TABLE 3.
Annotation of all ORFs located within pKLC102
| Gene identification | Coordinates
|
Direction | Length (aa)a | GC content (%) | Gene name | Annotation result and homologous gene products | BLAST search resultb | E value of best BLAST hit | |
|---|---|---|---|---|---|---|---|---|---|
| Left | Right | ||||||||
| CP1 | 113 | 997 | → | 294 | 60.23 | soj | Similar to chromosome partitioning-related protein (Xylella fastidiosa 9a5c) | NP_299073 | 6e-67 |
| CP2 | 999 | 1724 | → | 241 | 59.78 | Similar to hypothetical protein from Pseudomonas resinovorans | NP_758706 | 2e-25 | |
| CP3 | 1.721 | 2.218 | → | 165 | 62.25 | Hypothetical protein similar to PA2226 (P. aeruginosa) | NP_250916 | 5E-27 | |
| CP4 | 2.224 | 2.970 | → | 248 | 61.85 | Hypothetical protein similar to unknown protein encoded by gene Z2097 within prophage CP-933O (E. coli O157:H7 EDL933) | NP_287555 | 6E-10 | |
| CP5 | 2.967 | 3.653 | → | 228 | 64.05 | Hypothetical protein similar to Magn3145 (Magnetospirillum magnetotacticum) | ZP_00050489 | 1E-10 | |
| CP6 | 3.653 | 4.354 | → | 233 | 64.53 | Hypothetical protein similar to an intragenic region upstream of Psyr3996 (P. syringae pv. syringae B728a) | NZ_AABP02000009 | 2E-61 | |
| CP7 | 4.351 | 5.058 | → | 235 | 58.62 | Hypothetical protein homologous to EsV-1-119 ORF119 (Ectocarpus siliculosus virus) | NP_077604 | 0.039 | |
| CP8 | 5.042 | 5.260 | → | 72 | 57.08 | No significant similarity | |||
| CP9 | 5.323 | 6.600 | → | 425 | 61.11 | dnaB | Replicative DNA helicase PA4931 (dnaB) (P. aeruginosa) | NP_253618 | E-122 |
| CP10 | 7.039 | 7.395 | ← | 118 | 55.74 | No significant similarity | |||
| CP11 | 7.838 | 8.365 | → | 175 | 61.74 | No significant similarity | |||
| CP12 | 8.362 | 8.619 | → | 85 | 60.08 | No significant similarity | |||
| CP13 | 8.612 | 9.109 | → | 165 | 62.85 | No significant similarity | |||
| CP14 | 9.102 | 9.335 | → | 77 | 66.24 | Conserved hypothetical protein similar to Bcep0486 (B. fungorum) | ZP_00027718 | 1E-06 | |
| CP15 | 9.335 | 10.351 | → | 338 | 64.01 | Conserved hypothetical protein homologous to PA3849 (P. aeruginosa) and to a nucleoid associated protein (E. coli O157:H7) | NP_252538 | E-175 | |
| CP16 | 10.348 | 10.602 | → | 84 | 58.43 | Putative DNA-binding protein homologous to PA3385 (AlgZ) (P. aeruginosa) | AAD55364 | 0.028 | |
| CP17 | 10.599 | 12.332 | → | 577 | 58.36 | Conserved hypothetical protein similar to ORF SG102 (P. aeruginosa); ParB-like nuclease domain | AAN62323 | E-104 | |
| CP18 | 12.360 | 13.115 | → | 251 | 59.13 | Hypothetical protein Bcep0488 (B. fungorum) | ZP_00027720 | 1E-30 | |
| CP19 | 15.766 | 16.494 | → | 242 | 63.24 | Conserved hypothetical protein similar to ORF C104 (P. aeruginosa) | AAN62197 | 4E-64 | |
| CP20 | 16.500 | 17.048 | → | 182 | 60.84 | Conserved hypothetical protein similar to ORF C103 (P. aeruginosa) | AAN62196 | 1E-24 | |
| CP21 | 17.095 | 17.934 | → | 279 | 60.83 | Putative antirepressor homologous to sb41 (Salmonella enterica serovar Typhimurium phage ST64B) | NP_700414 | 6E-23 | |
