TABLE 1.
Predicted ORFs and features of pPMA4326A
| ORF or featurea | Position | Size (aa)b | %GC | Homology (BLAST)c | Accession no. | Score/E value; aa identity (no. with identity/total [%]) |
|---|---|---|---|---|---|---|
| A01 | 1-1311 | 437 | 60 | Replication protein (repA); PtoDC3000 (pDC3000A) | AAO59029 | 775/0.0; 388/437 (88) |
| A02 | 1514-1801 | 96 | 53 | ssDNA-binding protein (ssb); PtoDC3000 | AAO54791 | 165/5e−41; 86/93 (92) |
| A03 | 1946-2251 | 102 | 49 | Acetyltransferase; P. fluorescens | ZP_00086296 | 88.6/8e−18; 46/98 (46) |
| MFA01 | 2630-3091 | 462 bp | 56 | rulB; PtoDC3000 (pDC3000A) | AE016855 | 288/7e−78; 145/152 (95) |
| A04 | 3897-3427 | 157 | 50 | Hypothetical | ||
| MFA02 | 4209-4827 | 619 bp | 49 | Element 622 (IS-like element, no transposase) | ||
| A05 | 4895-5314 | 140 | 60 | Hypothetical | ||
| A06 | 5804-6127 | 108 | 50 | Conserved hypothetical; Photorhabdus luminescens | NP_931526 | 72/8e−13; 38/61 (62) |
| A07 | 6160-6585 | 142 | 60 | Conserved hypothetical; E. coli O157:H7 | BAB35465 | 77/2e−14; 42/134 (31) |
| A08 | 7102-7464 | 121 | 47 | Hypothetical | ||
| A09 | 7637-7945 | 103 | 55 | IS222 transposase orfA; Pseudomonas sp. strain ND6 | AAP44234 | 178/5e−45; 94/110 (85) |
| A10 | 8128-8799 | 224 | 55 | IS222 transposase orfB; PtoDC3000 | AAO56533 | 420/1e−116; 198/223 (88) |
| A11 | 9541-9338 | 68 | 53 | Hypothetical | ||
| A12 | 10649-9618 | 344 | 51 | Conserved hypothetical; PtoDC3000 (intergenic space) | AE016856 | 707/0.0; 47/197 (23) |
| A13 | 11647-10727 | 307 | 50 | Conserved hypothetical; PtoDC3000 | AAO53752 | 512/1e−162; 256/292 (87) |
| A14 | 12436-11795 | 214 | 58 | Partitioning/stability (stbA); PtoPT23 (pPT23B) | AAB81646 | 362/2e−99; 188/205 (91) |
| A15 | 12794-13447 | 218 | 49 | Partitioning/stability (yafB/parA); E. coli (R721) | BAB12593 | 239/8c−63; 129/217 (59) |
| A16 | 13469-13807 | 113 | 47 | Partitioning/stability (yafA); E. coli (R721) | BAB12592 | 65/9e−11; 38/87 (43) |
| A17 | 14012-14989 | 326 | 58 | IS1406 transposase; PtoDC3000 | AAO58162 | 639/0.0; 320/325 (98) |
| A18 | 15724-15338 | 129 | 46 | Hypothetical | ||
| A19 | 16436-15966 | 157 | 38 | Pyocin S3 immunity (bip); P. aeruginosa B56394 | AAR02169 | 304/1c−82; 151/156 (96) |
| A20 | 16874-16524 | 117 | 51 | Transcriptional regulator (pbsX); PtoDC3000 (pDC3000B) | AAO59134 | 78.2/1e−14; 40/109 (36) |
| A21 | 17139-17666 | 176 | 42 | Transcriptional regulator; PsyA2 (pPSR1) | AAR02171 | 326/4e−89; 170/175 (97) |
| A22 | 17732-17947 | 72 | 42 | Conserved hypothetical; PtoDC3000 (pDC3000B) | AAO59136 | 44.7/1e−04; 21/52 (40) |
| A23 | 17976-18674 | 233 | 60 | Conjugal transfer (virB1); PsyA2 (pPSR1) | AAR02172 | 421/1e−117; 212/235 (90) |
| A24 | 18671-19009 | 113 | 62 | Conjugal transfer (virB2); PsyA2 (pPSR1) | AAR02173 | 211/8e−55; 102/112 (91) |
| A25 | 19016-19498 | 161 | 56 | Conjugal transfer (virB3); PsyA2 (pPSR1) | AAR02174 | 313/3e−85; 154/158 (97) |
