Table 2

Examples of probable mosaic operons
Species	Predicted operon	General operon function	Horizontally acquired genes	Probable source of horizontally acquired genes	Functions of horizontally acquired genes

Cluster 1*
Rickettsia prowazekii Rickettsia conorii	RP633-661, RC0980-1008	Ribosomal operon	RP651 RC0998	Chlamydia	L29
Aquifex aeolicus	Aq001-021	Ribosomal operon	Aq018a	Archaea	L29

Cluster 2
Rickettsia prowazekii Rickettsia conorii	RP800-804, RC1234-1238	F0F1-type ATPase	RP804 RC1238 Gram-positive bacteria	Delta subunit
Ureaplasma urealyticum	UU128-138	F0F1-type ATPase	UU128, UU132_1, UU133, UU134	Gram-negative bacteria	Epsilon subunit, alpha subunit, delta subunit, delta subunit
Mycobacterium leprae	ML1139-1146	F0F1-type ATPase	ML1139	Gram-negative bacteria	A chain protein

Cluster 3
Rickettsia prowazekii Rickettsia conorii	RP134-139, RC175-180	Ribosomal proteins, transcription antiterminator, SecE	RP134 RC175	Gram-positive bacteria	Preprotein translocase subunit SecE

Cluster 5
Aquifex aeolicus	Aq1968_1_2 two domains	Histidine biosynthesis	Gram-negative bacteria	Phosphoribosyl-AMP cyclohydrolase

Cluster 8
Methanococcus jannaschii	MJ1037-1038	Tryptophan biosynthesis	MJ1037	Bacteria	Tryptophan synthase beta chain
Methanobacterium thermoautotrophicum	MTH1655-1661	Tryptophan biosynthesis	MTH1660	Gram-negative bacteria	Tryptophan synthase alpha chain
Halobacterium sp.	VNG0305-0309	Tryptophan biosynthesis	VNG0307G	Bacteria	Tryptophan synthase beta chain
Bacillus subtilis Bacillus halodurans	PabB-folK BH0090-0095	Tryptophan biosynthesis	PabB, BH0090	Gram-negative bacteria	Anthranilate/para-aminobenzoate synthases component I

Cluster 9
Halobacterium sp.	VNG0635G-0647G	NADH:ubiquinone oxidoreductase	VNG0640G	Gram-negative bacteria	NADH dehydrogenase-like protein

Cluster 18
Rickettsia prowazekii Rickettsia conorii	RP423-425, RC0588-0590	Lipid metabolism	RP425, RC0590	Spirochetes	Undecaprenyl pyrophosphate synthase

Cluster 27
Halobacterium sp.	VNG1306G-1310G	Succinate dehydrogenase/fumarate reductase	VNG1310G	Actinobacteria	Succinate dehydrogenase subunit C

Cluster 29
Mycoplasma genitalium Mycoplasma pneumoniae	MG461-466 MPN677-682	Housekeeping	MG466 MPN682	Gram-negative bacteria	Ribosomal protein L34

Cluster 34
Thermotoga maritima	TM0548-0556	Leucine/isoleucine biosynthesis	TM0552 TM0555 TM0554	2-Isopropylmalate synthase 3-Isopropylmalate dehydratase, small subunit 3-Isopropylmalate dehydratase, large subunit
Pyrococcus abyssi	PAB888-895	PAB0890 PAB0893	Bacteria	2-Isopropylmalate synthase (LeuA-1) 3-Isopropylmalate dehydrogenase (LeuB)
Clostridium acetobutylicum	CAC3169-3174	Leucine/isoleucine biosynthesis	CAC3172 CAC3173 CAC3174 Archaea	3-Isopropylmalate dehydratase, small subunit 3-Isopropylmalate dehydratase, large subunit 2-Isopropylmalate synthase

Cluster 41
Thermotoga maritima	TM1243-1251	Nucleotide metabolism	TM1243	Archaea	Phosphoribosylaminoimidazole-succinocarboxamide synthase

Cluster 42
Lactococcus lactis	L0104-0108	Arginine biosynthesis	L0107	Gram-negative bacteria	Acetylglutamate kinase
Thermotoga maritima	TM1780-1785	Arginine biosynthesis TM1784	Archaea	Acetylglutamate kinase

Cluster 48
Borrelia burgdorferi	BB0054-0061	Carbohydrate metabolism (glycolysis, gluconeogenesis)	BB0057	Gram-positive bacteria	Glyceraldehyde-3-phosphate dehydrogenase

Cluster 54
Thermotoga maritima	TM1780-1785	Arginine biosynthesis	TM1780	Gram-negative bacteria	Argininosuccinate synthase

Cluster 63
Mycoplasma pneumoniae Mycoplasma genitalium	MPN573-574 MG391-392	Molecular chaperones	MPN574 MG393	Gram-negative bacteria	Heat shock protein (groES)

Cluster 82
Mycoplasma pneumoniae, Mycoplasma genitalium	MPN535-536 MG358-359	DNA replication, recombination and repair	MPN536 MG359	Gram-negative bacteria	Holliday junction resolvasome helicase subunit
Ureaplasma urealyticum	UU448-449	DNA replication, recombination and repair	UU448	Gram-negative bacteria	Holliday junction resolvasome helicase subunit

Cluster 86
Halobacterium sp.	VNG6305CC-6306C	Tetrahydrobiopterin biosynthesis	VNG6305C	Gram-negative bacteria	Organic radical activating enzyme

Cluster 87
Halobacterium sp.	VNG0582C-0586C	Energy production and conversion	VNG0582, VNG0583G	Bacteria	Cytochrome b subunit of the bc complex Cytochrome b subunit of the bc complex

Cluster 103
Archaeoglobus fulgidus	AF0321-0325	Lipopolysaccharide biosynthesis	AF0323b	Bacteria	dTDP-4-dehydrorhamnose 3,5-epimerase and related enzymes
Deinococcus radiodurans	DRA0037-DRA0044	Lipopolysaccharide biosynthesis	DRA0044	Archaea	dTDP-4-dehydrorhamnose epimerase
Methanothermobacter thermoautotrophicus	MTH1789-1792	Lipopolysaccharide biosynthesis	MTH1789, MTH1790, MTH1791	Gram-positive bacteria Bacteria Bacteria	dTDP-D-glucose 4,6-dehydratase dTDP-4-dehydrorhamnose 3,5-epimerase dTDP-glucose pyrophosphorylase

*The numbering of gene clusters is from the previously published analysis of gene neighborhoods in prokaryotic genomes [25].
Omelchenko et al. Genome Biology 2003 4:R55 doi:10.1186/gb-2003-4-9-r55