MSRA - BACSU - GREMLIN Contacts

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MSRA - Peptide methionine sulfoxide reductase MsrA

UniProt:	P54154	Sequences: MSEKKEIATFAGGCFWCMVKPFDEQPGIEKVVSGYTGGHTENPTYEEVCSETTGHREAVQITFHPDVFPYEKLLELFWQQIDPTDAGGQFADRGSSYRAAIFYHNDKQKELAEASKQRLAESGIFKDPIVTDILKAEPFYEAEGYHQHFYKKNPAHYQRYRTGSGRAGFISEHWGAK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	177 (156)
Sequences:	5942 (3645)
Seq/√Len:	291.8

ECOLI - MSRA
BACSU - MSRA
HALSA - MSRA
SULSO - MSRA

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
109_K	113_E	3.321	1.00
9_T	104_H	3.212	1.00
8_A	70_Y	3.166	1.00
7_I	60_Q	3.025	1.00
78_W	115_S	2.749	1.00
103_Y	109_K	2.272	1.00
36_T	58_A	2.252	1.00
116_K	133_I	2.093	1.00
32_V	139_F	2.048	1.00
40_T	47_E	1.962	1.00
10_F	73_L	1.887	1.00
86_A	130_V	1.861	1.00
103_Y	135_K	1.860	1.00
78_W	116_K	1.811	1.00
5_K	29_E	1.804	1.00
25_Q	76_L	1.789	1.00
36_T	136_A	1.783	1.00
12_G	18_M	1.780	1.00
26_P	67_V	1.779	1.00
51_E	96_S	1.777	1.00
56_R	98_R	1.759	1.00
32_V	141_E	1.759	1.00
9_T	60_Q	1.755	1.00
6_E	105_N	1.739	1.00
11_A	58_A	1.711	1.00
71_E	111_L	1.700	1.00
33_S	147_Q	1.672	1.00
44_T	47_E	1.646	1.00
69_P	72_K	1.638	1.00
18_M	80_Q	1.615	1.00
32_V	60_Q	1.603	1.00
6_E	108_Q	1.587	1.00
117_Q	121_E	1.573	1.00
5_K	65_P	1.572	1.00
23_D	148_H	1.571	1.00
37_G	100_A	1.538	1.00
101_I	112_A	1.532	1.00
25_Q	68_F	1.521	1.00
71_E	114_A	1.508	1.00
106_D	109_K	1.479	1.00
56_R	134_L	1.475	1.00
110_E	114_A	1.475	1.00
23_D	151_K	1.451	1.00
88_G	93_R	1.437	1.00
85_D	88_G	1.422	1.00
56_R	100_A	1.420	1.00
38_G	55_H	1.394	1.00
81_I	99_A	1.369	1.00
32_V	62_T	1.366	1.00
7_I	62_T	1.362	1.00
9_T	58_A	1.335	1.00
15_F	35_Y	1.283	1.00
74_L	111_L	1.261	1.00
30_K	62_T	1.258	1.00
144_G	152_K	1.242	1.00
6_E	63_F	1.240	1.00
64_H	67_V	1.227	1.00
11_A	100_A	1.226	1.00
75_E	115_S	1.214	1.00
9_T	36_T	1.211	1.00
54_G	95_S	1.186	1.00
6_E	65_P	1.183	1.00
23_D	31_V	1.168	1.00
104_H	108_Q	1.135	1.00
36_T	137_E	1.119	1.00
114_A	118_R	1.119	1.00
12_G	80_Q	1.115	1.00
100_A	134_L	1.114	1.00
71_E	118_R	1.100	1.00
125_F	128_P	1.069	1.00
148_H	151_K	1.066	1.00
19_V	23_D	1.065	1.00
99_A	131_T	1.063	1.00
107_K	110_E	1.049	1.00
102_F	132_D	1.042	1.00
5_K	62_T	1.042	1.00
49_C	96_S	1.038	1.00
9_T	136_A	1.026	1.00
72_K	75_E	1.026	1.00
81_I	131_T	1.024	1.00
43_P	140_Y	0.997	1.00
100_A	132_D	0.997	1.00
103_Y	133_I	0.991	1.00
104_H	136_A	0.990	1.00
120_A	129_I	0.969	1.00
113_E	117_Q	0.968	1.00
10_F	74_L	0.955	1.00
28_I	68_F	0.954	1.00
20_K	161_R	0.954	1.00
21_P	80_Q	0.953	1.00
119_L	129_I	0.945	1.00
41_E	138_P	0.936	1.00
20_K	23_D	0.934	1.00
98_R	132_D	0.928	1.00
63_F	108_Q	0.926	1.00
7_I	104_H	0.925	1.00
48_V	53_T	0.916	1.00
46_E	145_Y	0.913	1.00
95_S	98_R	0.912	1.00
10_F	70_Y	0.903	1.00
70_Y	112_A	0.902	1.00
35_Y	143_E	0.901	1.00
22_F	61_I	0.889	1.00
41_E	140_Y	0.888	1.00
159_R	162_T	0.880	1.00
106_D	110_E	0.877	1.00
10_F	22_F	0.867	1.00
56_R	102_F	0.861	1.00
40_T	43_P	0.860	1.00
109_K	135_K	0.858	1.00
115_S	119_L	0.855	1.00
149_F	156_H	0.848	1.00
91_A	160_Y	0.827	1.00
74_L	101_I	0.827	1.00
113_E	116_K	0.826	1.00
116_K	129_I	0.825	1.00