| CP22 | 17.964 | 18.452 | → | 162 | 62.17 | ssb | Putative single-stranded DNA-binding protein homologous to ssb (P. aeruginosa); single-strand binding conserved domain | AAN62318 | 5E-30 |
| CP23 | 18.871 | 19.152 | ← | 93 | 53.90 | No significant similarity | |||
| CP24 | 19.289 | 19.549 | ← | 86 | 52.87 | No significant similarity | |||
| CP25 | 19.571 | 19.981 | ← | 136 | 60.83 | Putative nucleic acid binding protein; contains PIN conserved domain (similarity with an analogous gene from Salmonella enterica serovar Typhimurium LT2) | NP_461950 | 2E-51 | |
| CP26 | 19.981 | 20.211 | ← | 76 | 57.57 | Putative virulence-associated protein similar to cytoplasmic protein from Salmonella enterica serovar Typhimurium LT2; VagC conserved domain | NP_490591 | 2E-20 | |
| CP27 | 20.467 | 22.386 | → | 639 | 62.19 | topA | Topoisomerase I; similar to XFa0003 (X. fastidiosa) | NP_061659 | E-148 |
| CP28 | 22.694 | 22.903 | → | 69 | 51.90 | cspA | Cold acclimation protein similar to PA3266 (CspA) (P. aeruginosa) | NP_251956 | 2E-18 |
| CP29 | 23.124 | 25.013 | → | 629 | 60.37 | No significant similarity | |||
| CP30 | 25.010 | 26.983 | → | 657 | 64.18 | Putative helicase similar to Psyr4003 (P. syringae pv. syringae); SNF2 family N-terminal domain; DEAD-like helicase superfamily; helicase superfamily C-terminal domain | ZP_00127683 | 0.0 | |
| CP31 | 27.105 | 27.887 | → | 260 | 46.23 | Putative ABC transporter similar to mlr7981 (Mesorhizobium loti); ATP-binding protein | BAB53638 | 9E-85 | |
| CP32 | 27.920 | 29.173 | → | 417 | 41.55 | Hypothetical protein similar to SMa2241 (S. meliloti plasmid pSymA) | NP_436454 | E-126 | |
| CP33 | 29.347 | 30.471 | → | 374 | 65.16 | pilL | PilL (Yersinia pseudotuberculosis) | AAL05416 | 3E-36/PICK> |
| CP34 | 30.471 | 32.180 | → | 569 | 63.86 | pilN | PilN (E. coli) | AAL05518 | 8E-56 |
| CP35 | 32.298 | 33.509 | → | 403 | 64.03 | pilO | PilO (Salmonella enterica serovar Typhi) | AAF14815 | 5E-13 |
| CP36 | 33.499 | 34.032 | → | 177 | 70.97 | pilP | PilP (Salmonella enterica serovar Typhimurium plasmid R64) | BAA77976 | 2E-04 |
| CP37 | 34.041 | 35.621 | → | 526 | 63.25 | pilQ | PilQ (S. enterica subsp. enterica serovar Dublin) | AAF81213 | 7E-74 |
| CP38 | 35.621 | 36.700 | → | 359 | 63.80 | pilR | PilR (Salmonella enterica serovar Typhi) | AAC98886 | 2E-40 |
| CP39 | 36.779 | 37.252 | → | 157 | 60.13 | pilS | PilS; prepilin similar to hypothetical protein from P. syringae pv. syringae B728a and to type IV prepilin (Y. pseudotuberculosis) | ZP_00127690 | 3E-18 |
| CP40 | 37.249 | 38.190 | → | 313 | 66.03 | pilU | PilU; prepilin peptidase (P. aeruginosa) | S54702 | 1E-15 |
| CP41 | 38.195 | 39.523 | → | 442 | 63.81 | pilV | PilV; pilus tip adhesin (E. coli) | CAA44099 | 6E-48 |
| CP42 | 39.552 | 39.989 | → | 145 | 68.26 | pilM | PilM (Salmonella enterica serovar Typhimurium plasmid R64) | BAA77973 | 1.1 |
