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Table 6 Potential new type III secretion effectors found in X. fragariae LMG 25863

From: Draft genome sequence of Xanthomonas fragariaereveals reductive evolution and distinct virulence-related gene content

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%

  1. 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.
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BMC Genomics

ISSN: 1471-2164

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