Table S3. BLAST comparison of M. tuberculosis ESX region protein sequences with those of M. haemophilum.Shown are percent amino acid identities and similarities based on the BLAST results. Assignments were made taking into account both homology and gene context.

ESX-1 / ESX-2 / ESX-3 / ESX-4 / ESX-5
M. tb
H37Rv / M. haemo / M. tb
H37Rv / M. haemo / M. tb
H37Rv / M. haemo / M. tb
H37Rv / M. haemo / M. tb
H37Rv / M. haemo
Rv3864
(EspE) / Mh4230
205/391 (52%)
282/391 (64%) / Rv3884c
(EccA2) / Mh4253
373/603 (61%)
455/603 (75%) / Rv0282
(EccA3) / Mh0375
529/620 (85%)
562/620 (90%) / Rv3444c
(EsxT) / Mh0881
77/97 (79%)
87/97 (89%) / Rv1782
(EccB5) / Mh2257
437/506 (86%)
482/506 (95%)
Rv3865
(EspF) / Mh4231
52/91 (57%)
64/91 (70%) / Rv3885c
(EccE2) / Mh4254
294/524 (47%)
347/524 (66%) / Rv0283
(EccB3) / Mh0376
396/533 (74%)
436/533 (81%) / Rv3445c
(EsxU) / Mh0880
80/96 (83%)
85/96 (88%) / Rv1783
(EccC5) / Mh2258
1253/1391 (90%)
1320/1391 (94%)
Rv3866
(EspG1) / Mh4232
208/274 (75%)
243/274 (88%) / Rv3886c
(MycP2) / Mh4255
350/541 (64%)
414/541 (76%) / Rv0284
(EccC3) / Mh0377
1139/1331 (85%)
1218/1331 (91%) / Rv3446c / Mh0879
243/392 (61%)
269/392 (68%) / Rv1785c
(Cyp143) / Mh2259
324/393 (82%)
352/393 (89%)
Rv3867
(EspH) / Mh4233
104/169 (61%)
128/169 (75%) / Rv3887c
(EccD2) / Mh4256
265/511 (51%)
342/511 (66%) / Rv0285
(PE5) / Mh0378
87/101 (86%)
92/101 (91%) / Rv3447c
(EccC4) / Mh0878
866/1238 (69%)
978/1238 (78%) / Rv1786 / Mh2260
54/64 (84%)
56/64 (87%)
Rv3868
(EccA1) / Mh4234
521/573 (90%)
546/573 (95%) / Rv3888c / Mh4257
227/299 (75%)
254/299 (84%) / Rv0286
(PPE4) / Not present at locus / Rv3448
(EccD4) / Mh0877
274/471 (58%)
325/471 (69%) / Rv1787
(PPE25) / Mh2261*
230/393 (58%)
272/393 (69%)
Rv3869
(EccB1) / Mh4235
381/479 (79%)
426/479 (88%) / Rv3889c
(EspG2) / Mh4258
141/277 (50%)
184/277 (66%) / Rv0287
(EsxG) / Mh0379
71/84 (84%)
77/84 (91%) / Rv3449
(MycP4) / Mh0876
285/394 (72%)
317/394 (80%) / Rv1788
(PE18) / Not present at locus*
Rv3870
(EccCa1) / Mh4236
658/746 (88%)
693/746 (92%) / Rv3890c
(EsxC) / Mh4259
50/92 (54%)
63/92 (68%) / Rv0288
(EsxH) / Mh0380
71/96 (73%)
83/96 (86%) / Rv3450c
(EccB4) / Mh0875
340/476 (71%)
365/476 (76%) / Rv1789
(PPE26) / Mh2262*
274/412 (66%)
318/412 (77%)
Rv3871
(EccCb1) / Mh4237
502/592 (84%)
548/592 (92%) / Rv3891c
(EsxD) / Mh4260
35/95 (36%)
60/95 (63%) / Rv0289
(EspG3) / Mh0381
229/295 (77%)
252/295 (85%) / Rv1790
(PPE27) / Not present at locus*
Rv3872
(PE35) / Not present at locus / Rv3892c
(PPE69) / Mh0053
154/410 (37%)
209/410 (50%) / Rv0290
(EccD3) / Mh0382
383/471 (81%)
419/471 (88%) / Rv1791
(PE19) / Mh2263*
69/87(79%)
71/87(81%)
Rv3873
(PPE68) / Mh4238
246/371 (66%)
293/371 (78%) / Rv3893c
(PE36) / Mh0052
39/76 (51%)
46/76 (60%) / Rv0291
(MycP3) / Mh0383
312/404 (77%)
346/404 (85%) / Rv1792
(EsxM)
Pseudogene in H37Rv
due to in-frame stop codon / Mh2264
Encodes 93 amino acid
open reading frame
Rv3874
(EsxB) / Mh4239
41/97 (42%)
60/97 (61%) / Rv3894c
(EccC2) / Mh0051
807/1377 (58%)
1014/1377 (73%) / Rv0292
(EccE3) / Mh0384
214/328 (65%)
247/328 (75%) / Rv1793
(EsxN) / Mh2265
52/92 (56%)
56/92 (60%)
Rv3875
(EsxA) / Mh4240
34/84 (40%)
55/84 (65%) / Rv3895c
(EccB2) / Mh0050
311/485 (64%)
385/485 (79%) / Rv1794 / Mh2266
285/300 (95%)
295/300 (98%)
Rv3876
(EspI) / Mh4243
(truncated)
224/291 (76%)
255/291 (87%) / Rv1795
(EccD5) / Mh2267
408/503 (81%)
450/503 (89%)
Rv3877
(EccD1) / Mh4244
367/480 (76%)
412/480 (85%) / Rv1796
(MycP5) / Mh2268
449/577 (77%)
501/577 (86%)
Rv3878
(espJ) / Mh4245
113/220 (51%)
145/220 (65%) / Rv1797
(EccE5) / Mh2269
299/406 (73%)
333/406 (82%)
Rv3879c
(espK) / Mh4246
445/803 (55%)
512/803 (63%) / Rv1798
(EccA5) / Mh2270
550/595 (92%)
579/595 (97%)
Rv3880c
(espL) / Mh4249
70/108 (64%)
88/108 (81%)
Rv3881c
(espB) / Mh4250
263/467 (56%)
315/467 (67%)
Rv3882c
(EccE1) / Mh4251
336/433 (77%)
381/433 (87%)
Rv3883c
(MycP1) / Mh4252
373/446 (83%)
410/446 (91%)

* M. haemophilumlacks one pe gene and one ppe gene within the ESX-5 region as compared with M. tuberculosis, although it is difficult to define precisely which genes of this cluster are absent, as they are adjacent to one another and share homology.

3