Table 2 Presence of genes in gene clusters of all available finished and unfinished genome sequences
From: The ESAT-6 gene cluster of Mycobacterium tuberculosis and other high G+C Gram-positive bacteria
| Â | Â | Â | Â | Presence and names of genes in each species | |||||
|---|---|---|---|---|---|---|---|---|---|
Gene family | Description | Protein size (in M. tb) | ESAT-6 cluster region | M. tuberculosis H37Rv | M. tuberculosis CDC1551 (CSU#93) | M. tuberculosis* 210 | M. bovis* AF2122/97 (spoligotype 9) | M. bovis* BCG Pasteur 1173P2 | Â |
A | ABC transporter family signature, 19-27% homology | 283 | 1 | Rv3866 | MT3980 | ND | MB851A | No sequence data | |
| Â | Â | 276 | 2 | Rv3889c | MT4004 | MTB12A | MB727.3A (partly deleted #) | No sequence data | |
| Â | Â | 295 | 3 | Rv0289 | MT0302 | MTB203A | MB548A | No sequence data | |
| Â | Â | - | 4 | No duplication | No duplication | No duplication | No duplication | No duplication | |
| Â | Â | 300 | 5 | Rv1794 | MT1843 | MTB196A | MB557A | No sequence data | |
B | AAA+ class ATPases, CBXX/CFQX family, SpoVK, 1× ATP/GTP-binding site, 29-39% homology | 573 | 1 | Rv3868 | MT3981 | MTB44B | MB851B | No sequence data | |
| Â | Â | 619 | 2 | Rv3884c | MT3999 | MTB12B | MB727.1B | No sequence data | |
| Â | Â | 631 | 3 | Rv0282 | MT0295 | MTB23B | MB672B | No sequence data | |
| Â | Â | - | 4 | No duplication | No duplication | No duplication | No duplication | No duplication | |
| Â | Â | 610 | 5 | Rv1798 | MT1847 | MTB196B | MB542B | No sequence data | |
C | Amino-terminal transmembrane protein, possible ATP/GTP-binding motif, 31-41% homology | 480 | 1 | Rv3869 | MT3982 | MTB44C | MB851C | No sequence data | |
| Â | Â | 495 | 2 | Rv3895c | MT4011 | MTB136C | MB780.1C | No sequence data | |
| Â | Â | 538 | 3 | Rv0283 | MT0296 | MTB23C | MB672C | No sequence data | |
| Â | Â | 470 | 4 | Rv3450c | MT3556 | MTB45C | MB493.1C | No sequence data | |
| Â | Â | 506 | 5 | Rv1782 | MT1832 | MTB46C | MB771.1C | No sequence data | |
D | DNA segregation ATPase, ftsK chromosome partitioning protein, SpoIIIE, yukA, 3× ATP/GTP-binding sites, 2× amino-terminal transmembrane protein, 28-39% homology | 747 + 591 | 1 | Rv3870+71 | MT3983+85 | MTB44Da+Db | MB851D | MB851D (partly deleted) | |
| Â | Â | 1396 | 2 | Rv3894c | MT4010 | MTB3D | MB780.1D | No sequence data | |
| Â | Â | 1330 | 3 | Rv0284 | MT0297 | MTB23D | MB672D | No sequence data | |
| Â | Â | 1236 | 4 | Rv3447c | MT3553 | MTB45D | MB585.1D | No sequence data | |
| Â | Â | 435 + 932 | 5 | Rv1783+84 | MT1833 | MTB46Da+Db | MB771.1D | No sequence data | |
E | PE, 18-90% homology | 99 | 1 | Rv3872 | MT3986 | MTB44E | MB851E | Deleted | |
| Â | Â | 77 | 2 | Rv3893c | MT4008 | MTB3E | MB780.1E | No sequence data | |
| Â | Â | 102 | 3 | Rv0285 | MT0298 | MTB23E | MB389E | No sequence data | |
| Â | Â | - | 4 | No duplication | No duplication | No duplication | No duplication | No duplication | |
| Â | Â | 99 & 99 | 5 | Rv1788 & 91 | MT1837 & 40 | MTB196Ea & Eb | MB771.0E & MB557E | No sequence data | |
F | PPE, 19-88% homology | 368 | 1 | Rv3873 | MT3987 | MTB44F | MB851F | Deleted | |
| Â | Â | 399 | 2 | Rv3892c | MT4007 | MTB3F | MB780.1F | No sequence data | |
| Â | Â | 513 | 3 | Rv0286 | MT0299 | MTB472F | MB528F | No sequence data | |
| Â | Â | - | 4 | No duplication | No duplication | No duplication | No duplication | No duplication | |