| CP43 | 40.911 | 41.300 | → | 129 | 60.00 | No significant similarity | |||
| CP44 | 41.373 | 41.552 | → | 59 | 53.33 | No significant similarity | |||
| CP45 | 41.554 | 41.688 | → | 44 | 58.52 | No significant similarity | |||
| CP46 | 42.012 | 42.491 | → | 159 | 57.29 | Conserved hypothetical protein (P. fluorescens) | ZP_00087894 | 4E-46 | |
| CP47 | 42.861 | 43.058 | → | 65 | 53.54 | Conserved hypothetical protein (S. enterica subsp. enterica serovar Typhi) | NP_458626 | 1E-10 | |
| CP48 | 43.163 | 43.441 | → | 92 | 50.18 | No significant similarity | |||
| CP49 | 43.544 | 44.251 | → | 235 | 52.68 | Conserved hypothetical protein similar to Pflu5179 (P. fluorescens) | ZP_00087892 | 1E-41 | |
| CP50 | 44.487 | 44.837 | → | 116 | 63.25 | No significant similarity | |||
| CP51 | 44.894 | 45.685 | → | 263 | 61.62 | Conserved hypothetical protein similar to XF1760 (X. fastidiosa) | NP_299049 | 2E-42 | |
| CP52 | 45.788 | 46.150 | → | 120 | 58.13 | Conserved hypothetical protein similar to ORF C77 (P. aeruginosa) | AAN62171 | 9E-21 | |
| CP53 | 46.218 | 46.472 | → | 84 | 61.18 | Conserved hypothetical protein similar to XAC2240 (Xanthomonas axonopodis pv. citri) | NP_642557 | 2E-08 | |
| CP54 | 46.564 | 47.169 | → | 201 | 64.03 | Conserved hypothetical protein similar to XAC2241 (X. axonopodis pv. citri 306) | NP_642558 | 1E-50 | |
| CP55 | 47.199 | 48.644 | → | 481 | 63.69 | Hypothetical protein similar to Bcep3609 (B. fungorum), | ZP_00030785 | E-133 | |
| CP56 | 48.743 | 50.998 | → | 751 | 63.25 | Putative helicase similar to hypothetical protein Psyr4040 (P. syringae pv. syringae); SNF2 family N-terminal domain; DEAD-like helicase superfamily; helicase superfamily C-terminal domain | ZP_00127717 | 0.0 | |
| CP57 | 51.579 | 52.364 | ← | 261 | 55.47 | Putative polyketide synthase similar to XF2135 (X. fastidiosa); HCCA isomerase conserved domain | NP_299414 | 8E-23 | |
| CP58 | 52.303 | 52.644 | ← | 113 | 58.48 | Conserved hypothetical protein similar to Bcep7601 (B. fungorum); carboxymuconolactone decarboxylase conserved domain | ZP_00034706 | 2E-15 | |
| CP59 | 52.739 | 53.299 | ← | 186 | 54.55 | Putative TetR family transcription regulator protein similar to ORF43 (P. putida plasmid pWWO); TetR conserved domain | NP_542832 | 3E-17 | |
| CP60 | 53.362 | 54.147 | ← | 261 | 58.78 | Putative reductase protein similar to ORF44 (P. putida plasmid pWWO); short-chain dehydrogenase conserved domain | NP_542833 | 3E-76 | |
| CP61 | 54.303 | 54.716 | ← | 137 | 59.66 | Putative TetR family transcription regulator protein similar to MA2493 (Methanosarcina acetivorans) | NP_617399 | 0.12 | |
| CP62a | 54.709 | 55.560 | ← | 283 | 57.51 | Phage integrase similar to hypothetical protein Reut5633 (R. metallidurans); phage integrase domain | ZP_00026607 | 1E-23 | |
| CP62b | 54.904 | 55.407 | → | 167 | 59.52 | No significant similarity; inner ORF of the phage integrase CP62a | |||
