6.3.1.1	aspartate-ammonia ligase	-	
6.3.1.10	adenosylcobinamide-phosphate synthase	-	
6.3.1.11	glutamate-putrescine ligase	-	
6.3.1.12	D-aspartate ligase	-	
6.3.1.13	L-cysteine:1D-myo-inositol 2-amino-2-deoxy-alpha-D-glucopyranoside ligase	-	
6.3.1.14	diphthine-ammonia ligase	-	
6.3.1.15	8-demethylnovobiocic acid synthase	-	
6.3.1.16	carbapenam-3-carboxylate synthetase	transferred to EC 6.3.3.6	
6.3.1.17	beta-citrylglutamate synthase	-	
6.3.1.18	gamma-glutamylanilide synthase	-	
6.3.1.19	prokaryotic ubiquitin-like protein ligase	-	
6.3.1.2	glutamine synthetase	-	
6.3.1.20	lipoate-protein ligase	-	
6.3.1.21	phosphoribosylglycinamide formyltransferase 2	-	
6.3.1.3	phosphoribosyl-glycinamide synthetase	transferred to EC 6.3.4.13	
6.3.1.4	aspartate-ammonia ligase (ADP-forming)	-	
6.3.1.5	NAD+ synthase	-	
6.3.1.6	glutamate-ethylamine ligase	-	
6.3.1.7	4-methyleneglutamate-ammonia ligase	-	
6.3.1.8	glutathionylspermidine synthase	-	
6.3.1.9	trypanothione synthase	-	
6.3.2.1	pantoate-beta-alanine ligase (AMP-forming)	-	
6.3.2.10	UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase	-	
6.3.2.11	carnosine synthase	-	
6.3.2.12	dihydrofolate synthase	-	
6.3.2.13	UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase	-	
6.3.2.14	enterobactin synthase	-	
6.3.2.15	UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diamino-pimelate-D-alanyl-D-alanine ligase	deleted	
6.3.2.16	D-alanine-alanyl-poly(glycerolphosphate) ligase	-	
6.3.2.17	tetrahydrofolate synthase	-	
6.3.2.18	gamma-glutamylhistamine synthase	-	
6.3.2.19	ubiquitin-protein ligase	deleted. The ubiquitinylation process is now known to be performed by several enzymes in sequence, starting with EC 6.2.1.45 (ubiquitin-activating enzyme E1) and followed by several transfer reactions, including those of EC 2.3.2.23 (E2 ubiquitin-conjugating enzyme) and EC 2.3.2.27 (RING-type E3 ubiquitin transferase)	
6.3.2.2	glutamate-cysteine ligase	-	
6.3.2.20	indoleacetate-lysine synthetase	-	
6.3.2.21	ubiquitin-calmodulin ligase	deleted. The reaction is performed by the sequential action of EC 6.2.1.45 (ubiquitin-activating enzyme E1), several ubiquitin transferases and finally by EC 2.3.2.27 [ubiquitin transferase RING E3 (calmodulin-selective)]	
6.3.2.22	diphthine-ammonia ligase	transferred to EC 6.3.1.14	
6.3.2.23	homoglutathione synthase	-	
6.3.2.24	tyrosine-arginine ligase	-	
6.3.2.25	tubulin-tyrosine ligase	-	
6.3.2.26	N-(5-amino-5-carboxypentanoyl)-L-cysteinyl-D-valine synthase	-	
6.3.2.27	aerobactin synthase	deleted, now covered by EC 6.3.2.38 N2-citryl-N6-acetyl-N6-hydroxylysine synthase, and EC 6.3.2.39, aerobactin synthase	
6.3.2.28	L-amino-acid alpha-ligase	transferred to EC 6.3.2.49	