| Â | Â | 365, 393 & 350 | 5 | Rv1787 & 89 & 90 | MT1836 & 38 & 39 | MTB196Fa & Fb & Fc | MB771.0Fa & Fb & MB557F | No sequence data | |
G | lhp or CFP-10, also MTSA-10, grouped into ESAT-6 family, potent secreted T-cell antigens, 9-32% homology | 100 | 1 | Rv3874 | MT3988 | MTB44G | MB851G | Deleted | |
| Â | Â | 107 | 2 | Rv3891c | MT4006 | MTB12G | MB727.3G | No sequence data | |
| Â | Â | 97 | 3 | Rv0287 | MT0300 | MTB472G | MB548G | No sequence data | |
| Â | Â | 125 | 4 | Rv3445c | MT3550 | MTB45G | MB585.0G | No sequence data | |
| Â | Â | 98 | 5 | Rv1792 (Stop) | MT1841 (Stop) | MTB196G (Stop) | MB557G | No sequence data | |
H | ESAT-6 family, cfp7, L45 or l-esat, also Mtb9.9 family, potent secreted T-cell antigens, 15-27% homology | 95 | 1 | Rv3875 | MT3989 | MTB44H | MB851H †| Deleted | |
| Â | Â | 95 | 2 | Rv3890c | MT4005 | MTB12H | MB727.3H | No sequence data | |
| Â | Â | 96 | 3 | Rv0288 | MT0301 | MTB203H | MB548H | No sequence data | |
| Â | Â | 100 | 4 | Rv3444c | MT3549 | MTB45H | MB585.0H | No sequence data | |
| Â | Â | 94 | 5 | Rv1793 | MT1842 | MTB196H | MB557H | No sequence data | |
I | ATPases involved in chromosome partitioning, 1× ATP/GTP-binding motif, -33% homology- | 666 | 1 | Rv3876 | MT3990 | MTB60I | MB477I | Deleted | |
| Â | Â | 341 | 2 | Rv3888c | MT4003 | MTB12I | Deleted # | No sequence data | |
| Â | Â | - | 3 | No duplication | No duplication | No duplication | No duplication | No duplication | |
| Â | Â | - | 4 | No duplication | No duplication | No duplication | No duplication | No duplication | |
| Â | Â | - | 5 | No duplication | No duplication | No duplication | No duplication | No duplication | |
J | Integral inner membrane protein, binding-protein-dependent transport systems inner membrane component signature, putative transporter protein, 19-27% homology | 511 | 1 | Rv3877 | MT3991 | MTB369J | MB477J | Deleted | |
| Â | Â | 509 | 2 | Rv3887c | MT4002 | MTB12J | MB727.3J (partly deleted #) | No sequence data | |
| Â | Â | 472 | 3 | Rv0290 | MT0303 | MTB203J | MB548J | No sequence data | |
| Â | Â | 467 | 4 | Rv3448 | MT3554 | MTB45J | MB585.1J | No sequence data | |
| Â | Â | 503 | 5 | Rv1795 | MT1844 | MTB196J | MB506J | No sequence data | |
K | Mycosins, subtilisin-like cell-wall associated serine proteases, 43-49% homology | 446 | 1 | Rv3883c | MT3998 | MTB12Ka | MB727.0K | No sequence data | |
| Â | Â | 550 | 2 | Rv3886c | MT4001(Frame) | MTB12Kb | MB727.2K | No sequence data | |
| Â | Â | 461 | 3 | Rv0291 | MT0304 | MTB203K | MB548K | No sequence data | |
| Â | Â | 455 | 4 | Rv3449 | MT3555 | MTB45K | MB585.1K | No sequence data | |
| Â | Â | 585 | 5 | Rv1796 | MT1845 | MTB196K | MB506K | No sequence data | |
L | 2× amino-terminal transmembrane protein, 16-27% homology | 462 | 1 | Rv3882c | MT3997 | MTB12La | MB727.0L | No sequence data | |
| Â | Â | 537 | 2 | Rv3885c | MT4000 (Frame) | MTB12Lb | MB727.2L | No sequence data | |
| Â | Â | 331 | 3 | Rv0292 | MT0305 | MTB203L | MB694.0L | No sequence data | |
| Â | Â | - | 4 | No duplication | No duplication | No duplication | No duplication | No duplication | |
| Â | Â | 406 | 5 | Rv1797 | MT1846 | MTB196L | MB542L | No sequence data | |
| Â | Â | Â | Â | Presence and names of genes in each species | |||||
Gene family | Description | Protein size (in M. tb) | ESAT-6 cluster region | M. leprae TN | M. avium* 104 | M. paratuberculosis K 10 | M. smegmatis* MC2 155 | C. diphtheriae* NCTC13129 | S. coelicolor A3 (2) |
