TABLE 4.

List of functions putatively involved in promoting competition capabilities and nodule coinfection^a

COG ID	COG class(es)	COG functional category	Prokka annotation/other annotation	Biological process
COG0154	J	Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit or related amidase	Acylamidase	Aminoacyl-tRNA biosynthesis (glutaminyl-tRNAGln and l-asparaginyl-tRNAAsn)
COG0156	H	7-Keto-8-aminopelargonate synthetase or related enzyme	8-Amino-7-oxononanoate synthase	Biotin biosynthetic process
COG0242	J	Peptide deformylase	Peptide deformylase	Protein biosynthesis (cotranslational protein modification)
COG0376	P	Catalase (peroxidase I)	Catalase-peroxidase KatG	Hydrogen peroxide catabolic process; response to oxidative stress
COG0391*	GH	Archaeal 2-phospho-l-lactate transferase/bacterial gluconeogenesis factor, CofD/UPF0052 family	Putative phosphoenolpyruvate transferase FbiA	Coenzyme F420 biosynthesis
COG0410*	E	ABC-type branched-chain amino acid transport system, ATPase component	High-affinity branched-chain amino acid transport ATP-binding protein LivF	High-affinity branched-chain amino acid transport
COG0418*	F	Dihydroorotase	Dihydroorotase PyrC	Pyrimidine nucleotide biosynthesis
COG0494	V	8-Oxo-dGTP pyrophosphatase MutT and related housecleaning NTP	GDP-mannose pyrophosphatase NudK/nudix-type nucleoside diphosphatase (YffH/AdpP family)	Nucleoside phosphate metabolic process; ribose phosphate metabolic process
COG0507	L	ATP-dependent exoDNase (exonuclease V), alpha subunit, helicase superfamily I	ATP-dependent RecD-like DNA helicase	Recombinational DNA repair
COG0516	F	IMP dehydrogenase/GMP reductase	Inosine-5′-monophosphate dehydrogenase	Purine metabolism
COG0559	E	Branched-chain amino acid ABC-type transport system, permease component	High-affinity branched-chain amino acid transport system permease protein LivH	Branched-chain amino acid transport
COG0582	L	Integrase	Tyrosine recombinase XerC	Chromosome segregation; DNA recombination
COG0630	U	Type IV secretory pathway ATPase VirB11 (archaellum biosynthesis ATPase)	Type IV secretion system protein VirB11	Protein transport; infection
COG0683*	E	ABC-type branched-chain amino acid transport system, periplasmic component	Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein Brac	Branched-chain amino acid transport
COG1024*	I	Enoyl-CoA hydratase/carnitine racemase	Putative fatty acid oxidation complex subunit alpha–enoyl-CoA hydratase FadJ	Fatty acid metabolism
COG1028	IQR	NAD(P)-dependent dehydrogenase, short-chain alcohol dehydrogenase family	Putative dihydroanticapsin 7-dehydrogenase	Short-chain dehydrogenase
COG1060*	H	2-Iminoacetate synthase ThiH (tyrosine cleavage enzyme, thiamine biosynthesis)	FbiC FO synthase	Coenzyme F0 biosynthesis
COG1086	MO	NDP-sugar epimerase, includes UDP-GlcNAc-inverting 4,6-dehydratase FlaA1 and capsular polysaccharide biosynthesis protein EpsC	UDP-N-acetyl-alpha-d-glucosamine C6 dehydratase	Protein glycosylation
COG1137	M	ABC-type lipopolysaccharide export system, ATPase component	Lipopolysaccharide export system ATP-binding protein LptB	Lipopolysaccharide transmembrane transport
COG1171*	E	Threonine dehydratase	Diaminopropionate ammonia-lyase	Cellular amino acid catabolic process
COG1172	G	Ribose/xylose/arabinose/galactoside ABC-type transport system, permease component	Ribose import permease protein RbsC	Ribose transmembrane transport
COG1176	E	ABC-type spermidine/putrescine transport system, permease component I	Putrescine transport system permease protein PotH	Putrescine transport
COG1228	Q	Imidazolonepropionase or related amidohydrolase	Putative imidazolonepropionase	Nucleotide metabolism
COG1282*	C	NAD/NADP transhydrogenase beta subunit	NAD(P) transhydrogenase subunit beta PntB	Oxidation-reduction process; nicotinate and nicotinamide metabolism
COG1317	NU	Flagellar biosynthesis/type III secretory pathway protein FliH	Type III secretion protein L	Protein transport; infection
COG1478	H	F420-0:gamma-glutamyl ligase (F420 biosynthesis)	Bifunctional F420 biosynthesis protein FbiB	Coenzyme F420 biosynthesis (factor 420 polyglutamylation)
COG1529*	C	CO or xanthine dehydrogenase, Mo-binding subunit	Putative caffeine dehydrogenase subunit alpha	Oxidation-reduction process
COG1629	P	Outer membrane receptor proteins, mostly Fe transport	Heme/hemopexin utilization protein C	Siderophore transmembrane transport
COG1793	L	ATP-dependent DNA ligase	Multifunctional nonhomologous end joining protein LigD	DNA damage and repair
COG1920	H	2-Phospho-l-lactate guanylyltransferase, coenzyme F420 biosynthesis enzyme	Phosphoenolpyruvate guanylyltransferase FbiD	Coenzyme F420 biosynthesis
COG2081	R	Predicted flavoprotein YhiN	Putative protein/predicted flavoprotein (HI0933-like protein)	Unknown function
COG2898	S	Lysylphosphatidylglycerol synthetase, C-terminal domain, DUF2156 family	Putative phosphatidylglycerol lysyltransferase	Lipid metabolism
COG2948	U	Type IV secretory pathway, VirB10 components	Type IV secretion system protein VirB10	Protein transport; infection
COG3288*	C	NAD/NADP transhydrogenase alpha subunit	NAD(P) transhydrogenase subunit alpha PntA	Oxidation-reduction process; nicotinate and nicotinamide metabolism
COG3451	U	Type IV secretory pathway, VirB4 component	Type IV secretion system protein VirB4	Protein transport; infection
COG4178	R	ABC-type uncharacterized transport system, permease and ATPase components	Putative inner membrane ABC transporter ATP-binding protein YddA	Lipid transport

^aCOG description of gene hits identified by 50 top k-mers (P value 5.14 × 10⁻⁵) in the most competitive strains as single occupants and coinhabitants of mixed nodules (Sinorhizobium meliloti GR4, SM11, KH35c, KH46, AK58, and RU11/001). Function/annotation are reported according to the annotation performed with Prokka in this work and/or using original annotation. Asterisks indicate orthologous gene hits identified in both association analyses.