6.3.2.29	cyanophycin synthase (L-aspartate-adding)	-	
6.3.2.3	glutathione synthase	-	
6.3.2.30	cyanophycin synthase (L-arginine-adding)	-	
6.3.2.31	coenzyme F420-0:L-glutamate ligase	-	
6.3.2.32	coenzyme gamma-F420-2:alpha-L-glutamate ligase	-	
6.3.2.33	tetrahydrosarcinapterin synthase	-	
6.3.2.34	coenzyme F420-1:gamma-L-glutamate ligase	-	
6.3.2.35	D-alanine-D-serine ligase	-	
6.3.2.36	4-phosphopantoate-beta-alanine ligase	-	
6.3.2.37	UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-D-lysine ligase	-	
6.3.2.38	N2-citryl-N6-acetyl-N6-hydroxylysine synthase	-	
6.3.2.39	aerobactin synthase	-	
6.3.2.4	D-Alanine-D-alanine ligase	-	
6.3.2.40	cyclopeptine synthase	-	
6.3.2.41	N-acetylaspartylglutamate synthase	-	
6.3.2.42	N-acetylaspartylglutamylglutamate synthase	-	
6.3.2.43	[amino group carrier protein]-L-2-aminoadipate ligase	-	
6.3.2.44	pantoate-beta-alanine ligase (ADP-forming)	-	
6.3.2.45	UDP-N-acetylmuramate-L-alanyl-gamma-D-glutamyl-meso-2,6-diaminoheptanedioate ligase	-	
6.3.2.46	fumarate-(S)-2,3-diaminopropanoate ligase	-	
6.3.2.47	dapdiamide synthase	-	
6.3.2.48	L-arginine-specific L-amino acid ligase	-	
6.3.2.49	L-alanine-L-anticapsin ligase	-	
6.3.2.5	phosphopantothenate-cysteine ligase (CTP)	-	
6.3.2.50	tenuazonic acid synthetase	-	
6.3.2.51	phosphopantothenate-cysteine ligase (ATP)	-	
6.3.2.52	jasmonoyl-L-amino acid ligase	-	
6.3.2.53	UDP-N-acetylmuramoyl-L-alanine-L-glutamate ligase	-	
6.3.2.54	L-2,3-diaminopropanoate-citrate ligase	-	
6.3.2.55	2-[(L-alanin-3-ylcarbamoyl)methyl]-3-(2-aminoethylcarbamoyl)-2-hydroxypropanoate synthase	-	
6.3.2.56	staphyloferrin B synthase	-	
6.3.2.57	staphyloferrin A synthase	-	
6.3.2.58	D-ornithine-citrate ligase	-	
6.3.2.59	3-methyl-D-ornithine---L-lysine ligase	-	
6.3.2.6	phosphoribosylaminoimidazolesuccinocarboxamide synthase	-	
6.3.2.60	glutamate---[amino group carrier protein] ligase	-	
6.3.2.61	tubulin-glutamate ligase	-	
6.3.2.62	beta-tubulin-glutamate ligase	-	
6.3.2.7	UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-L-lysine ligase	-	
6.3.2.8	UDP-N-acetylmuramate-L-alanine ligase	-	
6.3.2.9	UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase	-	
6.3.2.B1	oligomer L-amino acid ligase	deleted, replaced by EC 6.3.2.30	
6.3.2.B10	L-asparagine:L-amino acid ligase	preliminary BRENDA-supplied EC number	
6.3.2.B11	beta-citrylglutamate synthase	preliminary BRENDA-supplied EC number	
6.3.2.B15	3-[[[(2R,3R)-3-carboxyoxiran-2-yl]carbonyl]amino]-L-alanine-L-valine ligase	preliminary BRENDA-supplied EC number	
6.3.2.B16	L-valine-specific L-amino acid ligase	preliminary BRENDA-supplied EC number	
6.3.2.B19	[LysW]-C-terminal-L-glutamate ligase	preliminary BRENDA-supplied EC number	