A | ABC transporter family signature, 19-27% homology | 283 | 1 | ML0057(pseudo) | ND | ND | MS29A | ND | ND |
|  |  | 276 | 2 | MLabc (pseudo)‡ | MA138A | MP3889c | ND | ND | ND |
| Â | Â | 295 | 3 | ML2530 | MA141A | MP0289 | MS32A | ND | ND |
| Â | Â | - | 4 | No duplication | No duplication | No duplication | No duplication | No duplication | No duplication |
| Â | Â | 300 | 5 | ML1540 | MA310A | MP1794 | ND | ND | ND |
B | AAA+ class ATPases, CBXX/CFQX family, SpoVK, 1x ATP/GTP binding site, 29-39% homology | 573 | 1 | ML0055 | ND | ND | MS29B | ND | ND |
| Â | Â | 619 | 2 | ML0039(pseudo) | MA177B | MP3884c | ND | ND | ND |
| Â | Â | 631 | 3 | ML2537 | MA78B | MP0282 | MS32B | ND | ND |
| Â | Â | - | 4 | No duplication | No duplication | No duplication | No duplication | No duplication | No duplication |
| Â | Â | 610 | 5 | ML1536 | MA310B | MP1798 | ND | ND | ND |
C | Amino-terminal transmembrane protein, possible ATP/GTP- binding motif, 31-41% homology | 480 | 1 | ML0054 | ND | ND | MS29C | ND | ND |
| Â | Â | 495 | 2 | Deleted | MA144C | MP3895c | ND | ND | ND |
| Â | Â | 538 | 3 | ML2536 | MA78C | MP0283 | MS32C | ND | ND |
| Â | Â | 470 | 4 | Deleted | MA94C | MP3450c | MS8C | CORDmem | SC3C3.07 |
| Â | Â | 506 | 5 | ML1544 | MA221C | MP1782 | ND | ND | ND |
D | DNA segregation ATPase, ftsK chromosome partitioning protein, SpoIIIE, yukA, 3× ATP/GTP-binding sites 2 × amino-terminal transmembrane protein, 28-39% homology | 747+591 | 1 | ML0053+52 | ND | ND | MS29D (Stop$) | ND | ND |
| Â | Â | 1396 | 2 | Deleted | MA144D | MP3894c | ND | ND | ND |
| Â | Â | 1330 | 3 | ML2535 | MA78D | MP0284 | MS32D | ND | ND |
| Â | Â | 1236 | 4 | Deleted | MA504D | MP3447c | MS8D | CORDyuk | SC3C3.20c |
| Â | Â | 435+932 | 5 | ML1543 | MA221D | MP1783 | ND | ND | ND |
E | PE, 18-90% homology | 99 | 1 | Deleted | ND | ND | MS29E | ND | ND |
| Â | Â | 77 | 2 | Deleted | MA138E | MP3893c | ND | ND | ND |
| Â | Â | 102 | 3 | ML2534 | MA78E | MP0285 | MS32E | ND | ND |
| Â | Â | - | 4 | No duplication | No duplication | No duplication | No duplication | No duplication | No |
| Â | Â | 99 & 99 | 5 | Deleted | MA310Ea & Eb | MP1788 & 91 | ND | ND | ND |
F | PPE, 19-88% homology | 368 | 1 | ML0051 | ND | ND | MS29F | ND | ND |
| Â | Â | 399 | 2 | Deleted | MA138F | MP3892c | ND | ND | ND |
| Â | Â | 513 | 3 | ML2533 (pseudo) | MA78F | MP0286 | MS32F | ND | ND |
| Â | Â | - | 4 | No duplication | No duplication | No duplication | No duplication | No duplication | No duplication |
| Â | Â | 365, 393 & 350 | 5 | Deleted | MA310Fa & Fb & Fc | MP1787 & 89 & 90 | ND | ND | ND |
G | lhp or CFP-10, also MTSA-10, grouped ESAT-6 family, potent secreted T-cell antigens, 9-32% homology | 100 | 1 | ML0050 | ND | ND | MS29G | ND | SC3C3.10 and SC3C3.11(c) |
|  |  | 107 | 2 | Deleted | MA138G | MP3891c § | ND | ND | ND |
| Â | Â | 97 | 3 | ML2532 | MA141G | MP0287 | MS32G | ND | ND |
| Â | Â | 125 | 4 | Deleted | MA319G | MP3445c | MS8G | CORDcfp10 | ND |
|  |  | 98 | 5 | MLcfp (pseudo)‡ | MA310G | MP1792 | ND | ND | ND |
H | ESAT-6 family, cfp7, L45 or l-esat, also Mtb9.9 family, potent secreted T-cell antigens, 15-27% homology | 95 | 1 | ML0049 | ND | ND | MS29H | ND | SC3C3.10 and SC3C3.11¶ |
|  |  | 95 | 2 | ML0034 (pseudo) | MA138H | MP3890c § | ND | ND | ND |