110_E	113_E	0.823	1.00
20_K	150_Y	0.822	1.00
25_Q	28_I	0.820	1.00
40_T	53_T	0.813	1.00
6_E	107_K	0.803	0.99
68_F	72_K	0.798	0.99
17_C	150_Y	0.797	0.99
134_L	137_E	0.794	0.99
36_T	138_P	0.789	0.99
75_E	118_R	0.784	0.99
19_V	31_V	0.782	0.99
116_K	120_A	0.781	0.99
112_A	133_I	0.781	0.99
114_A	117_Q	0.768	0.99
47_E	52_T	0.768	0.99
39_H	54_G	0.768	0.99
107_K	111_L	0.767	0.99
42_N	140_Y	0.766	0.99
87_G	95_S	0.763	0.99
21_P	76_L	0.756	0.99
74_L	115_S	0.751	0.99
28_I	61_I	0.749	0.99
156_H	159_R	0.748	0.99
24_E	151_K	0.747	0.99
155_A	159_R	0.745	0.99
85_D	130_V	0.738	0.99
71_E	115_S	0.737	0.99
76_L	79_Q	0.724	0.99
29_E	32_V	0.724	0.99
10_F	61_I	0.720	0.99
18_M	21_P	0.718	0.99
119_L	124_I	0.713	0.99
85_D	93_R	0.712	0.99
120_A	128_P	0.710	0.99
87_G	93_R	0.709	0.99
71_E	75_E	0.707	0.99
15_F	143_E	0.698	0.99
158_Q	162_T	0.694	0.99
76_L	80_Q	0.693	0.99
113_E	133_I	0.692	0.99
33_S	148_H	0.680	0.98
34_G	139_F	0.677	0.98
47_E	53_T	0.676	0.98
20_K	24_E	0.675	0.98
118_R	121_E	0.675	0.98
141_E	144_G	0.674	0.98
40_T	55_H	0.671	0.98
115_S	118_R	0.669	0.98
77_F	99_A	0.668	0.98
20_K	151_K	0.665	0.98
48_V	96_S	0.662	0.98
74_L	78_W	0.660	0.98
60_Q	104_H	0.659	0.98
21_P	161_R	0.655	0.98
156_H	160_Y	0.641	0.98
37_G	55_H	0.641	0.98
29_E	62_T	0.637	0.97
50_S	53_T	0.636	0.97
148_H	152_K	0.633	0.97
120_A	124_I	0.630	0.97
20_K	158_Q	0.630	0.97
70_Y	108_Q	0.628	0.97
33_S	59_V	0.625	0.97
37_G	102_F	0.624	0.97
84_T	125_F	0.623	0.97
111_L	115_S	0.621	0.97
11_A	56_R	0.619	0.97
150_Y	154_P	0.614	0.97
111_L	114_A	0.610	0.97
36_T	100_A	0.603	0.96
51_E	95_S	0.603	0.96
84_T	130_V	0.599	0.96
145_Y	153_N	0.596	0.96
91_A	159_R	0.590	0.96
29_E	67_V	0.590	0.96
91_A	161_R	0.586	0.96
77_F	81_I	0.586	0.96
20_K	25_Q	0.583	0.96
35_Y	49_C	0.582	0.96
17_C	21_P	0.581	0.96
103_Y	112_A	0.580	0.96
17_C	33_S	0.578	0.96
105_N	108_Q	0.576	0.95
18_M	59_V	0.575	0.95
53_T	95_S	0.575	0.95
36_T	102_F	0.574	0.95
157_Y	160_Y	0.571	0.95
28_I	31_V	0.570	0.95
103_Y	136_A	0.570	0.95
117_Q	120_A	0.568	0.95
106_D	135_K	0.568	0.95
43_P	47_E	0.567	0.95
50_S	95_S	0.566	0.95
31_V	59_V	0.560	0.95
40_T	44_T	0.559	0.95
56_R	99_A	0.553	0.94
89_Q	94_G	0.551	0.94
82_D	88_G	0.550	0.94
49_C	91_A	0.544	0.94
153_N	156_H	0.544	0.94
86_A	95_S	0.541	0.94
149_F	153_N	0.539	0.94
56_R	95_S	0.537	0.93
158_Q	161_R	0.536	0.93
82_D	127_D	0.536	0.93
26_P	68_F	0.534	0.93
18_M	77_F	0.532	0.93
44_T	49_C	0.529	0.93
85_D	125_F	0.516	0.92
102_F	134_L	0.515	0.92
49_C	160_Y	0.515	0.92
56_R	87_G	0.514	0.92
26_P	29_E	0.512	0.92
30_K	141_E	0.511	0.92
18_M	33_S	0.508	0.91
46_E	49_C	0.503	0.91
10_F	101_I	0.501	0.91
154_P	159_R	0.500	0.91

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
3bqhA	1	0.9153	100	0.049	Contact Map
3e0mA	4	0.9605	100	0.057	Contact Map
1ff3A	5	0.9605	100	0.059	Contact Map
1fvgA	1	0.8927	100	0.06	Contact Map
4d7lA	3	0.9661	100	0.075	Contact Map
3pimA	2	0.887	100	0.077	Contact Map
2j89A	1	0.9718	100	0.079	Contact Map
1nwaA	1	0.9153	100	0.086	Contact Map
4gwbA	2	0.9209	100	0.103	Contact Map
4lwlA	1	0.9209	100	0.171	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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