Table 6.
Potential new type III secretion effectors found in X. fragariae LMG 25863
| General characteristics | Most closely related knownXanthomonasT3SE | Best genbank match | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Locus | Moved start-codon compared to PGAAP annotation | Protein length | %GC | Putative PIP | Effector class | Best match for Xf | Worst match amongst the sequences within the effector class | Locus | Organism | Similarity with Xf-sequence |
| [Genbank:O1K_18811] | 424 AA | 52 | XopC2 | 52.8% | 94.4% | [Genbank:CCA89217] | Ralstonia | 66.6% | ||
| [Genbank:O1K_11082] | 147 bp to 5' side | 327 AA | 64 | ttcgcaaacgcgtgcatgctgttggc-(N)323-TTG | XopE3 | 55.4% | 97.8% | [Genbank:ZP_08184849] | X. gardneri | 78.5% |
| [Genbank:O1K_20482] | 492 bp to 5' side | 2578 AA | 64 | ttggcggccacgtgccgacgttgcc-(N)244-ATG | XopAD | 53.4% | 86.0% | [Genbank:ZP_09295361] | Mesorhizobium | 56.4% |
| [Genbank:O1K_01564] | 507 bp to 5' side | 570 AA | 56 | ttcggcaaacccactacgccttcgc-(N)222-ATG | XopD | 46.9% | 78.2% | [Genbank:EGH27374] | Pseudomonas | 55.7% |
| [Genbank:O1K_01569, Genbank: O1K_01579]a | 975 bp to 5' side | 580 AA | 56 | ttcggcaaacccactacgccttcgc-(N)222-ATG | XopD | 47.8% | 78.2% | [Genbank:EGH27374] | Pseudomonas | 54.7% |
| [Genbank:O1K_01589] | 399 bp to 5' side | 583 AA | 57 | ttcggcaaagccgctacgccttcgc-(N)206-ATG | XopD | 47.9% | 78.2% | [Genbank:EGH27374] | Pseudomonas | 55.1% |
| [Genbank:O1K_02164] | 453 bp to 5' side | 666 AA | 56 | ttcggcaagcccgctacgccttcgc-(N)193-ATG | XopD | 49.3% | 78.2% | [Genbank:EGH27374] | Pseudomonas | 53.2% |
| [Genbank:O1K_03146] | 633 bp to 5' side | 860 AA | 57 | ttcggcaaacctgctacgccttcgc-(N)156-ATG | XopD | 52.0% | 78.2% | [Genbank:EGH27374] | Pseudomonas | 47.8% |
| [Genbank:O1K_03991] | 342 bp to 5' side | 584 AA | 55 | XopD | 47.9% | 78.2% | [Genbank:EGH27374] | Pseudomonas | 54.0% | |
| [Genbank:O1K_13828] | 891 bp to 5' side | 675 AA | 55 | ttcggcaaacccgctacgccttcgc-(N)210-ATG | XopD | 47.5% | 78.2% | [Genbank:EGH27374] | Pseudomonas | 51.6% |
| [Genbank:O1K_20327] | 246 bp to 5' side | 619 AA | 56 | ttcggcaaacccgttacgccttcgc-(N)224-ATG | XopD | 47.9% | 78.2% | [Genbank:EGH27374] | Pseudomonas | 55.8% |
Overview of possible new type III secretion effectors in X. fragariae LMG 25863 together with their Genbank accessions, protein length in amino acids, %GC-content of the coding DNA sequences, and possible Plant-Inducible-Promoter (PIP) boxes. Putative start-codons of most open reading frames were moved from the start as identified by PGAAP as indicated in the table. The pairwise protein sequence similarity between each new Xf-effector and the most closely related Xanthomonas effector class is compared with the lowest pairwise similarity observed within this effector class. Finally, the accession number of the best protein blast match in Genbank for each putative new Xf-effector is given together with the organism it comes from, and its pairwise protein sequence similarity with the Xf-effector. aO1K_01579 is a possible incorrect double of O1K_01569, created by incorrect sequence assembly.