| Â | Â | 96 | 3 | ML2531 | MA141H | MP0288 | MS32H | ND | ND |
| Â | Â | 100 | 4 | ML0363 | MA319H | MP3444c | MS8H | CORDesat6 | ND |
|  |  | 94 | 5 | MLesat (pseudo)‡ | MA310H | MP1793 | ND | ND | ND |
I | ATPases involved in chromosome partitioning, 1x ATP/GTP-binding motif, 33% homology | 666 | 1 | ML0048 | ND | ND | MS29I | ND | SC3C3.03c |
| Â | Â | 341 | 2 | ML0035 (pseudo) | MA138I | MP3888c | ND | ND | ND |
| Â | Â | - | 3 | No duplication | No duplication | No duplication | No duplication | No duplication | No duplication |
| Â | Â | - | 4 | No duplication | No duplication | No duplication | No duplication | No duplication | No duplication |
| Â | Â | - | 5 | No duplication | No duplication | No duplication | No duplication | No duplication | No duplication |
J | Integral inner membrane protein, binding-protein-dependent transport systems inner membrane component signature, putative transporter protein, 19-27% homology | 511 | 1 | ML0047 | ND | ND | MS29J | ND | ND |
| Â | Â | 509 | 2 | ML0036 (pseudo) | MA138J | MP3887c | ND | ND | ND |
| Â | Â | 472 | 3 | ML2529 | MA141J | MP0290 | MS32J | ND | ND |
| Â | Â | 467 | 4 | Deleted | MA504J | MP3448 | MS8J | CORDtransporter | SC3C3.21 |
| Â | Â | 503 | 5 | ML1539 | MA310J | MP1795 | ND | ND | ND |
K | Mycosins, subtilisin-like cell-wall associated serine proteases, 43-49% homology | 446 | 1 | ML0041 | ND | ND | MS65K | ND | ND |
| Â | Â | 550 | 2 | ML0037 (pseudo) | MA177K | MP3886c | ND | ND | ND |
| Â | Â | 461 | 3 | ML2528 | MA141K | MP0291 | MS32K | ND | ND |
| Â | Â | 455 | 4 | Deleted | MA439K | MP3449 | MS8K | CORDsub | SC3C3.17c and SC3C3.08 |
| Â | Â | 585 | 5 | ML1538 | MA310K | MP1796 | ND | ND | ND |
L | 2× amino-terminal transmembrane protein, 16-27% homology | 462 | 1 | ML0042 | ND | ND | MS65L | ND | ND |
| Â | Â | 537 | 2 | ML0038 (pseudo) | MA177L | MP3885c | ND | ND | ND |
| Â | Â | 331 | 3 | ML2527 | MA81L | MP0292 | MS32L | ND | ND |
| Â | Â | - | 4 | No duplication | No duplication | No duplication | No duplication | No duplication | No duplication |
| Â | Â | 406 | 5 | ML1537 | MA310L | MP1797 | ND | ND | ND |
Other region-specific genes of known functions (not assigned to a family) | |||||||||
Region 5 (not present in M. smegmatis, C. diphtheriae and S. coelicolor) | Rv1785c | Probable member of the cytochrome P450 family (pseudogene in M. leprae) | |||||||
| Â | Rv1786 | Probable ferredoxin (pseudogene in M. leprae) | |||||||
Other region-specific genes of unknown functions (not assigned to a family) | |||||||||
Region 1(deleted in M. avium and M. paratuberculosis, not present in C. diphtheriae and S. coelicolor) | Rv3867 | Unknown, annotated as part of MT3980 (Rv3866) in M. tuberculosis CDC1551 sequence with a frameshift (functional in M. leprae) | |||||||
| Â | Rv3878 | Unknown, some similarity to PPE family, deleted with RD1 deletion region in M. bovis BCG (pseudogene in M. leprae) | |||||||
| Â | Â | Â | Rv3879c | Unknown, repetitive, highly proline-rich N-terminus, deleted with RD1 deletion region in M. bovis BCG (pseudogene in M. leprae) | |||||
| Â | Â | Â | Rv3880c | Unknown (functional in M. leprae) | |||||
| Â | Â | Â | Rv3881c | Unknown (pseudogene in M. leprae) | |||||
Region 4 (not present in S. coelicolor) | Rv3446c | Unknown, may contain a possible ABC transporter signature (deleted in M. leprae) | |||||||