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Table 2 Overview of the putative genes and their putative functions

From: Large plasmidome of dairy Lactococcus lactis subsp. lactis biovar diacetylactis FM03P encodes technological functions and appears highly unstable

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  
  1. 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