Table 2.
Overview of the putative genes and their putative functions
| Plasmid | Gene | Putative function | Best homolog found in: |
|---|---|---|---|
| pLd1 | repB | Replication initiator protein | |
| orf2* | Replication-associated protein | ||
| hsdS | Type I restriction-modification system specificity subunit S | ||
| orf4 | Hypothetical protein | ||
| orf5 | Hypothetical protein | ||
| orf6 | Hypothetical protein | ||
| tra | Transposase IS982 family | ||
| citQ | Leader peptide CitQ | ||
| citR | Translational regulator | ||
| citP | Citrate transporter | ||
| orf11 | Hypothetical protein | ||
| pLd2 | repB | Replication initiator protein | |
| orf2* | Replication-associated protein | ||
| hsdS | Type I restriction-modification system specificity subunit S | ||
| cadA | Cadmium-transporting ATPase | ||
| cadC | Cadmium efflux system accessory protein | ||
| cspC | Cold shock protein | ||
| orf7 | Serine/threonine protein phosphatase | ||
| tra | Transposase IS6 family | ||
| mobC | Mobilisation protein | ||
| mobA | Mobilisation protein | ||
| mobB | Mobilisation protein | ||
| mobD | Mobilisation protein | ||
| orf13 | HXXEE domain-containing protein | Streptococcus thermophilus | |
| orf14* | XRE family transcriptional regulator | Streptococcus thermophilus | |
| repC* | Replication initiator protein | Lactobacillus farciminis | |
| orf16 | Hypothetical protein | Enterococcus faecium | |
| pLd3 | repC | Replication initiator protein | |
| orf2 | Hypothetical protein | Lactobacillus reuteri | |
| pLd4 | repB | Replication initiator protein | |
| orf2 | Hypothetical protein | Enterococcus faecalis | |
| orf3 | Hypothetical protein | Enterococcus faecalis | |
| orf4 | Hypothetical protein | ||
| orf5 | Hypothetical protein | ||
| orf6 | Hypothetical protein | ||
| fmtB | Peptidoglycan-binding protein | Streptococcus thermophilus | |
| tra | Transposase IS982 family | ||
| orf9* | DNA-directed DNA polymerase | ||
| orf10 | Hypothetical protein | ||
| tnpR | Resolvase | ||
| pLd5 | repB | Replication initiator protein | |
| orf2 | Replication-associated protein | ||
| hsdS | Type I restriction-modification system specificity subunit S | ||
| tra | Transposase IS982 family | ||
| orf5 | Hypothetical protein | ||
| orf6 | Site-specific integrase | ||
| pLd6 | repB | Replication initiator protein | |
| orf2* | Hypothetical protein | ||
| hsdS | Type I restriction-modification system specificity subunit S | ||
| pLd7 | repB | Replication initiator protein | |
| orf2 | Replication-associated protein | ||
| hsdR | Type I restriction-modification system specificity subunit R | ||
| hsdM | Type I restriction-modification system specificity subunit M | ||
| hsdS | Type I restriction-modification system specificity subunit S | ||
| corA | Magnesium transporter | ||
| tra | Transposase IS982 family | ||
| orf8 | Hypothetical protein | ||
| orf9 | Hypothetical protein | ||
| orf10 | Hypothetical protein | ||
| tnpR | Resolvase | ||
| tra | Transposase IS6 family | ||
| orf13 | MFS transporter | ||
| orf14 | Acetyltransferase | ||
| orf15 | Polysaccharide biosynthesis protein | ||
| orf16 | Hypothetical protein | ||
| tra | Transposase IS6 family | ||
| dld | D-Lactate dehydrogenase | ||
| orf19 | Hypothetical protein | ||
| orf20 | Hypothetical protein | ||
| orf21 | Hypothetical protein | ||
| tra* | Transposase IS6 family | ||
| uspA | Universal stress protein | ||
| mntH | Manganese transporter | ||
| tra* | Transposase IS3 family | ||
| orf26* | integrase/recombinase | ||
| orf27 | Hypothetical protein | ||
| mobC | Mobilisation protein | ||
| mobA | Mobilisation protein | ||
| mobB | Mobilisation protein | ||
| mobD | Mobilisation protein | ||
| pLd8 | repB1 | Replication initiator protein | |
| parA | Chromosome partitioning protein | ||
| orf3 | Hypothetical protein | ||
| orf4 | Serine protease | ||
| repB2 | Replication initiator protein | ||
| orf6 | Hypothetical protein | ||
| orf7 | Hypothetical protein | ||
| orf8 | Hypothetical protein | ||
| orf9 | Hypothetical protein | ||
| orf10 | Nickase | ||
| tra | Transposase IS6 family | ||
| mntH | Manganese transporter | ||
| uspA | Universal stress protein | ||
| tra | Transposase IS6 family | ||
| tra* | Transposase IS6 family | ||
| orf16 | AAC(3) family N-acetyltransferase | ||
| tra | Transposase IS982 family | ||
| orf18 | C4-dicarboxylate ABC transporter | ||
| tra | Transposase IS982 family | ||
| orf20 | Hypothetical protein | ||
| orf21 | Hypothetical protein | ||
| orf22 | Large-conductance mechanosensitive channel | ||
| lacX | Hypothetical protein | ||
| lacG | 6-phospho-beta-galactosidase | ||
