StralSV: assessment of sequence variability within similar 3D structures and application to polio RNA-dependent RNA polymerase

Table 1 Excerpt of sample StralSV output "matrix" file for positions 229-269 from poliovirus RdRp analysis

AA	Rname	A	V	L	I	P	M	F	W	G	S	T	C	Y	N	Q	D	E	K	R	H	X
L	229	4	0	21	10	0	0	1	0	103	0	0	0	0	0	0	0	0	0	0	4	0
F	230	0	4	4	3	0	8	127	0	0	0	0	0	5	0	0	0	0	0	0	0	4
A	231	30	0	0	0	0	0	0	0	0	116	0	2	5	0	0	4	0	0	0	0	0
F	232	8	10	7	4	0	0	34	0	0	0	49	0	140	0	0	5	0	0	0	0	0
D	233	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	272	0	0	0	0	0
Y	234	0	49	4	11	0	0	0	0	0	0	152	0	60	0	0	0	0	0	0	0	0
T	235	5	0	0	0	0	0	0	0	0	91	25	0	0	0	0	0	4	7	144	0	0
G	236	23	0	0	0	0	0	0	0	23	0	0	139	0	13	5	48	0	11	13	0	1
Y	237	4	0	0	0	0	0	152	37	4	0	0	7	28	0	0	0	0	0	0	44	0
D	238	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	268	4	0	0	0	0
A	239	41	0	0	0	0	0	0	0	14	165	56	0	0	0	0	0	0	0	0	0	0
S	240	0	0	0	0	0	0	44	0	0	37	160	0	0	18	7	0	0	0	5	0	0
L	241	0	151	20	22	0	4	0	44	0	0	0	4	0	0	16	0	0	0	0	10	0
S	242	0	0	0	0	44	0	0	0	0	24	165	10	0	3	13	0	0	4	0	10	0
P	243	0	0	0	0	37	0	0	7	44	17	0	0	0	0	10	0	142	0	20	0	0
A	244	34	7	0	8	10	0	0	44	0	14	0	4	0	114	4	12	0	6	13	0	0
W	245	10	20	48	0	0	0	10	30	0	0	0	0	0	0	0	152	0	0	0	4	0
F	246	0	4	32	140	0	14	30	0	0	0	3	4	0	0	0	0	0	0	54	0	0
E	247	19	2	0	0	0	0	0	0	0	7	0	0	0	10	12	44	18	22	145	2	0
A	248	44	135	59	10	0	0	0	0	10	0	12	5	0	5	0	0	0	0	0	1	0
L	249	20	0	30	72	0	11	0	0	0	3	0	0	0	0	0	0	145	0	0	0	0
K	250	3	0	16	14	0	10	10	0	15	0	0	29	0	0	5	0	144	20	0	0	0
M	251	11	0	0	0	0	31	0	0	0	144	0	0	3	0	0	22	20	4	0	0	4
V	252	8	27	2	168	0	0	0	0	9	0	0	0	3	0	0	0	6	0	0	0	0
L	253	0	0	52	10	0	14	0	0	0	0	0	0	140	0	7	0	0	0	0	0	0
E	254	3	13	9	0	0	0	0	0	0	0	2	0	1	0	140	16	23	7	0	1	0
K	255	12	0	0	2	0	0	0	0	0	0	4	128	7	10	0	2	1	33	3	0	0
I	256	0	0	17	14	0	0	16	0	1	0	0	85	7	0	0	0	0	0	1	0	0
G	257	0	0	0	0	0	0	0	0	20	23	0	0	7	0	0	1	0	0	0	0	0
F	258	0	0	0	0	0	0	18	0	0	0	0	0	3	0	0	0	0	0	0	0	0
G	259	0	0	0	0	0	0	0	0	14	0	0	0	0	0	0	0	0	0	0	0	0
D	260	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	14	0	0	0	0	0
