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Table 2 General information about putatively intact Latilactobacillus sakei prophages. For this, prophages with the “questionable” completeness evaluation by PHASTER have been included, if all essential modules were present (checked manually). For the inducible Latilactobacillus sakei phages within this study, GC-content, ORFs total, ORFs with unknown function, ORF-% unknown and prophage length were adjusted after manual BLASTs. For all other as intact expected phage sequences, the values obtained by PHASTER were listed

From: Distribution, inducibility, and characterisation of prophages in Latilactobacillus sakei

Inducible Latilactobacillus sakei phages within this study:

Phage

Predicted region by PHASTER (if multiple)

GC-content [%]

ORFs total

ORFs with unknown function

ORF-% unknown

Prophage length [kb]

Completeness (score) by PHASTER

Region position by PHASTER

Most common phage (gene hits) by PHASTER

TMW 1.23 P1

 

39.9

52

24

46.2

39.3

Intact (100)

contig 17: 1888–39,112

PHAGE_Lister_2389_NC_003291 (12)

TMW 1.46 P1

 

40.8

57

25

43.9

39.6

Intact (150)

852,024–891,679

PHAGE_Lactob_CL1_NC_028888 (7)

TMW 1.46 P2 a

 

40.1

51

30

58.8

36.4

Intact (100)

1,197,847–1,227,163

PHAGE_Lister_B025_NC_009812 (9)

TMW 1.1290 P1

 

40.2

54

25

46.3

38.0

Intact (130)

contig 1: 45015–93,497

PHAGE_Lactob_PL_1_NC_022757 (10)

TMW 1.1393 P1

 

40.6

54

26

48.1

34.7

Intact (150)

contig 5: 69791–108,578

PHAGE_Lactob_phig1e_NC_004305 (9)

TMW 1.1397 P1

 

39.0

62

21

33.9

38.4

Intact (150)

contig 1: 442601–480,500

PHAGE_Lactob_Lrm1_NC_011104(8)

φ-DJ1812 b (strain TMW 1.1398)

region 1 region 2

39.3

54

18

33.3

40.6

Incomplete (50)

Intact (130)

774,846–805,244

805,573–828,066

PHAGE_Brocho_NF5_NC_015252 (2)

PHAGE_Lactob_LF1_NC_019486 (7)

Other putatively intact Latilactobacillus sakei phages:

C21B P1

 

41.4

58

12

20.7

44.8

Intact (150)

346,775–391,586

PHAGE_Lactob_A2_NC_004112 (8)

CBA3635 P1

 

39.6

66

22

33.3

43.3

Intact (140)

239,719–283,028

PHAGE_Oenoco_phiS13_NC_023560 (16)

CBA3635 P2

 

39.7

53

13

24.5

51.3

Intact (150)

1,672,801–1,724,115

PHAGE_Lister_B025_NC_009812 (10)

DS4 P1 c

 

39.8

58

19

32.8

41.2

Intact (150)

645,922–687,133

PHAGE_Entero_EFC_1_NC_025453 (4)

FAM18311 P1c

 

40.5

55

9

16.4

55.0

Intact (120)

1,267,830–1,322,910

PHAGE_Oenoco_phiS13_NC_023560 (14)

J54 P1

 

42.0

47

10

21.3

33.1

Questionable (70)

614,556–647,708

PHAGE_Lactoc_50101_NC_031040 (15)

J64 P1 c

 

39.7

53

11

20.8

39.8

Intact (150)

648,583–688,460

PHAGE_Lactob_PL_1_NC_022757 (8)

J64 P2 c

 

40.7

54

13

24.1

40.1

Intact (150)

887,011–927,148

PHAGE_Lactob_phig1e_NC_004305 (9)

J64 P3 a

 

40.5

36

10

27.8

30.4

Intact (120)

1,294,505–1,324,922

PHAGE_Strept_315.4_NC_004587 (7)

