TABLE 2.
Predicted ORFs and features of pPMA4326B
| ORF or featurea | Position | Size (aa)b | %GC | Homology (BLAST)c | Accession no. | Score/E value; aa identity (no. with identity/total [%]) |
|---|---|---|---|---|---|---|
| B01 | 1-1302 | 434 | 61 | Replication protein (repA); PtoDC3000 (pDC3000A) | AAO59029 | 771/0.0; 386/437 (88) |
| B02 | 1451-1744 | 98 | 54 | ssDNA-binding protein (ssb); PtoDC3000 | AAO54791 | 162/4e−40; 83/93 (89) |
| B03 | 1816-2016 | 67 | 57 | Conserved hypothetical; E. coli O157:H7 CP-933P | AAK16987 | 82.4/6e−16; 40/56 (71) |
| B04 | 2016-2309 | 98 | 51 | parE; E. coli O157:H7 | BAB35704 | 143/3e−34; 66/92 (71) |
| B05 | 2562-2975 | 138 | 51 | Hypothetical | ||
| MFB01 | 3181-4741 | 1,561 bp | 59 | IS801 transposase; PmaM6 (pFKN) | AAK49542 | 541/1e−153; 249/284 (87), 141/145 (97) |
| MFB02 | 5256-5094 | 163 bp | 52 | ISPsy transposase; PtoDC3000 | AAO56690 | 64.3/2e−16; 31/33 (93), 17/21 (80) |
| B06 | 5391-6809 | 473 | 59 | MFS sugar transporter; PtoDC3000 | AAO56003 | 881/0.0; 433/472 (91) |
| B07 | 8291-7062 | 410 | 61 | IS801 transposase; PmaM6 (pFKN) | AAK49542 | 828/0.0; 390/407 (95) |
| B08 | 9426-8608 | 273 | 53 | hopPmaA-like; PmaES4326 (candidate type III effector) | AAL84239 | 412/1e−114; 210/229 (91) |
| MFB03 | 9898-10196 | 299 bp | 48 | E622 (IS-like element, no transposase); PmaES4326 | ||
| B09 | 10161-10766 | 202 | 51 | Resolvase; S. enterica serovar Typhimurium LT2 (pSLT) | AAL23535 | 277/3e−74; 140/179 (78) |
| B10 | 10750-12408 | 553 | 58 | Integrase; S. enterica serovar Typhimurium LT2 (pSLT) | AAL23534 | 832/0.0; 393/555 (70) |
| B11 | 12398-13369 | 324 | 58 | exeA; Pseudomonas sp. strain TW3 | AAF23986 | 613/1e−175; 311/323 (96) |
| B12 | 15934-13610 | 775 | 55 | hopPmaA; PmaES4326 | AAL84239 | 1532/0.00; 774/774 (100) |
| MFB04 | 16247-16449 | 203 bp | 52 | E622 (IS-like element, no transposase); PmaES4326 | ||
| MFB05 | 17872-17513 | 360 bp | 56 | ISPsy12 transposase orfB; PtoDC3000 | AAO56533 | 224/3e−57; 104/120 (86) |
| B13 | 18973-18293 | 227 | 52 | Conserved hypothetical; Streptomyces violaceoruber (pSV2) | AAO50163 | 97.4/7e−20; 65/198 (32) |
| B14 | 19433-19161 | 91 | 47 | Conserved hypothetical; Listonella anguillarum (pEIB1, intergenic) | AY255699 | 159/2e−38; 64/91 (70) |
| B15 | 20162-19527 | 212 | 58 | Partitioning/stability (stbA); PtoPT23 (pPT23B) | AAB81646 | 359/9e−99; 187/204 (91) |
| B16 | 20570-21268 | 233 | 52 | Partitioning/stability (parA); Shewanella oneidensis MR-1 (megaplasmid) | AAN52997 | 157/7e−38; 89/223 (39) |
| B17 | 21261-21584 | 108 | 49 | Hypothetical | ||
| MFB06 | 22492-21711 | 782 bp | 59 | IS801 transposase; PmaM6 (pFKN) | AAK49542 | 204/5e−60; 88/97 (90), 97/104 (93) |
| MFB07 | 23698-22809 | 890 bp | 59 | Membrane protein; PtoDC3000 (pDC3000B) | AAO59103 | 338/1e−144; 181/187 (96), 95/98 (96) |
| B18 | 23898-25313 | 472 | 60 | MFS sugar transporter; PtoDC3000 (pDC3000B) | AAO59104 | 930/0.0; 470/471 (99) |
| MFB08 | 25401-25895 | 495 bp | 57 | rulB; PsyA2 (pPSR1) | AAC44639 | 295/6e−80; 145/165 (87) |
| B19 | 25979-26119 | 47 | 50 | Hypothetical | ||
| B20 | 27284-26316 | 323 | 55 | ISPssy transposase; PtoDC3000 | AAO58997 | 600/1e−171; 298/325 (91) |
| MFB09 | 27442-27634 | 193 bp | 61 | Transcriptional regulator (lysR); PsyB728a | ZP_00126456 | 70/1e−17; 32/43 (74%), 17/22 (77) |
| B21 | 28765-27641 | 375 | 56 | Conserved hypothetical; PtoDC3000 (pDC3000B) | AAO59105 | 699/0.0; 352/352 (100) |
| B22 | 29483-29010 | 158 | 47 | Conserved hypothetical; PtoDC3000 (pDC3000B) | AAO59098 | 301/8e−82; 141/157 (89) |
| B23 | 30490-29708 | 261 | 61 | Conserved hypothetical; PtoDC3000 (pDC3000B) | AAO59106 | 541/1e−153; 257/260 (98) |
| MFB10 | 30585-30673 | 89 bp | 57 | ISXc5 transposase; Xanthomonas campestris TAP44-3 (pKLH443) | CAB65711 | 53.9/3e−07; 24/29 (82) |
| B24 | 30768-31841 | 358 | 54 | ISPsy1 transposase; Pgy PG4180 (p4180A) | AAD50908 | 663/0.0; 328/357 (91) |
| MFB11 | 32002-32280 | 279 bp | 55 | ISPs1 transposase; PtoDC3000 | AAO57780 | 176/2e−44; 84/93 (90) |
| B25 | 32371-33348 | 326 | 55 | ISPssy transposase; PtoDC3000 | AAO58997 | 611/1e−174; 301/325 (92) |
| B26 | 33565-37038 | 1,157 | 59 | Relaxase/mobilization protein; PsyA2 (pPSR1) | AAR02188 | 1946/0.0; 973/1163 (83) |
| B27 | 37215-37415 | 67 | 52 | Conserved hypothetical; PtoDC3000 | AAO58724 | 68.6/1e−11; 31/41 (75) |
| MFB12 | 37480-37617 | 138 bp | 38 | Relaxase/mobilization protein; PsyA2 (pPSR1) | AAM64140 | 72.4/7e−13; 30/46 (65) |
| B28 | 37785-38213 | 143 | 62 | Transcriptional regulator (gntR); PtoDC3000 (pDC3000A) | AAO59095 | 261/5e−70; 129/142 (90) |
| B29 | 38549-39469 | 307 | 57 | Conserved hypothetical; P. aeruginosa PA14 | AAP84187 | 195/4e−49; 104/189 (55), 58/150 (38) |
a
MF, miscellaneous feature.
b
Unless otherwise stated.
c
Abbreviations: Psy, P. syringae pv. syringae; Pto, P. syringae pv. tomato; Pma, P. syringae pv. maculicola.