MSRA - SULSO - GREMLIN Contacts

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MSRA - Peptide methionine sulfoxide reductase MsrA

UniProt:	Q97Y45	Sequences: MEVATLGGGCFWCTEAVYKRVKGVISVKPGYSGGHVPNPTYEDVCTDTTGHAEVVQITFDSSIISYREILEIFFEIHDPTTLNRQGNDVGTQYRSIILYHNEEQRKIAEEMIREVEKRIGKKVVTELKPFEVFYEAEDYHHDFYDKHKYNPYCRLVISPKVKKFMKLFPDKVKIHEG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	177 (158)
Sequences:	5894 (3651)
Seq/√Len:	290.4

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
105_R	109_E	3.437	1.00
4_A	66_Y	3.281	1.00
5_T	100_H	3.269	1.00
3_V	56_Q	3.155	1.00
74_F	111_M	2.814	1.00
32_S	54_V	2.363	1.00
99_Y	105_R	2.345	1.00
112_I	127_L	2.139	1.00
28_K	133_F	2.054	1.00
36_V	43_D	1.966	1.00
28_K	135_E	1.939	1.00
99_Y	129_P	1.932	1.00
74_F	112_I	1.916	1.00
6_L	69_I	1.868	1.00
8_G	14_T	1.857	1.00
32_S	130_F	1.838	1.00
82_L	124_V	1.838	1.00
7_G	54_V	1.831	1.00
67_R	107_I	1.831	1.00
21_V	72_I	1.821	1.00
22_K	63_I	1.804	1.00
5_T	56_Q	1.800	1.00
47_D	92_Q	1.760	1.00
52_A	94_R	1.757	1.00
40_T	43_D	1.743	1.00
65_S	68_E	1.711	1.00
19_K	142_D	1.673	1.00
113_R	117_K	1.666	1.00
29_P	141_H	1.654	1.00
28_K	56_Q	1.641	1.00
21_V	64_I	1.634	1.00
97_I	108_A	1.618	1.00
14_T	76_I	1.573	1.00
52_A	128_K	1.564	1.00
102_E	105_R	1.558	1.00
19_K	145_D	1.549	1.00
2_E	104_Q	1.537	1.00
2_E	101_N	1.527	1.00
84_R	89_V	1.500	1.00
33_G	96_I	1.490	1.00
3_V	58_T	1.459	1.00
52_A	96_I	1.455	1.00
5_T	54_V	1.440	1.00
67_R	110_E	1.427	1.00
106_K	110_E	1.424	1.00
26_S	58_T	1.417	1.00
81_T	84_R	1.394	1.00
77_H	95_S	1.389	1.00
5_T	32_S	1.355	1.00
71_E	111_M	1.348	1.00
34_G	51_H	1.348	1.00
28_K	58_T	1.343	1.00
11_F	31_Y	1.271	1.00
70_L	107_I	1.231	1.00
7_G	96_I	1.217	1.00
50_G	91_T	1.201	1.00
60_D	63_I	1.198	1.00
19_K	27_V	1.178	1.00
2_E	61_S	1.175	1.00
138_D	146_K	1.165	1.00
110_E	114_E	1.160	1.00
100_H	104_Q	1.146	1.00
8_G	76_I	1.145	1.00
96_I	128_K	1.144	1.00
32_S	131_E	1.138	1.00
68_E	71_E	1.121	1.00
15_E	19_K	1.114	1.00
45_C	92_Q	1.096	1.00
103_E	106_K	1.094	1.00
96_I	126_E	1.091	1.00
67_R	114_E	1.078	1.00
142_D	145_D	1.062	1.00
59_F	104_Q	1.054	1.00
100_H	130_F	1.052	1.00
99_Y	127_L	1.042	1.00
17_V	76_I	1.040	1.00
98_L	126_E	1.031	1.00
95_S	125_T	1.031	1.00
39_P	134_Y	1.025	1.00
115_V	118_R	1.014	1.00
77_H	125_T	0.990	1.00
154_R	158_S	0.987	1.00
42_E	139_Y	0.983	1.00
94_R	126_E	0.973	1.00
91_T	94_R	0.972	1.00
116_E	123_V	0.961	1.00
2_E	59_F	0.955	1.00
6_L	70_L	0.946	1.00
109_E	113_R	0.941	1.00
37_P	132_V	0.941	1.00
115_V	123_V	0.940	1.00
24_V	64_I	0.940	1.00
3_V	100_H	0.938	1.00
16_A	156_V	0.933	1.00
44_V	49_T	0.932	1.00
5_T	130_F	0.917	1.00
