
| Frameshift | AW25_RS02890 | SDR family oxidoreductase | 59_60dupCG | Gly21fs | High |
| Intergenic region | AW25_RS06100-AW25_RS06105 | N/A | 1278988C > T | Modifier | |
| Fn StrepR | |||||
| No off-pathway mutations identified | |||||
| LVS CipR | |||||
| Frameshift | AW21_RS02545 | Outer membrane protein assembly factor BamB | 870delT | Asp290fs | High |
| Intergenic region | AW21_RS03145-AW21_RS03150 | N/A | 599763C > A | Modifier | |
| Synonymous | AW21_RS06025 | DUF3573 domain-containing protein FupA | 105G > C | Gly35Gly | Low |
| Frameshift | AW21_RS06025 | DUF3573 domain-containing protein FupA | 107dupC | Leu37fs | High |
| Missense | AW21_RS06205 | Transglycosylase SLT domain protein | 1868A > T | Lys623Ile | Moderate |
| Deletion (in-frame) | AW21_RS06850 | NAD-dependent epimerase/dehydratase family protein WbtC | 499_510delAAA CTTGCAAAG | Lys167_Lys170del | Moderate |
| Stop gained | AW21_RS09925 | Lipopolysaccharide-assembly family protein LptE | 179T > G | Leu60* | High |
| Frameshift and stop lost | AW21_RS10125 | IS630 family transposase, pseudogene | 502dupT | Ser168fs | High |
| LVS StrepR | |||||
| Intergenic region | AW21_RS00955-AW21_RS10080 | 10080-IS630 family transposase | 164135C > T | Modifier | |
| Frameshift and stop lost | AW21_RS10125 | IS630 family transposase, pseudogene | 133dupT | Tyr45fs | High |
| Missense | AW21_RS01780 | IS5/IS1182 family transposase, pseudogene | 425T > C | Ile142Thr | Moderate |
| Synonymous | AW21_RS10175 | IS630 family transposase, pseudogene | 162C > T | Ile54Ile | Low |
| Frameshift* | AW21_RS06710 | Two-component sensor histidine kinase | 457 A > T | ||
| AW21_RS06710 | Two-component sensor histidine kinase | 458 G > C | |||
| AW21_RS06710 | Two-component sensor histidine kinase | 459 T > C | |||
| AW21_RS06710 | Two-component sensor histidine kinase | 460 T > C | |||
| AW21_RS06710 | Two-component sensor histidine kinase | 462 del GAGGATC | |||
| AW21_RS06710 | Two-component sensor histidine kinase | 472 A > G | |||
| AW21_RS06710 | Two-component sensor histidine kinase | 473 G > T | |||
| Missense | AW21_RS06710 | Two-component sensor histidine kinase | 474 del C | ||
| Missense | AW21_RS06960 | Recombination factor protein RarA, pseudogene | 719C > A | Pro240Gln | Moderate |
| Nonsense | AW21_RS07120 | Aminotransferase, pseudogene | 620T > G | Leu207* | High |
| Missense | AW21_RS08665 | Hypothetical protein | 725C > T | Ala242Val | Moderate |
| Missense | AW21_RS08665 | Hypothetical protein | 737C > G | Thr246Arg | Moderate |
| Missense | AW21_RS09100 | NAD(P)/FAD-dependent oxidoreductase | 23G > T | Gly8Val | Moderate |
* Mutations identified in AW21_RS06710 ultimately result in frameshift, occurring downstream of the natural frameshift found in the native gene.