A phylogenomic analysis of the Actinomycetales mce operons

Casali, Nicola; Riley, Lee W

doi:10.1186/1471-2164-8-60

BMC Genomics

Table 3 Classification of Actinomycetales yrbE and mce genes ^a

From: A phylogenomic analysis of the Actinomycetales mce operons

Prefix^b	yrbE1A	yrbE1B	mce1A	mce1B	mce1C	mce1D	mce1E	mce1F
Rv	0167	0168	0169	0170	0171	0172	0173	0174
MT	0176	0177r^c	0178	0179	0180	0181	0182	0183
Mb	0173	0174	0175	0176	0177	0178	0179	0180
ML	2587	2588	2589	2590	2591	2592	2593	2594
MAP	3602	3603	3604	3605	3606	3607	3608	3609
MSMEG	0126	0127	0128	0129	0130	0131	0132	0133
	*yrbE2A*	*yrbE2B*	*mce2A*	*mce2B*	*mce2C*	*mce2D*	*mce2E*	*mce2F*
Rv	0587	0588	0589	0590	0591	0592	0593	0594
MT	0616	0617	0618	0619	0621	0622	0623	0624
Mb	0602	0603	0604	0605	0606	0607	0609	0610
MAP	4082	4083	4084	4085	4086	4087	4088	4089
	*yrbE3A*	*yrbE3B*	*mce3A*	*mce3B*	*mce3C*	*mce3D*	*mce3E*	*mce3F*
Rv	1964	1965	1966	1967	1968	1969	1970	1971
MT	2016	2017	2018	2019	2020	2021	2022	2023
Mb	1999
MAP	2117c	2117c.1^d	2116c	2115c	2114c	2113c	2112c	2111c
MSMEG	0335	0336^e	0337	0338	0339	0340	0341	0342
	*yrbE4A*	*yrbE4B*	*mce4A*	*mce4B*	*mce4C*	*mce4D*	*mce4E*	*mce4F*
Rv	3451c	3450c	3499c	3498c	3497c	3496c	3495c	3494c
MT	3605	3604	3603	3602	3601	3600	3599	3598
Mb	3531c	3530c	3529c	3528c	3527c	3526c	3525c	3524c
MAP	0562	0563	0564	0565	0566	0567	0568	0569
MSMEG	5861	5860	5859.3^e	5859.2^e	5859.1^e	5859	5858	5857.1^e
nfa	5350	5360	5370	5380	5390	5400	5410	5420
	*yrbE5A*	*yrbE5B*	*mce5A*	*mce5B*	*mce5C*	*mce5D*	*mce5E*	*mce5F*
MAP ^f	0757	0758	0759	0760	0761	0762/3^g	0764	0765
MAP			2189	2190	2191	2192	2193^h	2194
MSMEG	2855	2856	2857	2858	2859	2860	2861	2862
MSMEG ^f	4785	4784	4783	4782	meⁱ	4777	4776	4775
	*yrbE6A*	*yrbE6B*	*mce6A*	*mce6B*	*mce6C*	*mce6D*	*mce6E*	*mce6F*
nfa	51090	51080	51070	51060	51050	51040	51030	51020
SCO	5901	5900	5899	5898	5897	5896	5895	5894
SAV	2421	2420	2419	2418	2417	2416	2415	2514
	*yrbE7A*	*yrbE7B*	*mce7A*	*mce7B*	*mce7C*	*mce7D*	*mce7E*	*mce7F*
MAP ^j	meⁱ	0107	0108	0109	0110	0111	0112	0113
MAP	1849	1850	1851	1852	1853	1854	1855	1856
MSMEG ^j	1131	1132	1133	1134	1135	1136	1137	1138
nfa	50540	50530	50520	50510	50500	50490	50480	50470
nfa	56330	56320	56310	56300	56290	56280	56270	56260
	*yrbE8A*	*yrbE8B*	*mce8A*	*mce8B*	*mce8C*	*mce8D*	*mce8E*	*mce8F*
nfa	11130	11140	11150	11160	11170	11180	11190	11200
nfa	29780	29770	29760^h	29750	29740	29730	29720	29710

^a Operons mce1-4 designated as in TubercuList; mce5-8 designated herein. Gene names in organisms other than M. tuberculosis do not correspond to those given in genome annotation.
^b Organism specific gene number prefix: Rv, M. tuberculosis H37Rv; MT, M. tuberculosis CDC1551; Mb, M. bovis; ML, M. leprae; MAP, M. paratuberculosis; MSMEG, M. smegmatis; nfa, N. farcinica; SCO, S. coelicolor; SAV, S. avermitilis.
^c Orthologous sequence present, but ORF annotated in reverse direction.
^d Orthologous sequence present, but not annotated. ORF extends ~400 bp at 5'end.
^e Orthologous sequence present, but not annotated.
^f Orthology inferred from synteny.
^g Contains frameshift mutation, resulting in two ORFs.
^h Not a member of IPR003399 or IPR005693.
ⁱ Insertion of mobile element.
^j Orthology inferred from synteny.

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ISSN: 1471-2164

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