TABLE 2.
Predicted ORFs found in plasmid pEP36 from E. pyrifoliae strain Ep1/96
| pEp36 ORFa | Strand | Predicted protein size (kDa) | Size in amino acids (putative gene function) | Putative protein/organism/ GenBank accession no. | Alignment region | Homologue alignment | % Identity |
|---|---|---|---|---|---|---|---|
| Similar ORFs | |||||||
| repA/ORF 1 | + | 37.6 | 325 (replication protein) | RepA/Erwinia amylovora/AAG31039.1 | 1-325 | 1-325 (325)b | 93 |
| hns/ORF 4 | − | 14.4 | 128 (histone-like nucleotid structuring protein, DNA binding) | H-NS/Erwinia amylovora/AAG31058.1 | 1-128 | 1-128 (134) | 63 |
| trlA/ORF 6 | − | 31.1 | 285 (LysR transcriptional regulator) | MarR/Erwinia amylovora/AAG31051.1 | 1-285 | 1-285 (285) | 87 |
| aldD/ORF 8 | + | 49.3 | 461 (aldehyde dehydrogenase) | AldD/Erwinia amylovora/AAG31043.1 | 1-460 | 1-460 (461) | 85 |
| ctpE/ORF 10 | − | 54.3 | 507 (methyl-accepting chemotaxis protein) | CtpE/Erwinia amylovora/AAG31044.1 | 1-507 | 1-507 (507) | 84 |
| thiF/ORF 14 | − | 34.3 | 321 (thiamine biosynthesis) | ThiF/Erwinia amylovora/AAG31053.1 | 1-321 | 1-321 (321) | 80 |
| thiG/ORF 15 | − | 27.5 | 253 (thiamine biosynthesis) | ThiG/Erwinia amylovora/AAG31045.1 | 2-253 | 1-252 (252) | 90 |
| thiO/ORF 16 | − | 40.1 | 359 (amino acid oxidase flavoprotein) | ThiO/Erwinia amylovora/AAG31046.1 | 10-349 | 10-349 (349) | 87 |
| tnpR/ORF 17 | + | 21.3 | 194 (resolvase) | TnpR/Erwinia amylovora/AAG31042.1 | 1-193 | 1-193 (194) | 95 |
| ORF 18 | + | 18.9 | 171 (conserved hypothetical protein) | ORF 15/Erwinia amylovora/AAG31047.1 | 1-171 | 1-171 (171) | 85 |
| betT/ORF 19 | − | 76.2 | 676 (high-affinity choline transport gene) | BetT/Erwinia amylovora/AAG31040.1 | 1-676 | 1-676 (676) | 94 |
| msrA/ORF 29 | + | 19.7 | 178 (peptide methionine sulfoxide reductase) | MsrA/Erwinia amylovora/AAG31048.1 | 1-178 | 1-178 (178) | 92 |
| parA/ORF 31 | + | 22.2 | 208 (partitioning protein) | ParA/Erwinia amylovora/AAG31050.1 | 4-208 | 2-206 (206) | 50 |
| parB/ORF 32 | + | 7.7 | 68 (partitioning protein) | ParB/Erwinia amylovora/AAG31059.1 | 1-66 | 13-76 (76) | 38 |
| ORFs not found | |||||||
| ORF 2 | + | 45.3 | 403 (transposase A) | Transposase mutator/Yersinia pestis/ NP_403677.1 | 1-403 | 1-402 (402) | 90 |
| ORF 3 | + | 17.9 | 159 (unknown) | Hypothetical protein | |||
| ORF 5 | − | 34.7 | 312 (plasminogen activator) | Plasminogen activator precursor/ Yersinia pestis/A42928 | 1-312 | 1-312 (312) | 71 |
| ORF 7 | + | 24.0 | 213 (unknown) | Hypothetical protein | |||
| ORF 9 | − | 39.4 | 344 (unknown) | Hypothetical protein | |||
| ORF 11 | − | 10.9 | 94 (unknown) | Hypothetical protein/Yersinia pestis/ NP_404766.1 | 1-68 | 1-68 (81) | 73 |
| stbE/ORF 12 | − | 11.1 | 95 (plasmid stability) | Putative cytoplasmic protein/Salmonella enterica serovar Typhimurium/ | 1-93 | 1-93 (94) | 67 |
| NP_460510.1 or stbE/Morganella | 1-93 | 1-93 (93) | 56 | ||||
| morganii/AAC84004.1 | |||||||
| stbD/ORF 13 | − | 9.2 | 84 (plasmid stability) | Putative cytoplasmic protein/Salmonella | 1-84 | 1-82 (82) | 65 |
| enterica serovar Typhimurium/ | |||||||
| NP_460511.1 or StbD/Morganella | 1-84 | 1-83 (83) | 64 | ||||
| morganii/AAC84003.1 | |||||||
| ORF 20 | − | 29.5 | 270 (ABC transporter) | Hypothetical protein/Staphylococcus | 25-267 | 33-271 (273) | 51 |
| aureus/NP_371363.1 or YusA/ | 25-269 | 33-273 (274) | 48 | ||||
| Bacillus subtilis/B70020 | |||||||
| ORF 21 | − | 23.7 | 222 (ABC transporter-binding protein-dependent transport system) | YusB/Bacillus subtilis/C70020 | 1-222 | 1-222 (222) | 56 |
| ORF 22 | − | 35.7 | 326 (ABC transporter-ATP binding protein) | YusC/Bacillus subtilis/D70020 | 13-326 | 28-341 (341) | 57 |
| ORF 23 | − | 113.5 | 998 (transposase) | Tnp/plasmid F/NP_061389.1 | 1-998 | 1-998 (1002) | 76 |
| ORF 24 | + | 21.7 | 193 (resolvase) | TnpR/Pseudomonas putida/P30739 | 1-178 | 1-178 (181) | 51 |
| ORF 25 | − | 32.9 | 284 (transposase) | Integrase/Escherichia coli/CAC43414.1 | 1-284 | 1-284 (284) | 89 |
| ORF 26 | − | 11.4 | 99 (transposase) | Tnp/Salmonella enterica serovar Typhimurium LT2/NP_461695 | 1-99 | 1-99 (99) | 83 |
| ORF 27 | + | 19.3 | 178 (conserved hypothetical protein) | Putative membrane protein/Yersinia pestis/NP_407480.1 | 1-166 | 12-179 (193) | 37 |
| ORF 28 | − | 14.0 | 126 (unknown) | Hypothetical protein | |||
| ORF 30 | + | 15.3 | 138 (conserved hypothetical protein) | Hypothetical protein/Escherichia coli/ BAB33986.1 | 1-93 | 1-93 (135) | 87 |
a
Similar ORFs, ORFs similar to those found in E. amylovora plasmid pEA29; ORFs not found, ORFs not found in E. amylovora plasmid pEA29.
b
Total length of ORF in GenBank.