TABLE 1.
General features of the ORFs in pRV500 and putative functions for their products
| ORF | Position | Size (amino acids) | GC content (%) | Proposed function | Organism and protein or plasmid with protein database similarity (SPTREMBL or Swissprot accession no.)a | % Amino acid identityb |
|---|---|---|---|---|---|---|
| Orf1 (hsdR) | 6759-9923 | 1,054 | 41.5 | Type I R-M system: restriction subunit | Campylobacter jejuni, HsdR (q9pmc0) | 43 |
| Xylella fastidiosa, R-M I endonuclease (q9p9y1) | 42 | |||||
| Methanosarcina mazei, MM0431 (q8pzr1) | 40 | |||||
| Orf2 | 6571-5612 | 319 | 38.3 | Recombinase of the integrase family (Int/rec) (tyrosine DNA recombinase) | Streptococcus pneumoniae TIGR4, integrase/recombinase SP0890 (q97rd2) | 53 |
| Staphylococcus aureus MW2, XerC (q8nwz8) | 28 | |||||
| Lactobacillus leichmannii, XerC recombinase (q48733) | 26 | |||||
| Orf3 (hsdS) | 5616-4491 | 375 | 40.5 | Type I R-M system: specificity subunit | Pasteurella haemolytica, HsdS (P95511) | 25 |
| Campylobacter jejuni, HsdS (q8rj16) | 30 | |||||
| Orf4 (hsdS) | 4039-4494 | 151 | 38.4 | Type I R-M system: specificity subunit (truncated) | Klebsiella pneumoniae, HsdS (034140) | 50 |
| Methanosarcina mazei, type I R-M specificity subunit MM0430 (q8pzr2) | 48 | |||||
| Salmonella enterica, Sty SBLI (P72419) | 45 | |||||
| Orf5 (hsdM) | 2517-4049 | 510 | 43.3 | Type I R-M system: methylase | Xylella fastidiosa, type I R-M methylase (q9p9x8) | 55 |
| Methanosarcina mazei, type I R-M MM2198 (q8puy0) | 53 | |||||
| Campylobacter jejuni, HsdM (q9pmb6) | 52 | |||||
| Orf6 | 1782-2351 | 189 | 35.3 | Unknown | Plasmid pJW563, Lactococcus lactis, OrfX (q48655)c | 58 |
| Plasmid pSRQ700, Lactococcus lactis, OrfX (q93k29)c | 35 | |||||
| Plasmid pUCL287, Tetragenococcus halophilus, RepBd | 30 | |||||
| Orf7 (repA) | 721-1656 | 311 | 34.4 | Initiator protein (replication) | Plasmid pMD5057, Lactobacillus plantarum, RepA (AAN40880)d | 94 |
| Plasmid pUCL287, Tetragenococcus halophilus, RepA (q51863)d | 79 | |||||
| Plasmid pLKS, Lactobacillus plantarum, RepA (q9s0j9)d | 66 | |||||
| Orf8 | 12747-12959 | 70 | 31.2 | Unknown | Plasmid pRC18, Lactobacillus casei, hypothetical protein (q8vual)d | 92 |
| Plasmid pLP9000, Lactobacillus plantarum, hypothetical protein (q8kjs5) | 74 | |||||
| Plasmid pMD136, Pediococcus pentosaceus, Orf7 (q9X3b8)c | 43 | |||||
| Orf9 | 12487-12287 | 66 | 35.8 | Unknown | No similarity | |
| Orf10 | 11803-12390 | 195 | 38.3 | Putative integrase/recombinase (Int/rec) (tyrosine DNA recombinase) | Plasmid pLP9000, Lactobacillus plantarum, putative integrase/recombinase (q8kjs4) | 94 |
| Plasmid pRC18, Lactobacillus casei, putative integrase/recombinase (q8vua2)d | 94 | |||||
| Plasmid pLH1, Lactobacillus helveticus, Orf195a integrase/recombinase (O50346)e | 90 | |||||
| Orf11 | 11664-11314 | 116 | 35.3 | Unknown | Plasmid pSRQ800 Lactococcus lactis, Orf3 (O07029)c | 86 |
| Orf12 | 11317-11033 | 94 | 36.1 | Unknown—HTH motif | Plasmid pSRQ800 Lactococcus lactis, Orf4 (O07030)c | 85 |
| Orf13 | 10999-10211 | 262 | 31.6 | Unknown | Streptococcus pneumoniae R6, hypothetical protein SP0558 (q97s55) | 38 |
a
Only three selected hits among E values above 1 E-05 (blast program) are indicated.
b
% identity is on whole length except where values are indicated in bold.
c
Theta-type plasmid belonging to the pUCL22 family.
d
Theta-type plasmid belonging to the pUCL287 family.
e
Theta-type plasmid belonging to the pLS32 family.