6.3.2.B2	murein peptide ligase	preliminary BRENDA-supplied EC number	
6.3.2.B23	3-formyl-tyrosine ligase	preliminary BRENDA-supplied EC number	
6.3.2.B24	beta-tubulin-glutamate ligase	deleted, replaced by EC 6.3.2.62, beta-tubulin-glutamate ligase	
6.3.2.B3	tubulin-glutamate ligase	deleted, replaced by EC 6.3.2.61, tubulin-glutamate ligase	
6.3.2.B4	polyglycylase	preliminary BRENDA-supplied EC number	
6.3.3.1	phosphoribosylformylglycinamidine cyclo-ligase	-	
6.3.3.2	5-formyltetrahydrofolate cyclo-ligase	-	
6.3.3.3	dethiobiotin synthase	-	
6.3.3.4	(carboxyethyl)arginine beta-lactam-synthase	-	
6.3.3.5	O-ureido-D-serine cyclo-ligase	-	
6.3.3.6	carbapenam-3-carboxylate synthase	-	
6.3.3.7	Ni-sirohydrochlorin a,c-diamide reductive cyclase	-	
6.3.4.1	GMP synthase	transferred to EC 6.3.5.2	
6.3.4.10	biotin-[propionyl-CoA-carboxylase (ATP-hydrolysing)] ligase	-	
6.3.4.11	biotin-[methylcrotonoyl-CoA-carboxylase] ligase	-	
6.3.4.12	glutamate-methylamine ligase	-	
6.3.4.13	phosphoribosylamine-glycine ligase	-	
6.3.4.14	biotin carboxylase	-	
6.3.4.15	biotin-[biotin carboxyl-carrier protein] ligase	-	
6.3.4.16	carbamoyl-phosphate synthase (ammonia)	-	
6.3.4.17	formate-dihydrofolate ligase	-	
6.3.4.18	5-(carboxyamino)imidazole ribonucleotide synthase	-	
6.3.4.19	tRNAIle-lysidine synthase	-	
6.3.4.2	CTP synthase (glutamine hydrolysing)	-	
6.3.4.20	7-cyano-7-deazaguanine synthase	-	
6.3.4.21	nicotinate phosphoribosyltransferase	-	
6.3.4.22	tRNAIle2-agmatinylcytidine synthase	-	
6.3.4.23	formate-phosphoribosylaminoimidazolecarboxamide ligase	-	
6.3.4.24	tyramine-L-glutamate ligase	-	
6.3.4.25	2-amino-2'-deoxyadenylo-succinate synthase	-	
6.3.4.3	formate-tetrahydrofolate ligase	-	
6.3.4.4	adenylosuccinate synthase	-	
6.3.4.5	argininosuccinate synthase	-	
6.3.4.6	urea carboxylase	-	
6.3.4.7	ribose-5-phosphate-ammonia ligase	-	
6.3.4.8	imidazoleacetate-phosphoribosyldiphosphate ligase	-	
6.3.4.9	biotin-[methylmalonyl-CoA-carboxytransferase] ligase	-	
6.3.5.1	NAD+ synthase (glutamine-hydrolysing)	-	
6.3.5.10	adenosylcobyric acid synthase (glutamine-hydrolysing)	-	
6.3.5.11	cobyrinate a,c-diamide synthase	-	
6.3.5.12	Ni-sirohydrochlorin a,c-diamide synthase	-	
6.3.5.13	lipid II isoglutaminyl synthase (glutamine-hydrolysing)	-	
6.3.5.2	GMP synthase (glutamine-hydrolysing)	-	
6.3.5.3	phosphoribosylformylglycinamidine synthase	-	
6.3.5.4	asparagine synthase (glutamine-hydrolysing)	-	
6.3.5.5	carbamoyl-phosphate synthase (glutamine-hydrolysing)	-	
6.3.5.6	asparaginyl-tRNA synthase (glutamine-hydrolysing)	-	
6.3.5.7	glutaminyl-tRNA synthase (glutamine-hydrolysing)	-	
6.3.5.8	aminodeoxychorismate synthase	transferred to EC 2.6.1.85	
6.3.5.9	hydrogenobyrinic acid a,c-diamide synthase (glutamine-hydrolysing)	-