R	261	0	0	0	0	0	2	0	0	2	0	0	0	0	0	0	0	0	0	14	0	0
V	262	0	46	0	2	5	0	0	0	0	7	3	0	0	0	13	0	0	4	2	0	0
D	263	2	13	0	0	0	0	0	10	0	2	5	3	0	7	12	14	0	32	0	0	0
Y	264	4	13	44	12	0	0	3	0	0	0	10	0	17	0	0	0	0	0	0	2	0
I	265	13	0	12	37	2	0	32	0	0	0	7	0	0	0	10	0	0	0	0	0	0
D	266	2	3	0	10	0	0	0	0	0	2	0	0	0	8	2	26	50	10	0	0	0
Y	267	3	0	4	0	0	0	0	0	0	2	42	0	17	10	0	16	0	0	10	7	0
L	268	0	2	63	2	0	5	0	0	0	31	0	0	2	0	0	0	0	0	0	3	2
N	269	0	13	38	3	0	10	0	0	0	3	6	15	0	13	2	0	0	0	0	0	0

The first column contains the amino acid of the query sequence at the position indicated in the second column. Each row in the table comprises a tally of the amino acids of each type (including non-standard indicated by 'X') from the corresponding positions in all qualified template fragments (positional hits). The following heading from the output provides the total number of templates searched plus other run parameters. Number of all PDB chains (SEQRES.all_list.11_03_09): 147,634; Structure: Polio RNApolym; Length: 461; MIN span: 5; Structure similarity: 55; LGA distance: 4.0; Window: 90; Legend: 's' AA reference sequence, 'd' dominant amino acid, '+' number of hits per position (max '+': n = 398).

ISSN: 1471-2105

AA	Rname	A	V	L	I	P	M	F	W	G	S	T	C	Y	N	Q	D	E	K	R	H	X
L	229	4	0	21	10	0	0	1	0	103	0	0	0	0	0	0	0	0	0	0	4	0
F	230	0	4	4	3	0	8	127	0	0	0	0	0	5	0	0	0	0	0	0	0	4
A	231	30	0	0	0	0	0	0	0	0	116	0	2	5	0	0	4	0	0	0	0	0
F	232	8	10	7	4	0	0	34	0	0	0	49	0	140	0	0	5	0	0	0	0	0
D	233	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	272	0	0	0	0	0
Y	234	0	49	4	11	0	0	0	0	0	0	152	0	60	0	0	0	0	0	0	0	0
T	235	5	0	0	0	0	0	0	0	0	91	25	0	0	0	0	0	4	7	144	0	0
G	236	23	0	0	0	0	0	0	0	23	0	0	139	0	13	5	48	0	11	13	0	1
Y	237	4	0	0	0	0	0	152	37	4	0	0	7	28	0	0	0	0	0	0	44	0
D	238	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	268	4	0	0	0	0
A	239	41	0	0	0	0	0	0	0	14	165	56	0	0	0	0	0	0	0	0	0	0
S	240	0	0	0	0	0	0	44	0	0	37	160	0	0	18	7	0	0	0	5	0	0
L	241	0	151	20	22	0	4	0	44	0	0	0	4	0	0	16	0	0	0	0	10	0