| A26 | 19359-21911 | 851 | 58 | Conjugal transfer (virB4); PsyA2 (pPSR1) | AAR02175 | 1617/0.0; 795/848 (93) |
| A27 | 21908-22594 | 229 | 58 | Conjugal transfer (virB5); PsyA2 (pPSR1) | AAR02176 | 407/1e−113; 204/228 (89) |
| A28 | 22897-23130 | 78 | 46 | Hypothetical | ||
| A29 | 23141-24073 | 311 | 54 | Conjugal transfer (virB6); PsyA2 (pPSR1) | AAR02177 | 531/1e−150; 268/310 (86) |
| A30 | 24141-24455 | 104 | 66 | Conjugal transfer (virB7); PsyA2 (pPSR1) | AAR02178 | 159/9e−39; 85/105 (80) |
| A31 | 24492-25280 | 263 | 58 | Conjugal transfer (virB8); PsyA2 (pPSR1) | AAR02179 | 489/1e−138; 242/262 (92) |
| A32 | 25270-26079 | 270 | 62 | Conjugal transfer (virB9); PsyA2 (pPSR1) | AAR02180 | 500/1e−141; 245/269 (91) |
| A33 | 26204-27415 | 404 | 61 | Conjugal transfer (virB10); PsyA2 (pPSR1) | AAR02181 | 705/0.0; 355/406 (87) |
| A34 | 27425-28483 | 353 | 62 | Conjugal transfer (virB11); PsyA2 (pPSR1) | AAR02182 | 620/1e−177; 294/341 (86) |
| A35 | 28493-28858 | 122 | 60 | Conserved hypothetical; PgyPG4180 | AF346402 | 287/6e−77; 111/118 (94) |
| A36 | 29219-29485 | 89 | 54 | Hypothetical | ||
| MFA03 | 29919-30008 | 90 bp | 59 | virD4; PsyA2 (pPSR1) | AAR02183 | 50.4/3e−06; 27/30 (90) |
| A37 | 30074-31090 | 339 | 51 | Hypothetical | ||
| A38 | 31626-33299 | 558 | 59 | Conjugal transfer (virD4); PsyA2 (pPSR1) | AAR02183 | 848/0.0; 418/555 (75) |
| A39 | 33340-33702 | 121 | 62 | Killer protein (kikA); E. coli (R721) | BAB12662 | 100/1e−21; 48/97 (49) |
| A40 | 33730-35895 | 722 | 61 | Conjugal transfer (traE); PsyA2 (pPSR1) | AAR02184 | 1355/0.0; 684/721 (94) |
| A41 | 35892-36446 | 185 | 58 | Hypothetical | ||
| A42 | 36474-37034 | 187 | 61 | ssDNA-binding protein (ssb); PtoDC3000 | AAO54198 | 360/3e−99; 175/189 (92) |
| MFA04 | 37088-37285 | 198 bp | 67 | Conserved hypothetical; P. aeruginosa PA01 (phage Pf1 PA0719) | AAG04108 | 60/2e−09; 39/66 (59) |
| A43 | 37376-38095 | 240 | 47 | Partitioning/stability (stbB); PsyA2 (pPSR1) | AAR02186 | 385/1e−106; 189/238 (79) |
| A44 | 38092-38664 | 191 | 48 | Conserved hypothetical; E. amylovora (pEU30) | AAQ97965 | 82/2e−15; 52/180 (28) |
| A45 | 39102-38683 | 140 | 51 | Conserved hypothetical (yciA); E. coli (R721) | BAB12622 | 43:1/3e−04; 24/67 (35) |
| A46 | 39444-40169 | 242 | 49 | Conjugal transfer (relaxosome component); PsyA2 (pPSR1) | AAR02187 | 445/1e−124; 222/241 (92) |
| A47 | 40159-43893 | 1245 | 58 | Conjugal transfer (relaxase); PsyA2 (pPSR1) | AAR02188 | 2224/0.0; 1114/1250 (89) |
| A48 | 44073-44228 | 52 | 55 | Conserved hypothetical; PtoDC3000 | AAO58724 | 79.3/5e−15; 37/53 (69) |
| A49 | 44373-44801 | 143 | 62 | Transcriptional regulator (gntR); PtoDC3000 (pDC3000A) | AAO59095 | 261/2e−69; 129/142 (90) |
| A50 | 45137-46057 | 307 | 57 | Conserved hypothetical; P. aeruginosa PA14 | AAP84187 | 195/4e−49; 104/189 (55) |
a
MF, miscellaneous feature.
b
Unless otherwise indicated.
c
Abbreviations: Psy, P. syringae pv. syringae; Pto, P. syringae pv. tomato; Pma, P. syringae pv. maculicola.