Table 2

Presence of genes in gene clusters of all available finished and unfinished genome sequences




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
A
 ABC transporter family signature, 19-27% homology
 283
 1
 Rv3866
 MT3980
 ND
 MB851A
 No sequence data


276
 2
 Rv3889c
 MT4004
 MTB12A
 MB727.3A (partly deleted #)
 No sequence data


295
 3
 Rv0289
 MT0302
 MTB203A
 MB548A
 No sequence data


-
 4
 No duplication
 No duplication
 No duplication
 No duplication
 No duplication


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


619
 2
 Rv3884c
 MT3999
 MTB12B
 MB727.1B
 No sequence data


631
 3
 Rv0282
 MT0295
 MTB23B
 MB672B
 No sequence data


-
 4
 No duplication
 No duplication
 No duplication
 No duplication
 No duplication


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


495
 2
 Rv3895c
 MT4011
 MTB136C
 MB780.1C
 No sequence data


538
 3
 Rv0283
 MT0296
 MTB23C
 MB672C
 No sequence data


470
 4
 Rv3450c
 MT3556
 MTB45C
 MB493.1C
 No sequence data


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)


1396
 2
 Rv3894c
 MT4010
 MTB3D
 MB780.1D
 No sequence data


1330
 3
 Rv0284
 MT0297
 MTB23D
 MB672D
 No sequence data


1236
 4
 Rv3447c
 MT3553
 MTB45D
 MB585.1D
 No sequence data


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


77
 2
 Rv3893c
 MT4008
 MTB3E
 MB780.1E
 No sequence data


102
 3
 Rv0285
 MT0298
 MTB23E
 MB389E
 No sequence data


-
 4
 No duplication
 No duplication
 No duplication
 No duplication
 No duplication


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


399
 2
 Rv3892c
 MT4007
 MTB3F
 MB780.1F
 No sequence data


513
 3
 Rv0286
 MT0299
 MTB472F
 MB528F
 No sequence data


-
 4
 No duplication
 No duplication
 No duplication
 No duplication
 No duplication


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


107
 2
 Rv3891c
 MT4006
 MTB12G
 MB727.3G
 No sequence data


97
 3
 Rv0287
 MT0300
 MTB472G
 MB548G
 No sequence data


125
 4
 Rv3445c
 MT3550
 MTB45G
 MB585.0G
 No sequence data


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


95
 2
 Rv3890c
 MT4005
 MTB12H
 MB727.3H
 No sequence data


96
 3
 Rv0288
 MT0301
 MTB203H
 MB548H
 No sequence data


100
 4
 Rv3444c
 MT3549
 MTB45H
 MB585.0H
 No sequence data


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


341
 2
 Rv3888c
 MT4003
 MTB12I
 Deleted #
 No sequence data


-
 3
 No duplication
 No duplication
 No duplication
 No duplication
 No duplication


-
 4
 No duplication
 No duplication
 No duplication
 No duplication
 No duplication


-
 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


509
 2
 Rv3887c
 MT4002
 MTB12J
 MB727.3J (partly deleted #)
 No sequence data


472
 3
 Rv0290
 MT0303
 MTB203J
 MB548J
 No sequence data


467
 4
 Rv3448
 MT3554
 MTB45J
 MB585.1J
 No sequence data


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


550
 2
 Rv3886c
 MT4001(Frame)
 MTB12Kb
 MB727.2K
 No sequence data


461
 3
 Rv0291
 MT0304
 MTB203K
 MB548K
 No sequence data


455
 4
 Rv3449
 MT3555
 MTB45K
 MB585.1K
 No sequence data


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


537
 2
 Rv3885c
 MT4000 (Frame)
 MTB12Lb
 MB727.2L
 No sequence data


331
 3
 Rv0292
 MT0305
 MTB203L
 MB694.0L
 No sequence data


-
 4
 No duplication
 No duplication
 No duplication
 No duplication
 No duplication


406
 5
 Rv1797
 MT1846
 MTB196L
 MB542L
 No sequence data




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


295
 3
 ML2530
 MA141A
 MP0289
 MS32A
 ND
 ND


-
 4
 No duplication
 No duplication
 No duplication
 No duplication
 No duplication
 No duplication


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


619
 2
 ML0039(pseudo)
 MA177B
 MP3884c
 ND
 ND
 ND


631
 3
 ML2537
 MA78B
 MP0282
 MS32B
 ND
 ND


-
 4
 No duplication
 No duplication
 No duplication
 No duplication
 No duplication
 No duplication






