Table 4.
Putative C. coli BFR-CA-9557 restriction modification systems
| ORF #1 | Strand | Position in genome | Description | Type/subunit | Predicted rec. seq. |
|---|---|---|---|---|---|
| 465 | + | 86828-89146 | hsdR, Type I restriction-modification system2C restriction subunit R (EC 3.1.21.3) | I/R | - |
| 485 | + | 92205-93437 | hsdS, Type I restriction-modification system2C specificity subunit S (EC 3.1.21.3), EcoKI specificity protein | I/S | - |
| 495 | + | 94709-96196 | Type I restriction-modification system2C DNA-methyltransferase subunit M (EC 2.1.1.72) | I/M | - |
| 6540 | - | 1246404-1250480 | Type I restriction-modification system2C DNA-methyltransferase subunit M (EC 2.1.1.72) / Type I restriction-modification system2C specificity subunit S (EC 3.1.21.3) | I/MS | (GAGNNNNNGT)3,4 |
| 720 | + | 139123-140043 | fokIM_1, Modification methylase FokI, (EC 2.1.1.72), homologue to ulcer associated adenine specific DNA methyltransferase | II/M | (GGATG)3 |
| 1470 | - | 275768-271959 | Type IIS restriction enzyme Eco57I | II/S | - |
| 2605 | + | 488272-489375 | DNA modification methylase (Adenine-specific methyltransferase), fokIM_2, Modification methylase FokI, (EC 2.1.1.72) | II/M | GAATTC |
| 2895 | + | 541751-542602 | DNA modification methyltransferase, dpnA, Modification methylase DpnIIB (EC 2.1.1.72) | II/M | GATC |
| 6520 | - | 1240865-1243951 | N-6 adenine specific DNA methyltransferase | II/M | - |
| 7730 | + | 1464470-1465285 | DNA adenine methylase, dpnM, Modification methylase DpnIIA, EC 2.1.1.72 | II/M | - |
| 8910 | + | 1701685-1702374 | 16S rRNA (guanine(966)-N(2))-methyltransferase (EC 2.1.1.171) | II/M | GATC5 |
| 2225 | + | 409683-409970 | McrBC 5-methylcytosine-specific restriction endonuclease system2C McrB subunit2C putative | IV/R | - |
| 22302 | + | 409982-411148 | McrBC 5-methylcytosine-specific restriction endonuclease system2C McrB_1 subunit2C putative | IV/R | - |
| 22302 | + | 411208-412158 | McrBC 5-methylcytosine-specific restriction endonuclease system2C McrB_2 subunit2C putative | IV/R | - |
| 2235 | + | 412124-413494 | McrBC 5-methylcytosine-specific restriction enzyme subunit McrC | IV/R | - |
1ORF # according to the NCBI annotation pipeline for RAST and Prodigal ORF # see Additional files 3 and 4
2disrupted ORF
3predicted sequence does not correspond to any motif detected by SMRT sequencing
4According to REBASE ORF #6540 encodes a Type II RM-system
5In contrast to RAST and Prodigal REBASE predicts a second candidate for a GATC-specific DNA modification methyltransferase for this ORF
Restriction modification systems have been identified as outlined in section “Methods”. Column 1 to 3 denote the number, strand direction and genome position of the ORF as identified by the NCBI annotation pipeline. Column 4 contains the description of the ORF in terms of aggregated annotations from NCBI, RAST and Prodigal. The type and predicted recognition sequence of the motif are shown in columns 5 and 6