S	242	0	0	0	0	44	0	0	0	0	24	165	10	0	3	13	0	0	4	0	10	0
P	243	0	0	0	0	37	0	0	7	44	17	0	0	0	0	10	0	142	0	20	0	0
A	244	34	7	0	8	10	0	0	44	0	14	0	4	0	114	4	12	0	6	13	0	0
W	245	10	20	48	0	0	0	10	30	0	0	0	0	0	0	0	152	0	0	0	4	0
F	246	0	4	32	140	0	14	30	0	0	0	3	4	0	0	0	0	0	0	54	0	0
E	247	19	2	0	0	0	0	0	0	0	7	0	0	0	10	12	44	18	22	145	2	0
A	248	44	135	59	10	0	0	0	0	10	0	12	5	0	5	0	0	0	0	0	1	0
L	249	20	0	30	72	0	11	0	0	0	3	0	0	0	0	0	0	145	0	0	0	0
K	250	3	0	16	14	0	10	10	0	15	0	0	29	0	0	5	0	144	20	0	0	0
M	251	11	0	0	0	0	31	0	0	0	144	0	0	3	0	0	22	20	4	0	0	4
V	252	8	27	2	168	0	0	0	0	9	0	0	0	3	0	0	0	6	0	0	0	0
L	253	0	0	52	10	0	14	0	0	0	0	0	0	140	0	7	0	0	0	0	0	0
E	254	3	13	9	0	0	0	0	0	0	0	2	0	1	0	140	16	23	7	0	1	0
K	255	12	0	0	2	0	0	0	0	0	0	4	128	7	10	0	2	1	33	3	0	0
I	256	0	0	17	14	0	0	16	0	1	0	0	85	7	0	0	0	0	0	1	0	0
G	257	0	0	0	0	0	0	0	0	20	23	0	0	7	0	0	1	0	0	0	0	0
F	258	0	0	0	0	0	0	18	0	0	0	0	0	3	0	0	0	0	0	0	0	0
G	259	0	0	0	0	0	0	0	0	14	0	0	0	0	0	0	0	0	0	0	0	0
D	260	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	14	0	0	0	0	0
R	261	0	0	0	0	0	2	0	0	2	0	0	0	0	0	0	0	0	0	14	0	0
V	262	0	46	0	2	5	0	0	0	0	7	3	0	0	0	13	0	0	4	2	0	0
D	263	2	13	0	0	0	0	0	10	0	2	5	3	0	7	12	14	0	32	0	0	0
Y	264	4	13	44	12	0	0	3	0	0	0	10	0	17	0	0	0	0	0	0	2	0
I	265	13	0	12	37	2	0	32	0	0	0	7	0	0	0	10	0	0	0	0	0	0
D	266	2	3	0	10	0	0	0	0	0	2	0	0	0	8	2	26	50	10	0	0	0
Y	267	3	0	4	0	0	0	0	0	0	2	42	0	17	10	0	16	0	0	10	7	0
L	268	0	2	63	2	0	5	0	0	0	31	0	0	2	0	0	0	0	0	0	3	2
N	269	0	13	38	3	0	10	0	0	0	3	6	15	0	13	2	0	0	0	0	0	0

AA	Rname	A	V	L	I	P	M	F	W	G	S	T	C	Y	N	Q	D	E	K	R	H	X
L	229	4	0	21	10	0	0	1	0	103	0	0	0	0	0	0	0	0	0	0	4	0
F	230	0	4	4	3	0	8	127	0	0	0	0	0	5	0	0	0	0	0	0	0	4
A	231	30	0	0	0	0	0	0	0	0	116	0	2	5	0	0	4	0	0	0	0	0
F	232	8	10	7	4	0	0	34	0	0	0	49	0	140	0	0	5	0	0	0	0	0
D	233	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	272	0	0	0	0	0
Y	234	0	49	4	11	0	0	0	0	0	0	152	0	60	0	0	0	0	0	0	0	0
T	235	5	0	0	0	0	0	0	0	0	91	25	0	0	0	0	0	4	7	144	0	0
G	236	23	0	0	0	0	0	0	0	23	0	0	139	0	13	5	48	0	11	13	0	1
Y	237	4	0	0	0	0	0	152	37	4	0	0	7	28	0	0	0	0	0	0	44	0