| lacE | PTS lactose transporter subunit IIBC | ||
| lacF | PTS lactose transporter subunit IIA | ||
| lacD | Tagatose 1,6-diphosphate aldolase | ||
| lacC | Tagatose-6-phosphate kinase | ||
| lacB | Galactose-6-phosphate isomerase subunit LacB | ||
| lacA | Galactose-6-phosphate isomerase subunit LacA | ||
| lacR* | Lactose repressor | ||
| tra* | Transposase IS3 family | ||
| orf33 | Type II restriction modification system | Leuconostoc mesenteroides | |
| orf34 | Type II restriction modification system | Leuconostoc mesenteroides | |
| orf35 | Hypothetical protein | ||
| tnpR | Resolvase | ||
| orf37 | Hypothetical protein | ||
| orf38 | Hypothetical protein | ||
| pepO | Neutral endopeptidase | ||
| oppA | Peptide-binding protein | ||
| oppC | Peptide ABC transporter permease | ||
| oppB | Peptide ABC transporter permease | ||
| oppF | Oligopeptide transport ATP-binding protein | ||
| oppD | Oligopeptide transport ATP-binding protein | ||
| tra | Transposase IS982 family | ||
| pLd9 | repB | Replication initiator protein | |
| orf2 | Hypothetical protein | ||
| hsdS | Type I restriction-modification system specificity subunit S | ||
| abi* | Abortive phage resistance protein | ||
| tra | Transposase IS6 family | ||
| dld | D-lactate dehydrogenase | ||
| tra | Transposase IS6 family | ||
| orf8 | Hypothetical protein | ||
| orf9 | MFS transporter | ||
| tra | Transposase IS6 family | ||
| tra* | Transposase IS982 family | ||
| orf12 | Amidohydrolase of peptidase M20 family | ||
| orf13 | Hypothetical protein | ||
| orf14 | Site-specific integrase | ||
| orf15 | Integrase-associated protein | ||
| pLd10 | repB1 | Replication initiator protein | |
| orf2 | Replication-associated protein | ||
| tra | Transposase IS982 family | ||
| epsR | XRE family transcriptional regulator | ||
| epsX | Polysaccharide biosynthesis protein | ||
| epsA | Tyrosine protein kinase transmembrane modulator | ||
| epsB | Tyrosine protein kinase | ||
| epsC | Tyrosine protein phosphatase | ||
| epsD | Undecaprenyl-phosphate galactosephosphotransferase | ||
| epsE | Group 1 glycosyltransferase | ||
| epsL | Exopolysaccharide biosynthesis protein | ||
| orfY | LytR family transcriptional regulator | ||
| tra* | Transposase IS6 family | ||
| tra | Transposase IS3 family | ||
| tra | Transposase IS3 family | ||
| tra | Transposase IS256 family | ||
| orf17 | XRE family transcriptional regulator | ||
| orf18 | Replication-associated protein | ||
| repB2 | Replication initiator protein | ||
| mobD | Mobilisation protein | ||
| mobB | Mobilisation protein | ||
| mobA | Mobilisation protein | ||
| mobC | Mobilisation protein | ||
| orf24 | Hypothetical protein | ||
| orf25 | Integrase | ||
| orf26 | Hypothetical protein | ||
| tra* | Transposase IS6 family | ||
| orf28 | Hypothetical protein | ||
| epsG | Glycosyltransferase family 2 protein | ||
| epsH | Glycosyltransferase family 2 protein | ||
| tra | Transposase IS6 family | ||
| epsI* | Glycosyltransferase | ||
| wzxA | Flippase | ||
| tra | Transposase IS6 family | ||
| tra* | Transposase | Lactobacillus/Oenococcus/Enterococcus | |
| tra* | Transposase | Lactobacillus | |
| tra | Transposase IS30 family | Lactobacillus | |
| wzxB | Flippase | Lactobacillus | |
| wzy | Polymerase | Lactobacillus | |
| orf40 | Hypothetical protein | ||
| epsM | Glycosyltransferase family 2 protein | Lactobacillus | |
| epsN | Glycosyltransferase | Lactobacillus | |
| epsO | Glycosyltransferase family 1 protein | Lactobacillus | |
| orf44 | DUF4411 domain-containing protein | Lactobacillus plantarum | |
| tra | Transposase ISL3 family | Lactobacillus | |
| orf46 | Hypothetical protein | Lactobacillus | |
| orf47 | Hypothetical protein | ||
| orf48 | Hypothetical protein | ||
| orf49 | Resolvase | ||
| pLd11 | repB | Replication initiator protein | |
| orf2 | Replication-associated protein | ||
| orf3 | Relaxase/mobilisation nuclease domain protein | ||
| pepE | Peptidase E | ||
| tra | Transposase IS6 family | ||
| tra* | Transposase IS6 family | ||
| orf7 | DUF1919 domain-containing protein | ||
| orf8 | DUF3883 domain-containing protein | ||
| orf9 | Relaxase | ||
| orf10 | Hypothetical protein | ||
| orf11 | Hypothetical protein | ||
| mobC | Mobilisation relaxosome protein | ||
| pLd12 | repB | Replication initiator protein | |
| hsdS | Type I restriction-modification system specificity subunit S |
Putative functions that could be beneficial in the dairy environment are shown in bold. Pseudogenes are indicated with an asterisk. The species that contains the best homolog is given of genes that are rarely found in L. lactis