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. 2019 Nov 7;5(11):e000312. doi: 10.1099/mgen.0.000312

Table 4.

Putative plasmid sequences of the complete B. fragilis assemblies

Putative plasmid sequences from the hybrid assemblies of B. fragilis CCUG4856T and the six MDR B. fragilis isolates were screened using the PLSDB. The best hit to plasmids from cultured isolates is shown. Only three putative plasmids from the MDR B. fragilis isolate assemblies could be identified with confident % ID. For most sequences, plasmid replication family proteins were identified in the putative plasmids using ABRicate with a database of sequences downloaded from the Pfam database, strengthening the interpretation that the circularized putative plasmid sequences do in fact represent plasmids harboured by the isolates.

Strain

Sequence

Length (bp)

Relative read depth

mol% G+C

PLSDB results

Plasmid replicon family (% COV, % ID)

Best hit accession no.

Plasmid hit name

% ID

Length of the sequence of best hit (bp)

CCUG4856T

Chr

5 205 133

1.00×

43.19

–

–

–

–

–

pBF9343

36 560

7.42×

32.19

NC_006873.1

pBF9343

100

36 560

Rep_3 (100/100)

BFO17

Chr

5 474 541

1.00×

43.51

–

–

–

–

–

pBFO17_1

85 671

1.85×

36.78

NC_006873.1

pBF9343

80.7

36 560

None

pBFO17_2

5594

23.03×

39.65

NC_011073.1

pBFP35

99.9

5594

Rep_1 (100/100)

BFO18

Chr

5 302 644

1.00×

43.34

–

–

 –

–

–

pBFO18_1

7221

25.98×

42.32

NC_015168.1

pBACSA02

85.6

19 280

Rep_3 (99.69/99.69)

pBFO18_2

4137

50.80×

45.40

NC_019534.1

pBFUK1

92.2

12 817

Rep_3 (100.00/98.24)

pBFO18_3

2782

59.91×

41.45

NC_005026.1

pBI143

94.6

2747

RepL (89.66/49.22)*

S01

Chr

5 325 251

1.00×

43.57

–

 –

–

–

–

pBFS01_1

78 085

2.29×

36.04

NC_006873.1

pBF9343

80.7

36 560

None

pBFS01_2

8331

20.99×

41.17

NC_015166.1

pBACSA03

95.6

6277

Rep_3 (100.00/97.85)

pBFS01_3

5595

22.67×

39.62

NC_011073.1

pBFP35

99.9

5594

Rep_1 (100.00/99.48)

BFO42

Chr

5 141 257

1.00×

43.35

–

-

–

–

–

pBFO32_1

8306

40.06×

43.34

KJ830768.1

pBF69566b

96.0

11 019

RHH_1 (92.94/64.63) Rep_3 (93.64/68.31)

pBFO32_2

5594

40.15×

39.63

NC_011073.1

pBFP35

99.9

5594

Rep_1 (100.00/99.48)

BFO67

Chr

5 478 614

1.00×

43.85

–

–

–

–

–

pBFO67_1

6129

94.15×

41.67

NC_011073.1

pBFP35

76.9

5594

Rep_3 (100.00/99.69)

BFO85

Chr

5 504 076

1.00×

43.60

–

–

–

–

–

Chr, Chromosome.

*Annotated as RepA protein in the pgap annotation.