| CP63 | 56.331 | 57.023 | → | 230 | 63.78 | Conserved hypothetical protein similar to Psyr4041 (P. syringae pv. syringae) | ZP_00127718 | 2E-26 | |
| CP64 | 57.034 | 57.789 | → | 251 | 65.21 | Conserved hypothetical protein similar to Psyr4042 (P. syringae pv. syringae) | ZP_00127719 | 5E-53 | |
| CP65 | 57.774 | 58.355 | → | 193 | 65.64 | Hypothetical protein similar to ORF SG70 (P. aeruginosa) | AAN62161 | 5E-35 | |
| CP66 | 58.352 | 58.852 | → | 166 | 66.27 | Hypothetical protein similar to ORF SG69 (P. aeruginosa) | AAN62291 | 7E-31 | |
| CP67 | 59.134 | 61.365 | → | 743 | 65.10 | Putative conjugation protein TraG similar to hypothetical protein Psyr4044 (P. syringae pv. syringae); TraG/TraD family conserved domain | ZP_00127721 | 0.0 | |
| CP68 | 61.365 | 62.111 | → | 248 | 61.18 | Conserved hypothetical protein similar to ORF SG67 (P. aeruginosa) | AAN62289 | 5E-52 | |
| CP69 | 62.122 | 63.603 | → | 493 | 59.85 | Putative helicase similar to hypothetical protein Psyr4046 (P. syringae pv. syringae); UvrD helicase conserved domain | ZP_00127723 | 0.0 | |
| CP70 | 63.735 | 64.844 | → | 369 | 46.58 | Hypothetical protein similar to a probable RND efflux transporter mll1426 (M. loti) | NP_103018 | 4.4 | |
| CP71 | 64.889 | 65.200 | ← | 103 | 49.68 | Conserved hypothetical protein similar to PA0713 (P. aeruginosa) | NP_249404 | 5E-16 | |
| CP72 | 65.373 | 65.672 | → | 99 | 57.00 | No significant similarity | |||
| CP73 | 65.883 | 66.104 | → | 73 | 67.57 | Hypothetical protein similar to Avin1322 (A. vinelandii) | ZP_00089650 | 3E-24 | |
| CP74 | 66.107 | 66.340 | → | 77 | 64.53 | Hypothetical protein similar to Avin1321 (A. vinelandii) | ZP_00089649 | 2E-8 | |
| CP75 | 66.358 | 66.714 | → | 118 | 57.98 | Hypothetical protein similar to Avin1320 (A. vinelandii) | ZP_00089648 | 3E-15 | |
| CP76 | 66.725 | 67.111 | → | 128 | 66.93 | Hypothetical protein similar to Avin1319 (A. vinelandii) | ZP_00089647 | 1E-32 | |
| CP77 | 67.108 | 67.767 | → | 219 | 61.06 | Hypothetical protein similar to Avin1318 (A. vinelandii) | ZP_00089646 | 4E-78 | |
| CP78 | 67.764 | 68.648 | → | 294 | 66.33 | Hypothetical protein similar to Avin1317 (A. vinelandii) | ZP_00089645 | 5E-88 | |
| CP79 | 68.710 | 70.137 | → | 475 | 64.15 | Hypothetical protein similar to Avin1316 (A. vinelandii) | ZP_00089644 | E-149 | |
| CP80 | 70.211 | 70.558 | → | 115 | 64.94 | Hypothetical protein similar to Avin1315 (A. vinelandii) | ZP_00089643 | 1E-47 | |
| CP81 | 70.558 | 73.500 | → | 980 | 63.00 | Hypothetical protein similar to Avin1314 (A. vinelandii) | ZP_00089642 | 0.0 | |
| CP82 | 73.497 | 73.781 | → | 94 | 58.25 | Hypothetical protein similar to Avin1313 (A. vinelandii) | ZP_00089641 | 2E-19 | |
| CP83 | 73.778 | 74.434 | → | 218 | 62.25 | Conserved hypothetical outer membrane protein similar to PA0982 (P. aeruginosa) | NP_249673 | 3E-87 | |
| CP84 | 75.208 | 76.395 | → | 395 | 62.88 | Putative flavoprotein reductase similar to hypothetical protein PA2566 (P. aeruginosa) | NP_251256 | 0.0 | |
