TABLE 1.
Characteristics of the sequenced ORFs and encoded proteins examined in this study
| DNA sequence characteristic
|
Translation product characteristic
|
|||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| ORFa | % G+C | Start | Stop | RBSb | Dist1c | Dist2d | Length (no. of amino acids) | Related proteine | Origin | % Identity (no. of amino acids)f |
| fda | 38.3 | NDg | TAA | ND | ND | ND | ND | Fructose-1,6-biphosphate aldolase Fba (AJ005697) | Chromosome of S. pneumoniae | 80 (77) |
| int | 33.6 | ATG | TAA | TAAGGAGG | 7 | −1 | 448 | Integrase Int (U93688)h | Pathogenicity island SaPI1 of S. aureus | 26 |
| Integrase Int (M27965)h | Phage φL54a of S. aureus | 28 | ||||||||
| Integrase Int (M62697)h | Phage φadh of Lactobacillus gasseri | 32 (227) | ||||||||
| Integrase Int (L27649)h | Conjugative transposon Tn5276 of L. lactis | 24 | ||||||||
| Integrase Int (L29324)h | Conjugative transposon Tn5252 of S. pneumoniae | 26 (266) | ||||||||
| xis | 35.7 | ATG | TAA | AAAGGAGT | 5 | +13 | 82 | Excisionase Xis (L29324) | Conjugative transposon Tn5252 of S. pneumoniae | 41 |
| Excisionase Xis (L27649) | Conjugative transposon Tn5276 of L. lactis | 41 | ||||||||
| orfA | 43.3 | ATG | TAG | AAAGGAGA | 4 | +25 | 370 | Putative transfer protein TraG (AF051917) | Conjugative plasmid pSK41 of S. aureus | 30 |
| Putative transfer protein TrsG (L11998) | Conjugative plasmid pGO1 of S. aureus | 30 | ||||||||
| Immunogenic secreted protein Isp (U31811) | Chromosome of Streptococcus pyogenes D471 | 57 (325) | ||||||||
| orfB | 37.8 | ATG | TAA | AGAGGAGA | 5 | +1 | 74 | No similarity | ND | ND |
| orfC | 41.5 | ATG | TAG | TTAGGAGG | 7 | +11 | 626 | Putative membrane protein Orf15 (U09422) | Conjugative transposon Tn916 of E. faecalis | 18 (267) |
| orfD | 42.1 | ATG | TAG | AAAGGAGG | 4 | ND | 834 | Putative transfer protein Orf16 (U09422) | Conjugative transposon Tn916 of E. faecalis | 21 |
| Unknown protein YddE (AB001488) | Chromosome of B. subtilis 168 | 30 | ||||||||
ORFs are listed from the right to the left of the map.
The RBS consensus sequence of the gram-positive low-G+C bacterium Bacillus subtilis is AAAGGAGG.
Dist1, distance between the RBS and the start codon.
Dist2, distance between the start codon of an ORF and the stop codon of the previous ORF on the map (Fig. 1). A negative value indicates an overlapping of two ORFs.
Functions of proteins and GenBank accession numbers (in parentheses) of nucleotide sequences encoding proteins related to the product of the ORFs sequenced in this study are indicated.
Identities stretch over the entire length of each of the amino acid sequences of proteins encoded by ICESt1, except when indicated in parentheses.
ND, not determined.
Many other related integrases were found in databases, but in this table, we have only indicated a selection of the ones more related to the integrase encoded by var1C.