D	238	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	268	4	0	0	0	0
A	239	41	0	0	0	0	0	0	0	14	165	56	0	0	0	0	0	0	0	0	0	0
S	240	0	0	0	0	0	0	44	0	0	37	160	0	0	18	7	0	0	0	5	0	0
L	241	0	151	20	22	0	4	0	44	0	0	0	4	0	0	16	0	0	0	0	10	0
S	242	0	0	0	0	44	0	0	0	0	24	165	10	0	3	13	0	0	4	0	10	0
P	243	0	0	0	0	37	0	0	7	44	17	0	0	0	0	10	0	142	0	20	0	0
A	244	34	7	0	8	10	0	0	44	0	14	0	4	0	114	4	12	0	6	13	0	0
W	245	10	20	48	0	0	0	10	30	0	0	0	0	0	0	0	152	0	0	0	4	0
F	246	0	4	32	140	0	14	30	0	0	0	3	4	0	0	0	0	0	0	54	0	0
E	247	19	2	0	0	0	0	0	0	0	7	0	0	0	10	12	44	18	22	145	2	0
A	248	44	135	59	10	0	0	0	0	10	0	12	5	0	5	0	0	0	0	0	1	0
L	249	20	0	30	72	0	11	0	0	0	3	0	0	0	0	0	0	145	0	0	0	0
K	250	3	0	16	14	0	10	10	0	15	0	0	29	0	0	5	0	144	20	0	0	0
M	251	11	0	0	0	0	31	0	0	0	144	0	0	3	0	0	22	20	4	0	0	4
V	252	8	27	2	168	0	0	0	0	9	0	0	0	3	0	0	0	6	0	0	0	0
L	253	0	0	52	10	0	14	0	0	0	0	0	0	140	0	7	0	0	0	0	0	0
E	254	3	13	9	0	0	0	0	0	0	0	2	0	1	0	140	16	23	7	0	1	0
K	255	12	0	0	2	0	0	0	0	0	0	4	128	7	10	0	2	1	33	3	0	0
I	256	0	0	17	14	0	0	16	0	1	0	0	85	7	0	0	0	0	0	1	0	0
G	257	0	0	0	0	0	0	0	0	20	23	0	0	7	0	0	1	0	0	0	0	0
F	258	0	0	0	0	0	0	18	0	0	0	0	0	3	0	0	0	0	0	0	0	0
G	259	0	0	0	0	0	0	0	0	14	0	0	0	0	0	0	0	0	0	0	0	0
D	260	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	14	0	0	0	0	0
R	261	0	0	0	0	0	2	0	0	2	0	0	0	0	0	0	0	0	0	14	0	0
V	262	0	46	0	2	5	0	0	0	0	7	3	0	0	0	13	0	0	4	2	0	0
D	263	2	13	0	0	0	0	0	10	0	2	5	3	0	7	12	14	0	32	0	0	0
Y	264	4	13	44	12	0	0	3	0	0	0	10	0	17	0	0	0	0	0	0	2	0
I	265	13	0	12	37	2	0	32	0	0	0	7	0	0	0	10	0	0	0	0	0	0
D	266	2	3	0	10	0	0	0	0	0	2	0	0	0	8	2	26	50	10	0	0	0
Y	267	3	0	4	0	0	0	0	0	0	2	42	0	17	10	0	16	0	0	10	7	0
L	268	0	2	63	2	0	5	0	0	0	31	0	0	2	0	0	0	0	0	0	3	2
N	269	0	13	38	3	0	10	0	0	0	3	6	15	0	13	2	0	0	0	0	0	0

AA	Rname	A	V	L	I	P	M	F	W	G	S	T	C	Y	N	Q	D	E	K	R	H	X
L	229	4	0	21	10	0	0	1	0	103	0	0	0	0	0	0	0	0	0	0	4	0
F	230	0	4	4	3	0	8	127	0	0	0	0	0	5	0	0	0	0	0	0	0	4
A	231	30	0	0	0	0	0	0	0	0	116	0	2	5	0	0	4	0	0	0	0	0
F	232	8	10	7	4	0	0	34	0	0	0	49	0	140	0	0	5	0	0	0	0	0
