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Table 4 Mutational analysis of the PPE39 and PPE40 genes from 15 publicly available whole genome M. tuberculosis isolates and 8 non-M. tuberculosis MTBC members.

From: Evidence for a rapid rate of molecular evolution at the hypervariable and immunogenic Mycobacterium tuberculosis PPE38 gene region

Isolate PPE39 PPE40 Comment
M. bovis Deleted downstream from position 1358. 3 bp in-frame deletion removes aa 164 (A). PPE39 part of RD5 region (Figure 3).
M. bovis BCG PPE39/40 gene fusion. 3 bp in-frame deletion seen in M. bovis PPE40 also present.   Fused PPE39/40 (Figure 3).
CPHL_A + IS6110 integration at position 47. PPE40 function predicted to be abolished.
K85 sSNP G→ T position 1548 +  
GM041182 sSNP C→ T position 1563. 33bp in-frame deletion of nucleotides 190 -- 222. Removes aa sequence AAAAAMVVAAA. PPE40 function predicted to be altered.
M. microti Deleted downstream of position 325. + PPE39 is part of the RD5micregion (Figure 3).
Oryx bacillus Deleted Deleted PPE39 and PPE40 are parts of the RD5oryxregion (Figure 3).
Dassie bacillus Deleted Gene present. Deletion analysis suggests that PPE40 is intact but exact sequence is unknown.
T17 + +  
EAS054 3 bp (GCG) in-frame deletion removes alanine at aa position 27. +  
T92 Deleted Deleted from position 1592. See Figure 3.
94_M4241A PPE39/40 gene fusion.   Fused PPE39/40 (Figure 3).
02_1987 Deleted IS6110 integration at position 47. 3' region of gene deleted. Most of genes deleted as part of major genomic structural alterations. (Figure S23).
T85 G insertion position 830, A deletion position 942. Stop codon aa position 278. + PPE39 function predicted to be abolished or highly modified.
KZN 4207 + +  
KZN 1435 + 6 nsSNPs between positions 1094 and 1105. 2 aa changes: 367 T→ N and 368 G→ N.  
KZN 605 + +  
F11 IS6110 integration at position 47. + PPE39 function predicted to be abolished.
Strain C N.D. sSNP T→ C position 969. Unable to characterise PPE39 sequence due to the numerous 'N's'. Full length gene present.
CDC1551 3 bp (GCG) in-frame deletion removes alanine at aa position 27. +  
Haarlem IS6110 integration at position 47. + PPE39 function predicted to be abolished.
H37Rv IS6110 integration at position 20. Following IS PPE39 sequence commences at position 821. + PPE39 function predicted to be abolished.
H37Ra As for H37Rv. + PPE39 function predicted to be abolished.
  1. + indicates homology to consensus sequence.