J112 P1 b,3

region 1

region 2

39.0

42.5

35

20

10

2

28.6

10.0

31.4

17.6

Incomplete (50)

Questionable (80)

784,685–816,113

807,012–824,611

PHAGE_Lister_LP_030_3_NC_024384 (2)

PHAGE_Lactob_CL1_NC_028888 (5)

LK-145 P1 c

 

39.5

54

11

20.4

39.1

Questionable (70)

457,907–497,029

PHAGE_Lactob_PLE2_NC_031036 (10)

LZ217 P1 c

 

40.4

52

12

23.1

42.7

Intact (150)

941,734–984,525

PHAGE_Lactob_phig1e_NC_004305 (8)

MFPB16A1401 P1 c

 

40.4

51

12

23.5

37.1

Intact(150)

654,201–691,310

PHAGE_Lactob_phig1e_NC_004305 (10)

MFPB19 P1 c

 

39.6

48

10

20.8

37.6

Intact(150)

670,108–707,803

PHAGE_Lactob_Lrm1_NC_011104 (9)

ob4.1 P1 a,2

region 1

region 2

37.7

40.3

28

19

11

0

39.3

0.0

20.2

16.5

Incomplete (20)

Questionable (70)

128,217–148,461

148,791–165,294

PHAGE_Lister_B054_NC_009813 (3)

PHAGE_Oenoco_phi9805_NC_023559 (16)

ob4.1 P2 b

region 3

region 4

40.5

39.7

23

28

0

8

0.0

28.6

19.9

27.5

Intact (130)

Incomplete (10)

1,509,399–1,529,314

1,522,108–1,549,633

PHAGE_Lactob_LF1_NC_019486 (7)

PHAGE_Lactob_Lrm1_NC_011104 (4)

Probio65 P1 c,d

region 3

40.4

90

27

30.0

58.8

Intact (150)

1,994,946–2,053,762

PHAGE_Lactob_phig1e_NC_004305 (9)

Probio65 P2 c,d

region 1

region 3

TMW 1.411 P1 c,e

 

40.4

24

5

20.8

18.6

Intact (110)

QOSE01000002: 492–19,135

PHAGE_Lactob_PL_1_NC_022757 (7)

WiKim0063 P1 c

 

40.2

52

12

23.1

39.2

Intact (150)

355,716–394,962

PHAGE_Lactob_phig1e_NC_004305 (10)

WiKim0072 P1 c

 

40.7

60

16

26.7

41.9

Intact (150)

1,659,755–1,701,753

PHAGE_Lactob_phig1e_NC_004305 (10)

  1. a: Phage had proximal parts not detected by PHASTER, indicating a novel phage and leading to lower completeness scores assigned by PHASTER [12]
  2. b: Phage was predicted as two or more (incomplete or questionable) phage fragments by PHASTER, putatively due to BLAST hit paucity [12]
  3. c: Phage was already as intact predicted in [7]. The labeling of as intact predicted phages in both studies is mostly identical. An exception is phage FAM18311 P1 (this study), which corresponds to phage FAM18311P2 of [7]
  4. d: The genome of Latilactobacillus sakei strain Probio65 is commented by the authors as not circularized and to putatively contain a gap at the end. We found two identical prophage sequences at the proximal ends of the genome with the second one being halfed with one fragment on each proximal end of the chromosome. This may be an artefact during assembly, so we listed and counted the second prophage sequence for completeness, but excluded it from later analyses. The here as P1 listed and as intact predicted prophage by PHASTER included the first half of the second prophage sequence, artificially increasing its length and ORF count
  5. e: Albeit this phage was listed as intact by PHASTER, it was missing its lysogeny module and most of the replication module. The phage showed neither inducibility by UV light nor mitomycin C during the screening. The predicted sequence was located on a proximal end of a genome contig, so it might be possible, that those missing modules are located on other contigs, yet, with exception of its putative integrase gene, located at a proximal end of a contig as well, they could not be identified (neither by alignments nor manually)