| CP85 | 76.418 | 76.840 | → | 140 | 66.43 | Hypothetical protein similar to PA2565 (P. aeruginosa) | NP_251255 | 5E-25 | |
| CP86 | 76.830 | 77.696 | → | 288 | 63.78 | cheR | CheR; trans-aconitate 2-methyltransferase similar to PA2564 (P. aeruginosa) | NP_251254 | E-126 |
| CP87 | 77.834 | 78.265 | → | 143 | 61.81 | Conserved hypothetical protein similar to Avin1308 (A. vinelandii) | ZP_00089637 | 6E-20 | |
| CP88 | 78.265 | 79.203 | → | 312 | 64.86 | Hypothetical protein similar to Avin1307 (A. vinelandii) | ZP-00089636 | E-123 | |
| CP89 | 79.038 | 80.603 | → | 521 | 64.56 | Putative integral membrane protein similar to ORF C42 (P. aeruginosa) | AAN62272 | E-122 | |
| CP90 | 80.603 | 80.950 | → | 115 | 62.64 | Hypothetical protein similar to Avin1305 (A. vinelandii) | ZP_00089634 | 0.001 | |
| CP91 | 80.947 | 82.482 | → | 511 | 58.72 | Hypothetical protein similar to Avin1304 (A. vinelandii) | ZP_00089633 | 0.0 | |
| CP92 | 82.924 | 83.256 | → | 110 | 60.61 | Hypothetical protein (P. fluorescens); conserved domain of NikR transcriptional regulator | ZP_00086716 | 8E-16 | |
| CP93 | 83.260 | 83.610 | → | 116 | 62.68 | Conserved hypothetical protein similar to AGR_C_2415 (A. tumefaciens strain C58; Cereon); ParE conserved domain of plasmid stabilization system protein | G97518 | 5E-15 | |
| CP94 | 83.988 | 92.501 | ← | 2,837 | 65.32 | chvB | Beta (1->2) glucan biosynthesis protein similar to ChvB (A. tumefaciens) | NP_533395 | 0.0 |
| CP95 | 93.343 | 93.567 | → | 74 | 61.33 | Hypothetical protein similar to Pflu4565 (P. fluorescens) | ZP_00087289 | 0.13 | |
| CP96 | 93.782 | 94.501 | → | 239 | 61.25 | Transcriptional regulator-related protein similar to SO2551 (Shewanella oneidensis); helix-turn-helix and cAMP regulatory protein conserved domains | NP_718137 | 5E-78 | |
| CP97 | 94.572 | 94.934 | → | 120 | 60.33 | No significant similarity | |||
| CP98 | 94.852 | 95.532 | → | 226 | 64.02 | Hypothetical protein similar to XF0240 (X. fastidiosa) | NP_297533 | 7.1 | |
| CP99 | 95.641 | 97.659 | → | 672 | 62.51 | Fusion protein; putative fatty acid synthase similar to cyclopropane-fatty-acyl-2 phospholipid synthase mll4091 (M. loti) | BAB50831 | 3E-67 | |
| CP100 | 97.815 | 99.008 | ← | 397 | 61.81 | Probable fatty acid desaturase similar to PA0286 (P. aeruginosa) | AAG03675 | E-124 | |
| CP101 | 99.396 | 99.752 | → | 118 | 45.94 | Hypothetical protein similar to Avin0596 (A. vinelandii) | ZP_00088936 | 3E-21 | |
| CP102 | 99.964 | 101.883 | → | 639 | 58.70 | Conserved hypothetical protein; putative conjugative relaxase Tral; similar to hypothetical protein Avin0927 (A. vinelandii) | ZP_00089260 | 0.0 | |
| CP103a | 101.880 | 103.163 | → | 427 | 60.00 | xerC | Phage integrase similar to XerC (P. syringae) | AAM77365 | E-101 |
| CP103b | 101.970 | 102.476 | ← | 168 | 60.36 | No significant similarity; inner ORF of phage integrase CP103a | |||
a
aa, amino acids.
b
GenBank accession number.