Table 1 Pneumococcal genes flanking either side of the 93 integrated full-length prophage sequences.

From: Pneumococcal prophages are diverse, but not without structure or history

Cat a

N b

Genes upstream of phage integrase

PI c

Genes downstream of phage amidase

a

35 d

P-loop-containing kinase

transporter

putative sporulation transcription regulator whiA

I

pyridine nucleotide-disulfide oxidoreductase

ABC transporter permease

lipoprotein

b

7

transposase

recombination regulator RecX

adenylosuccinate synthetase

II

hypothetical protein

cytidine/deoxycytidylate deaminase

deoxyuridine 5’-triphosphate nucleotidohydrolase

b

6

transposase

recombination regulator RecX

adenylosuccinate synthetase

II

DNA-binding protein

hypothetical protein

cytidine/deoxycytidylate deaminase

b

5

IS1167 transposase

recombination regulator RecX

adenylosuccinate synthetase

II

DNA-binding protein

cytidine/deoxycytidylate deaminase

deoxyuridine 5’-triphosphate nucleotidohydrolase

b

3

IS1167 transposase

recombination regulator RecX

adenylosuccinate synthetase

II

DNA-binding protein

hypothetical protein

cytidine/deoxycytidylate deaminase

b

2

tRNA-Asn

recombination regulator RecX

adenylosuccinate synthetase

II

DNA-binding protein

cytidine/deoxycytidylate deaminase

deoxyuridine 5’-triphosphate nucleotidohydrolase

b

2

tRNA-Asn

recombination regulator RecX

adenylosuccinate synthetase

II

DNA-binding protein

hypothetical protein

cytidine/deoxycytidylate deaminase

b

2

transposase

recombination regulator RecX

adenylosuccinate synthetase

II

DNA-binding protein

cytidine/deoxycytidylate deaminase

phage integrase

b

1

assembly gap

recombination regulator RecX

adenylosuccinate synthetase

II

DNA-binding protein

hypothetical protein

cytidine/deoxycytidylate deaminase

b

1

transposase

recombination regulator RecX

adenylosuccinate synthetase

II

hypothetical protein

arginine deiminase

arginine deiminase

b

1

transposase-like protein, IS630

recombination regulator RecX

adenylosuccinate synthetase

II

DNA-binding protein

cytidine/deoxycytidylate deaminase

deoxyuridine 5’-triphosphate nucleotidohydrolase

b

1

transposase-like protein, IS630

recombination regulator RecX

adenylosuccinate synthetase

II

DNA-binding protein

hypothetical protein

cytidine/deoxycytidylate deaminase

b

1

tRNA-Asn

recombination regulator RecX

adenylosuccinate synthetase

II

DNA-binding protein

integrase

assembly gap

b

1

—

—

assembly gap

II

DNA-binding protein

cytidine/deoxycytidylate deaminase

deoxyuridine 5’-triphosphate nucleotidohydrolase

c

3

recombination regulator RecX

adenylosuccinate synthetase

cytidine/deoxycytidylate deaminase

III

deoxyuridine 5’-triphosphate nucleotidohydrolase

phosphoglycerate mutase

DNA repair protein RadA

c

1

phage lytic amidase

DNA-binding protein

cytidine/deoxycytidylate deaminase

III

deoxyuridine 5’-triphosphate nucleotidohydrolase

phosphoglycerate mutase

DNA repair protein RadA

c

1

DNA-binding protein

hypothetical protein

cytidine/deoxycytidylate deaminase

III

deoxyuridine 5’-triphosphate nucleotidohydrolase

phosphoglycerate mutase

DNA repair protein RadA

c

1

recombination regulator RecX

adenylosuccinate synthetase

cytidine/deoxycytidylate deaminase

V

deoxyuridine 5’-triphosphate nucleotidohydrolase

phosphoglycerate mutase

DNA repair protein RadA

d

3

superoxide dismutase

competence protein CglA

competence protein CglB

IV

hypothetical protein

competence protein CglC

competence protein CglD

e

3

leucyl-tRNA synthetase

acetyltransferase

GNAT family acetyltransferase

II

DNA-binding protein

Holliday junction DNA helicase RuvB

hypothetical protein ProS

  1. aCat = pneumococcal genome insertion site category. 13 examples of genomes with miscellaneous prophage integration sites, including assembly gaps on either side of the prophage sequence, are not shown here. A more detailed list of the integration sites and flanking genes may be found in Table S5, which includes the flanking genes associated with the 193 putatively full-length prophage sequences.
  2. bN = number of prophages.
  3. cPI = prophage integrase group, determined by the nucleotide sequence of the integrase.
  4. dTwo pneumococcal genomes had assembly gaps after the prophage amidase.
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