TABLE 2.

List of functions putatively involved in promoting competing abilities^a

COG ID	COG class(es)	COG functional category	Prokka annotation/other annotation	Biological process(es)
COG0210	L	Superfamily I DNA or RNA helicase	ATP-dependent DNA helicase PcrA	Mismatch repair, nucleotide excision repair
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
COG0624	E	Acetylornithine deacetylase/succinyl-diaminopimelate desuccinylase or related deacylase	Probable N-formyl-4-amino-5-aminomethyl-2-methylpyrimidine deformylase	Unknown function
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 NAD-dependent glycerol dehydrogenase	Glycerol metabolic process
COG1060	H	2-Iminoacetate synthase ThiH (tyrosine cleavage enzyme, thiamine biosynthesis)	FbiC F0 synthase	Coenzyme F0 biosynthesis
COG1129	G	ABC-type sugar transport system, ATPase component	Ribose import ATP-binding protein RbsA, CUT2 family	Ribose 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	Autoinducer 2 import system permease protein LsrD	AI-2 transport system
COG1282	C	NAD/NADP transhydrogenase beta subunit	NAD(P) transhydrogenase subunit beta PntB	Oxidation-reduction process; nicotinate and nicotinamide metabolism
COG1529	C	CO or xanthine dehydrogenase, Mo-binding subunit	Putative caffeine dehydrogenase subunit alpha	Oxidation-reduction process
COG1788	I	Acyl-CoA:acetate/3-ketoacid-CoA transferase, alpha subunit	Glutaconate CoA-transferase GctA subunit A	Glutamate catabolic process (via hydroxyglutarate)
COG1802	K	DNA-binding transcriptional regulator, GntR family	HTH-type transcriptional repressor RspR	DNA-binding transcriptional regulation
COG2057	I	Acyl-CoA:acetate/3-ketoacid-CoA transferase, beta subunit	Glutaconate CoA-transferase GctB subunit B	Glutamate catabolic process (via hydroxyglutarate)
COG2141	HR	Flavin-dependent oxidoreductase, luciferase family (includes alkanesulfonate monooxygenase SsuD and methylene tetrahydromethanopterin reductase)	F420-dependent glucose-6-phosphate dehydrogenase	Carbohydrate metabolic process, oxidation-reduction process
COG2188	K	DNA-binding transcriptional regulator, GntR family	Putative transcriptional repressor	DNA-binding transcriptional regulation
COG2205	T	K+-sensing histidine kinase KdpD	Two-component system sensor histidine kinase KdpD	Two-component regulatory system K+ sensing that regulates kdpABCF operon for potassium transport
COG3158	P	K+ transporter	Low affinity potassium transport system protein Kup	Potassium ion transport
COG3288	C	NAD/NADP transhydrogenase alpha subunit	NAD(P) transhydrogenase subunit alpha PntA	Oxidation-reduction process; nicotinate and nicotinamide metabolism

^aCOG description of gene hits identified by 51 k-mers (P value 1.13 × 10⁻⁴) in the most competitive strains (Sinorhizobium meliloti GR4, KH35c, KH46, SM11). Function/annotation are reported according to the annotation performed with Prokka in this work and/or using original annotation.