Gene duplications in prokaryotes can be associated with environmental adaptation

Bratlie, Marit S; Johansen, Jostein; Sherman, Brad T; Huang, Da Wei; Lempicki, Richard A; Drabløs, Finn

doi:10.1186/1471-2164-11-588

BMC Genomics

Table 3 A representative subset of 6 clusters with relatively specific GO terms

From: Gene duplications in prokaryotes can be associated with environmental adaptation

Cluster 1 - COG classification C (Energy production and conversion)
GO terms	GO:0005507	copper ion binding	function
	GO:0043167	ion binding	function
	GO:0043169	cation binding	function
	GO:0046872	metal ion binding	function
	GO:0046914	transition metal ion binding	function
Organisms	Dinoroseobacter_shibae_DFL_12	bacteria	Alphaprot.
	Mycobacterium_gilvum_PYR-GCK	bacteria	Actinobac.
	Nitrobacter_hamburgensis_X14	bacteria	Alphaprot.
Cluster 2 - COG classification N (Cell motility and secretion)
GO terms	GO:0009288	bacterial-type flagellum	component
	GO:0019861	flagellum	component
	GO:0042995	cell projection	component
	GO:0044460	flagellum part	component
	GO:0044461	bacterial-type flagellum part	component
	GO:0044463	cell projection part	component
Organisms	Alkaliphilus_metalliredigens_QYMF	bacteria	Firmicutes
	Desulfovibrio_desulfuricans_G20	bacteria	Deltaprot.
	Magnetococcus_MC-1	bacteria	Other Bacteria
	Xanthomonas_oryzae_PXO99A	bacteria	Gammaprot.
Cluster 3 - COG classification R (General function prediction only)
GO terms	GO:0004553	hydrolase activity, hydrolyzing O-glycosyl compounds	function
	GO:0016798	hydrolase activity, acting on glycosyl bonds	function
Organisms	Anaerocellum_thermophilum_DSM_6725	bacteria	Firmicutes
	Escherichia_coli_O157_H7_EC4115	bacteria	Gammaprot.
	Escherichia_coli_O157H7	bacteria	Gammaprot.
	Sodalis_glossinidius_morsitans	bacteria	Gammaprot.
	Streptococcus_pyogenes_MGAS315	bacteria	Firmicutes
	Streptococcus_pyogenes_SSI-1	bacteria	Firmicutes
	Streptomyces_coelicolor	bacteria	Actinobac.
Cluster 4 - COG classification L (DNA replication, recombination and repair)
GO terms	GO:0008168	methyltransferase activity	function
	GO:0008757	S-adenosylmethionine-dependent methyltransferase activity	function
	GO:0009008	DNA-methyltransferase activity	function
	GO:0016741	transferase activity, transferring one-carbon groups	function
Organisms	Bartonella_tribocorum_CIP_105476	bacteria	Alphaprot.
	Cyanothece_PCC_7424	bacteria	Cyanobac.
	Frankia_EAN1pec	bacteria	Actinobac.
	Orientia_tsutsugamushi_Boryong	bacteria	Alphaprot.
	Orientia_tsutsugamushi_Ikeda	bacteria	Alphaprot.
Cluster 5 - COG classification P (Inorganic ion transport and metabolism)
GO terms	GO:0006811	ion transport	process
	GO:0006812	cation transport	process
	GO:0015674	di-, tri-valent inorganic cation transport	process
Organisms	Escherichia_coli_K_12_substr__DH10B	bacteria	Gammaprot.
	Methanosarcina_barkeri_fusaro	archaea	Euryarchaeota
	Ralstonia_metallidurans_CH34	bacteria	Betaprot.
Cluster 6 - COG classification D (Cell division and chromosome partitioning)
GO terms	GO:0004359	glutaminase activity	function
	GO:0042242	cobyrinic acid a, c-diamide synthase activity	function
Organisms	Borrelia_burgdorferi_ZS7	bacteria	Spirochaetes
	Halobacterium_sp	archaea	Euryarchaeota
	Methanosarcina_barkeri_fusaro	archaea	Euryarchaeota
	Xanthobacter_autotrophicus_Py2	bacteria	Alphaprot.

The cluster numbering is for local reference only. The COG classification, based on the most represented COG category in each cluster (see Methods), is shown in the heading of each cluster. The table shows GO number, description and ontology for each GO term, and name, kingdom, and group for each species.

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ISSN: 1471-2164

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