D	233	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	272	0	0	0	0	0
Y	234	0	49	4	11	0	0	0	0	0	0	152	0	60	0	0	0	0	0	0	0	0
T	235	5	0	0	0	0	0	0	0	0	91	25	0	0	0	0	0	4	7	144	0	0
G	236	23	0	0	0	0	0	0	0	23	0	0	139	0	13	5	48	0	11	13	0	1
Y	237	4	0	0	0	0	0	152	37	4	0	0	7	28	0	0	0	0	0	0	44	0
D	238	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	268	4	0	0	0	0
A	239	41	0	0	0	0	0	0	0	14	165	56	0	0	0	0	0	0	0	0	0	0
S	240	0	0	0	0	0	0	44	0	0	37	160	0	0	18	7	0	0	0	5	0	0
L	241	0	151	20	22	0	4	0	44	0	0	0	4	0	0	16	0	0	0	0	10	0
S	242	0	0	0	0	44	0	0	0	0	24	165	10	0	3	13	0	0	4	0	10	0
P	243	0	0	0	0	37	0	0	7	44	17	0	0	0	0	10	0	142	0	20	0	0
A	244	34	7	0	8	10	0	0	44	0	14	0	4	0	114	4	12	0	6	13	0	0
W	245	10	20	48	0	0	0	10	30	0	0	0	0	0	0	0	152	0	0	0	4	0
F	246	0	4	32	140	0	14	30	0	0	0	3	4	0	0	0	0	0	0	54	0	0
E	247	19	2	0	0	0	0	0	0	0	7	0	0	0	10	12	44	18	22	145	2	0
A	248	44	135	59	10	0	0	0	0	10	0	12	5	0	5	0	0	0	0	0	1	0
L	249	20	0	30	72	0	11	0	0	0	3	0	0	0	0	0	0	145	0	0	0	0
K	250	3	0	16	14	0	10	10	0	15	0	0	29	0	0	5	0	144	20	0	0	0
M	251	11	0	0	0	0	31	0	0	0	144	0	0	3	0	0	22	20	4	0	0	4
V	252	8	27	2	168	0	0	0	0	9	0	0	0	3	0	0	0	6	0	0	0	0
L	253	0	0	52	10	0	14	0	0	0	0	0	0	140	0	7	0	0	0	0	0	0
E	254	3	13	9	0	0	0	0	0	0	0	2	0	1	0	140	16	23	7	0	1	0
K	255	12	0	0	2	0	0	0	0	0	0	4	128	7	10	0	2	1	33	3	0	0
I	256	0	0	17	14	0	0	16	0	1	0	0	85	7	0	0	0	0	0	1	0	0
G	257	0	0	0	0	0	0	0	0	20	23	0	0	7	0	0	1	0	0	0	0	0
F	258	0	0	0	0	0	0	18	0	0	0	0	0	3	0	0	0	0	0	0	0	0
G	259	0	0	0	0	0	0	0	0	14	0	0	0	0	0	0	0	0	0	0	0	0
D	260	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	14	0	0	0	0	0
R	261	0	0	0	0	0	2	0	0	2	0	0	0	0	0	0	0	0	0	14	0	0
V	262	0	46	0	2	5	0	0	0	0	7	3	0	0	0	13	0	0	4	2	0	0
D	263	2	13	0	0	0	0	0	10	0	2	5	3	0	7	12	14	0	32	0	0	0
Y	264	4	13	44	12	0	0	3	0	0	0	10	0	17	0	0	0	0	0	0	2	0
I	265	13	0	12	37	2	0	32	0	0	0	7	0	0	0	10	0	0	0	0	0	0
D	266	2	3	0	10	0	0	0	0	0	2	0	0	0	8	2	26	50	10	0	0	0
Y	267	3	0	4	0	0	0	0	0	0	2	42	0	17	10	0	16	0	0	10	7	0
L	268	0	2	63	2	0	5	0	0	0	31	0	0	2	0	0	0	0	0	0	3	2
N	269	0	13	38	3	0	10	0	0	0	3	6	15	0	13	2	0	0	0	0	0	0