Table 2.

Detrimental mutations and their corresponding stability changes that influence holoenzyme assembly, rifampin and RNA interactions.

Method	Wild-type residue	Residue position	Average stability effect	Maximum stabilizing effect	Mutant residue	Maximum destabilizing effect	Mutant residue
mCSM-Stability (ΔΔG in kcal/mol)	S	437	−0.795	−0.072	L	−1.701	H
	H	451	−1.214	−0.104	Y	−1.898	S
	G	459	−0.713	−0.381	V	−1.201	W
	P	489	−1.135	−0.507	R	−1.771	G
	K	884	−1.227	−0.190	L	−2.298	S
	H	1035	−0.419	0.600	Y	−1.421	G
mCSM-ppi (ΔΔG in kcal/mol)	S	437	−0.254	0.395	H	−0.820	R
	H	451	−0.652	−0.050	S	−1.451	M
	G	459	−0.397	0.237	H	−1.042	R
	P	489	−0.738	−0.138	W	−1.372	R
	K	884	−0.105	0.160	D	−0.685	R
	H	1035	−0.754	0.115	W	−1.726	R
mCSM-NA2 (ΔΔG in kcal/mol)	S	437	−1.538	4.922	W	−3.857	D
	H	451	−1.300	5.147	W	−3.632	D
	G	459	2.289	8.556	W	−0.221	D
	P	489	1.926	8.195	W	−0.582	D
	K	884	0.221	6.647	W	−2.130	D
	H	1035	0.847	7.295	W	−1.484	D
mCSM-lig (log-affinity change)	S	437	−0.646	−0.484	L	−1.062	R
	H	451	−0.510	−0.076	W	−0.777	E
	G	459	−0.981	−0.715	A	−1.236	R
	P	489	−0.598	−0.254	L	−0.917	R
	K	884	−0.156	−0.368	D	−0.925	R
	H	1035	−0.121	0.097	V	−0.501	E
SDM (ΔΔG in kcal/mol)	S	437	0.087	2.320	V	−1.900	P
	H	451	−0.756	1.290	L	−2.800	G
	G	459	−2.842	−1.780	V	−3.800	P
	P	489	−0.432	1.440	Y	−1.070	E
	K	884	0.108	1.270	V	−1.820	P
	H	1035	−0.200	0.590	V	−1.410	P
MAESTRO (ΔΔG in kcal/mol)	S	437	−0.21	−0.14	K	0.24	F
	H	451	−0.12	−0.05	G	0.22	R
	G	459	−0.23	−0.17	S	0.33	W
	P	489	−0.26	−0.22	H	0.31	M
	K	884	−0.20	−0.14	G	0.25	M
	H	1035	−0.27	−0.25	P	0.31	Y
CUPSAT (ΔΔG in kcal/mol)	S	437	2.70	7.98	I	−1.12	G
	H	451	2.01	6.92	W	−3.25	K
	G	459	−2.51	5.00	K	−5.53	C
	P	489	−2.76	−0.84	A	−5.47	M
	K	884	−2.99	3.42	I	−8.03	H
	H	1035	−1.07	2.15	C	−3.23	Y
Imutant 2.0 Structure (Sign of prediction)	S	437	4.05	9.00	A	1.00	F
	H	451	6.00	8.00	G	3.00	L
	G	459	6.63	9.00	N	3.00	I
	P	489	7.11	9.00	G	3.00	L
	K	884	6.42	9.00	G	2.00	M
	H	1035	4.63	8.00	G	2.00	L
PROVEAN (ΔΔG in kcal/mol)	S	437	−4.79	−3.00	A	−7.00	W
	H	451	−8.66	−5.73	Y	−10.37	C
	G	459	−8.10	−6.00	A	−10.00	L
	P	489	−9.04	−7.99	A	−10.99	F
	K	884	−5.97	−2.91	R	−7.75	C
	H	1035	−8.98	−5.79	Y	−10.61	C
Imutant 2.0 Sequence (Sign of prediction)	S	437	4.47	7.00	F	0.00	H
	H	451	3.21	7.00	P	0.00	F
	G	459	3.53	7.00	H	0.00	A
	P	489	6.89	9.00	G	5.00	L
	K	884	3.53	8.00	V	0.00	G
	H	1035	2.95	6.00	G	0.00	V
FOldX4 (ΔΔG in kcal/mol)	S	437	2.79	−1.44	I	12.39	R
	H	451	1.78	−0.74	L	4.39	W
	G	459	9.14	3.96	A	20.76	H
	P	489	3.04	2.11	N	4.79	R
	K	884	1.06	−2.12	Y	9.77	L
	H	1035	0.77	−1.47	P	5.69	Y
ENCoM (ΔΔSvib in kcal/mol/K)	S	437	−0.44	0.48	G	−1.50	W
	H	451	0.34	0.97	G	−0.46	W
	G	459	−0.91	−0.29	A	−1.55	W
	P	489	−0.16	0.14	G	−0.82	F
	K	884	0.18	0.96	G	−0.60	W
	H	1035	0.19	0.73	G	−0.26	W
DynaMut (ΔΔG in kcal/mol)	S	437	2.87	6.99	L	−2.08	G
	H	451	−0.74	2.17	Y	−3.43	T
	G	459	1.93	3.29	N	−0.25	S
	P	489	0.94	3.26	F	−0.72	S
	K	884	0.14	3.69	W	−1.87	E
	H	1035	0.21	2.38	W	−2.29	G