| Gene(s) | Description | Functional Consequence |
| dam | DNA adenine methylase mutation (GATC) | Preparing unmethylated DNA, important when trying to cut with certain restriction enzymes (ex: ClaI or XbaI) |
| dcm | DNA cytosine methylase mutation (CCWGG) | Preparing unmethylated DNA, important when trying to cut with certain restriction enzymes that are methylation sensitive. |
| dnaJ | Mutation in a chaperonin gene | Increases the stability of certain expressed proteins |
| endA, endA1 | Endonuclease I (nonspecific cleavage of dsDNA ) mutation | Improves plasmid yield |
| F | Host does (F’) or does not (F-) contain the fertility plasmid. | A low copy-number plasmid, encodes proteins needed for bacterial conjugation. Genes listed on F´ are wild-type unless indicated otherwise |
| fhuA (formerly tonA) | ferric hydroxamate uptake, iron uptake receptor mutation. | T1/T5 Phage resistance |
| gal | Mutation in galactose metabolism pathway | Cells cannot grow on galactose only |
| gyrA, gyrA96 | DNA gyrase mutation | Confers resistance to nalidixic acid |
| hsdRMS | hsdR(rk-, mk+) | Unmethylated DNA not degraded, cell still can methylate DNA |
| hsdS(rk-,mk-) | Unmethylated DNA not degraded, cell cannot methylate DNA | |
| lac | Lac operon mutations | Blue/white screening of clones |
| lacIq | lac repressor overproduced, expression from pLac repressed more | |
| LacZ | β-galactosidase activity abolished | |
| lacY | Lactose permease inactivated, lactose cannot be taken up by cell | |
| mcrA, mcrBC | Inactivation of pathway that cleaves methylated cytosine DNA | Allows for uptake of foreign (methylated) DNA |
| mrr, Δ(mcrC-mrr) | Inactivation of pathway that cleaves methylated adenine or cytosine DNA | Allows for uptake of foreign (methylated) DNA |
| recA, recA1, recA13 | Mutation in a DNA-dependent ATPase that is essential for recombination and general DNA repair | Reduces plasmid recombination, increases plasmid stability |
| recBCD | Exonuclease V activity abolished | Increased plasmid stability, reduced recombination |
| relA or relA1 | Relaxed phenotype, mutation eliminating stringent factor | Allows RNA synthesis in absence of protein synthesis |
| Ptrc-ccdA | Propagation of ccdB-containing plasmids | |
| Hte | High transformation efficiency | |
| deoR | constitutive expression of genes for deoxyribose synthesis | Allows uptake of large plasmids |
| hee | High electroporation efficiency | |
| supE44 (glnV44) | Suppression of the amber (UAG) stop codon by glutamine insertion | |
| supF (tyrT) | Suppression of the amber (UAG) stop codon by tyrosine insertion | |
| λ-thi-1 or thi1 | Mutation in thiamine metabolism | Requires exogenous thiamine for growth |
| ara | disruption of arabinose metabolism pathway | Inability to utilize arabinose as a carbon source |
| leuB | β-isopropyl malate dehydrogenase inactivated | Requires exogenous leucine source for growth |
| proAB | mutation in proline biosynthesis pathway | Requires exogenous proline source for growth |
| rpsL | Mutation in subunit S12 of 30S ribosome | Confers resistance to streptomycin |
| Tn10 | Confers resistance to tetracycline |
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