TABLE 1.
List of identified ORFs of plasmid pHel4
| ORF | Codon position (start-stop) | Sequencea | Molecular mass (kDa) | pI | Net charge | Propertiesb | Homology (BLASTP)c |
|---|---|---|---|---|---|---|---|
| orf4A | 1166-3 | AATTTATAGAGTTTCTTAATATG | 43.9 | 9.3 | 9 | TM; SP; α-β | HP1165, 1e-92; JHP1092, 2e-92; BB126, 7e-34; TetA(P), 2e-06; MccC, 5e-5 |
| orf4B | 2254-1178 | AAAGTTTTATCGGAGTAGAGTTG | 41.0 | 6.6 | −2 | α-β | MccB, 1e-18 |
| orf4C | 4488-2506 | TTAGAACAACTAAGAGCTAAATG | 78.1 | 10.4 | 26 | Mix; cc | MbeAy, 7e-30; MbeA, 23-27; MobA, 5e-24; BdrC3, 0.026 |
| orf4D | 3245-2739 | CCAAGAAATAAGGGGAAAACATG | 19.6 | 5.3 | −4 | Leucine zipper; α | |
| orf4E | 3785-3255 | ATTAAAAGGATTTTACTACCATG | 20.4 | 10.1 | 8 | TM; cc; α | MobB2, 0.65 |
| orf4F | 4822-4478 | TAAGGGATAGCCAAAAAAATATG | 13.2 | 10.6 | 8 | Mix | MbeCy, 0.021 |
| orf4G | 5020-5298 | GATTGAGTTAAGGAGATAAGATG | 10.8 | 10.1 | 5 | cc; α | JHP0828, 2e-16; HP0316, 0.002 |
| orf4H | 5285-5551 | ATGAGTTAAAAAGAGAGTATATG | 10.7 | 8.7 | 2 | Mix | HP0894, 4e-26; HP0892, 1e-21; JHP0831, 4e-21; JHP0825, 2e-18; ORF10, 1e-10; YafQ, 6e-09 |
| orf4I | 6671-8296 | AAGCATTAAAAGGTGCTTAAATG | 64.1 | 10.2 | 19 | cc; mix | RepA, 0.0 |
| orf4J | 8854-8483 | GAAAAACAAGGGGATCACTAATG | 13.6 | 8.5 | 4 | TM; α-β | |
| orf4K | 8490-8990 | TTGTAATAGGAGTTTAAAAAATG | 20.0 | 9.8 | 6 | α (cc) | |
| orf4L | 8990-9322 | AGTTATGTAAAGAGCATGTAGTG | 13.4 | 9.6 | 3 | TM; cc; mix | |
| orf4M | 9326-10099 | TCAATCGTTTGGAGTAGCATGTG | 29.6 | 6.5 | −5 | Mix | Orf6-pHPM8, 4e-57; JHP0651, 5e-33; HP0712, 7e-22; pHPM180-Orf2, 1e-08; HP0713, 5e-07 |
| orf4N | 10406-10086 | TATTCTAAACTCAAAGGTTCTTG | 12.2 | 9.2 | 1 | TM; α-β | |
| orf4O | 10149-10856 | ACAGGTGAAAAGACAGATGCATG | 27.6 | 7.9 | 1 | Mix | pHPM180-ORF2, e-115; JHP0651, 6e-11; HP0713, 7e-09; ZK593.8, 5e-08; Tou1, 5e-06; ORF56-TP901-1, 0.20; ORF178-wss virus, 0.23 |
a
The putative Shine-Dalgarno sequence is underlined; the start codon is in boldface.
b
TM, transmembrane domain; SP, signal peptide; α, α-β, and mix, secondary structure elements as predicted by PREDICTPROTEIN; cc, coiled-coil structure.
c
BB126, AAC66191; TetA(P), BAA19230; MccC, CAA40810; MccB, CAA40809; MbeAy, AAB05464; MbeA, CAA33883; MobA, AAA69498; BdrC3, AAF19116; BobB2, AAD02406; MbeCy, AAB05463; ORF10, AAF05106; YafQ, Q47149; ZK593.8, T27927; Tou1, AAF08816; ORF56-TP901-1, AAK38073; ORF178-white spot syndrome (wss) virus, AAK77847.