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


495
 2
 Deleted
 MA144C
 MP3895c
 ND
 ND
 ND


538
 3
 ML2536
 MA78C
 MP0283
 MS32C
 ND
 ND


470
 4
 Deleted
 MA94C
 MP3450c
 MS8C
 CORDmem
 SC3C3.07


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


1396
 2
 Deleted
 MA144D
 MP3894c
 ND
 ND
 ND


1330
 3
 ML2535
 MA78D
 MP0284
 MS32D
 ND
 ND


1236
 4
 Deleted
 MA504D
 MP3447c
 MS8D
 CORDyuk
 SC3C3.20c


435+932
 5
 ML1543
 MA221D
 MP1783
 ND
 ND
 ND
E
 PE, 18-90% homology
 99
 1
 Deleted
 ND
 ND
 MS29E
 ND
 ND


77
 2
 Deleted
 MA138E
 MP3893c
 ND
 ND
 ND


102
 3
 ML2534
 MA78E
 MP0285
 MS32E
 ND
 ND


-
 4
 No duplication
 No duplication
 No duplication
 No duplication
 No duplication
 No


99 & 99
 5
 Deleted
 MA310Ea & Eb
 MP1788 & 91
 ND
 ND
 ND
F
 PPE, 19-88% homology
 368
 1
 ML0051
 ND
 ND
 MS29F
 ND
 ND


399
 2
 Deleted
 MA138F
 MP3892c
 ND
 ND
 ND


513
 3
 ML2533 (pseudo)
 MA78F
 MP0286
 MS32F
 ND
 ND


-
 4
 No duplication
 No duplication
 No duplication
 No duplication
 No duplication
 No duplication


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


97
 3
 ML2532
 MA141G
 MP0287
 MS32G
 ND
 ND


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


96
 3
 ML2531
 MA141H
 MP0288
 MS32H
 ND
 ND


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


341
 2
 ML0035 (pseudo)
 MA138I
 MP3888c
 ND
 ND
 ND


-
 3
 No duplication
 No duplication
 No duplication
 No duplication
 No duplication
 No duplication


-
 4
 No duplication
 No duplication
 No duplication
 No duplication
 No duplication
 No duplication


-
 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


509
 2
 ML0036 (pseudo)
 MA138J
 MP3887c
 ND
 ND
 ND


472
 3
 ML2529
 MA141J
 MP0290
 MS32J
 ND
 ND


467
 4
 Deleted
 MA504J
 MP3448
 MS8J
 CORDtransporter
 SC3C3.21


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


550
 2
 ML0037 (pseudo)
 MA177K
 MP3886c
 ND
 ND
 ND


461
 3
 ML2528
 MA141K
 MP0291
 MS32K
 ND
 ND


455
 4
 Deleted
 MA439K
 MP3449
 MS8K
 CORDsub
 SC3C3.17c and SC3C3.08


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


537
 2
 ML0038 (pseudo)
 MA177L
 MP3885c
 ND
 ND
 ND


331
 3
 ML2527
 MA81L
 MP0292
 MS32L
 ND
 ND


-
 4
 No duplication
 No duplication
 No duplication
 No duplication
 No duplication
 No duplication


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)

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)

Rv3878
 Unknown, some similarity to PPE family, deleted with RD1 deletion region in M. bovis BCG (pseudogene in M. leprae)



Rv3879c
 Unknown, repetitive, highly proline-rich N-terminus, deleted with RD1 deletion region in M. bovis BCG (pseudogene in M. leprae)



Rv3880c
 Unknown (functional in M. leprae)



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)

*Names of genes of these organisms were given arbitrarily by the authors of this paper. †Gene not identified by BLAST, data obtained from [1], GenBank accession no. U34848 and AAC44033. ‡The gene is present in the sequence, but not annotated (name given arbitrarily by authors of this paper). §Genes identified by BLAST as well as data obtained from GenBank, accession no. AJ250015. Orthologs in S. coelicolor are equally similar to family G and H. ND, Not detected - not necessarily absent from genome but possibly not detected because of unfinished sequencing process. No duplication, no duplication of this gene is present in this region. No sequence data, no sequence data is available for this organism, published deletion information is included ([1] and others). Deleted, deleted from the genome of this particular species or strain (# = deleted in only some strains of this species). Frame, frameshift. Stop, in-frame stop codon. Stop$, stop codon corresponds to stop codon in M. tuberculosis H37Rv, which splits gene into Rv3870 and Rv3871. Pseudo, confirmed pseudogene due to multiple frameshifts and stop codons.

Gey van Pittius et al. Genome Biology 2001 2:research0044.1   doi:10.1186/gb-2001-2-10-research0044

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