Table 1

Distribution of variable peptidases and peptide transporters in Lactococcus lactis strains by CGH analysis (genes which are either present or absent in all query and reference strains are excluded)

Strains a

ssp

origin

PrtP

PrtM

Pcp

PepF1

OppA1

PepO2

PepF2

OppA2

OppB2

OppC2

OppD2

OppF2

DppB

PepX2 (YmgC)


KF24

lactis

plant

1

1

1

1

1

1

1

1

1

1

1

1

1

1


NIZOB2244W

lactis

plant

1

1

1

1

1

1

1

1

1

1

1

1

1

1


LMG9446

lactis

plant

1

1

1

1

1

1

1

1

1

1

1

1

1

1


KF196

lactis

plant

0?

0?

0?

1

1

0?

0?

0?

0?

0?

0?

0?

1

0?


KF201

lactis

plant

0?

0?

0?

1

1

0?

0?

0?

0?

0?

0?

0?

1

0?


N42

lactis

plant

1

1

0

1

1

0

0

0

0

0

0

0

1

1


KF134

lactis

plant

0

0

0

1

1

0

0

0

0

0

0

0

1

0


E34

lactis

plant

0

0

0

1

1

0

0

0

0

0

0

0

1

0


Li-1

lactis

plant

0

0

0

1

1

0

0

0

0

0

0

0

1

0


M20

lactis

plant

0

0

0

1

0

0

0

0

0

0

0

0

1

0


K231

lactis

plant

0

0

0

1

1

0

0

0

0

0

0

0

1

0


LMG9449

lactis

plant

0

0

0

1

1

0

0

0

0

0

0

0

0

1


KF146

lactis

plant

0

0

0

1

1

0

0

0

0

0

0

0

0

0


KF147

lactis

plant

0

0

0

1

1

0

0

0

0

0

0

0

0

0


K337

lactis

plant

0

0

0

1

0

0

0

0

0

0

0

0

0

0


KF67

lactis

plant

0

0

0

1

1

0

0

0

0

0

0

0

0

0


KF7

lactis

plant

0

0

0

1

1

0

0

0

0

0

0

0

0

0


LMG8520

lactis

plant

0

0

0

1

1

0

0

0

0

0

0

0

0

0


KF282

lactis

plant

0

0

0

0

0

0

0

0

0

0

0

0

1

0


LMG8526

lactis

plant

0

0

0

0

0

0

0

0

0

0

0

0

0

0


UC317

lactis

dairy

1

1

0?

1

1

0?

0?

0?

0?

0?

0?

0?

1

1


ML8

lactis

dairy

1

1

0

1

1

0

0

0

0

0

0

0

1

1


LMG14418

lactis

dairy

0

0

0

1

1

0

0

0

0

0

0

0

1

1


IL1403

lactis

dairy

0

0

0

1

1

0

0

0

0

0

0

0

1

1


DRA4

lactis

dairy

0

0

0?

1

1

0

0

0

0

0

0

0

1

1


NCDO895

lactis

dairy

0

0?

0?

1

1

0

0?

0?

0?

0

0

0

1

1


ATCC19435T

lactis

dairy

1

1

1

1

1

1

1

1

1

1

1

1

1

1


KW10

cremoris

plant

1

1

1

1

1

1

1

1

1

1

1

1

1

1


N41

cremoris

plant

1

1

1

1

1

1

1

1

1

1

1

1

1

0


NCDO763

cremoris

dairy

1

1

1

1

1

1

1

1

1

1

1

1

1

0


SK11

cremoris

dairy

1

1

1

1

1

1

1

1

1

1

1

1

1

0


AM2

cremoris

dairy

1

1

1

1

1

1

1

1

1

1

1

1

1

0


FG2

cremoris

dairy

1

1

1

1

1

1

1

1

1

1

1

1

1

0


LMG6897T

cremoris

dairy

1

1

0?

0

1

1

1

1

1

1

1

1

1

0


V4

cremoris

dairy

0?

0?

0?

0

1

1

1

1

1

1

1

1

1

0


HP

cremoris

dairy

0

0

1

1

1

1

1

1

1

1

1

1

1

0


MG1363

cremoris

dairy

0

0

1

0

1

1

1

1

1

1

1

1

1

0


a. Two Lactococcus strains P7304 and P7266 are not shown in this table since they are grouped separately from other strains phylogenetically [53] and present a distinct pattern of presence and absence of proteolytic genes. For instance, PepC, PepA, PepO, PepF, PepV, PepX, and PepP appear to be absent in these two strains, but this could also be the result of poor hybridization due to lower sequence homology.

? The score of the signal is not significant enough to conclude the presence or absence of a gene. Most of the assignments of absence/presence are assumed based on coexistence patterns of genes, e.g. PrtP and PrtM, or OppABCDF are usually encoded in the same operons, thus should be all present or all absent in the genomes. In these cases, a stricter cut-off value for deciding the presence of a gene (5.6-5.7 instead of 5.5) is used.

Liu et al. BMC Genomics 2010 11:36   doi:10.1186/1471-2164-11-36

Open Data