16_A	19_K	0.913	1.00
109_E	112_I	0.908	1.00
105_R	129_P	0.906	1.00
6_L	66_Y	0.897	1.00
31_Y	137_E	0.886	1.00
36_V	39_P	0.886	1.00
106_K	109_E	0.879	1.00
52_A	98_L	0.875	1.00
112_I	123_V	0.874	1.00
18_Y	57_I	0.869	1.00
150_N	154_R	0.866	1.00
70_L	97_I	0.866	1.00
16_A	144_Y	0.865	1.00
21_V	24_V	0.864	1.00
154_R	157_I	0.862	1.00
111_M	115_V	0.856	1.00
15_E	27_V	0.846	1.00
119_I	122_K	0.842	1.00
6_L	18_Y	0.836	1.00
102_E	106_K	0.831	1.00
108_A	127_L	0.825	1.00
66_Y	108_A	0.810	1.00
143_F	150_N	0.809	1.00
128_K	131_E	0.808	1.00
37_P	134_Y	0.802	0.99
70_L	111_M	0.802	0.99
103_E	107_I	0.801	0.99
36_V	49_T	0.801	0.99
112_I	116_E	0.801	0.99
110_E	113_R	0.800	0.99
25_I	28_K	0.794	0.99
71_E	114_E	0.787	0.99
38_N	134_Y	0.783	0.99
35_H	50_G	0.765	0.99
32_S	132_V	0.762	0.99
116_E	120_G	0.760	0.99
64_I	68_E	0.759	0.99
153_C	157_I	0.758	0.99
83_N	91_T	0.755	0.99
115_V	119_I	0.755	0.99
16_A	20_R	0.752	0.99
13_C	144_Y	0.745	0.99
87_N	156_V	0.741	0.99
83_N	89_V	0.740	0.99
67_R	111_M	0.740	0.99
151_P	154_R	0.739	0.99
2_E	103_E	0.737	0.99
87_N	159_P	0.736	0.99
67_R	71_E	0.734	0.99
43_D	48_T	0.734	0.99
116_E	122_K	0.732	0.99
81_T	124_V	0.729	0.99
81_T	89_V	0.721	0.99
14_T	17_V	0.719	0.99
148_K	151_P	0.716	0.99
20_R	145_D	0.715	0.99
109_E	127_L	0.712	0.99
17_V	72_I	0.707	0.99
142_D	146_K	0.705	0.99
72_I	75_E	0.704	0.99
87_N	155_L	0.701	0.99
25_I	58_T	0.693	0.98
36_V	51_H	0.692	0.98
72_I	76_I	0.686	0.98
43_D	49_T	0.685	0.98
29_P	142_D	0.683	0.98
24_V	57_I	0.679	0.98
30_G	133_F	0.673	0.98
114_E	117_K	0.672	0.98
56_Q	100_H	0.669	0.98
144_Y	158_S	0.667	0.98
111_M	114_E	0.665	0.98
11_F	137_E	0.663	0.98
44_V	92_Q	0.656	0.98
80_T	119_I	0.656	0.98
135_E	138_D	0.650	0.98
6_L	57_I	0.648	0.98
7_G	52_A	0.645	0.98
139_Y	147_H	0.644	0.98
151_P	155_L	0.640	0.97
66_Y	104_Q	0.637	0.97
16_A	145_D	0.636	0.97
32_S	96_I	0.634	0.97
29_P	55_V	0.633	0.97
47_D	91_T	0.629	0.97
33_G	51_H	0.627	0.97
99_Y	130_F	0.622	0.97
25_I	63_I	0.622	0.97
99_Y	108_A	0.612	0.97
107_I	111_M	0.611	0.97
27_V	55_V	0.611	0.97
70_L	74_F	0.610	0.97
73_F	95_S	0.610	0.97
102_E	129_P	0.603	0.96
33_G	98_L	0.600	0.96
156_V	159_P	0.592	0.96
113_R	116_E	0.588	0.96
147_H	150_N	0.588	0.96
114_E	118_R	0.587	0.96
101_N	104_Q	0.586	0.96
107_I	110_E	0.584	0.96
52_A	91_T	0.581	0.96
32_S	98_L	0.575	0.95
42_E	45_C	0.566	0.95
157_I	160_K	0.565	0.95
73_F	77_H	0.565	0.95
155_L	158_S	0.564	0.95
36_V	40_T	0.562	0.95
16_A	21_V	0.562	0.95
49_T	91_T	0.559	0.95
28_K	141_H	0.553	0.94
39_P	43_D	0.550	0.94
85_Q	90_G	0.550	0.94
80_T	124_V	0.548	0.94
13_C	17_V	0.548	0.94
36_V	48_T	0.546	0.94
14_T	55_V	0.546	0.94
46_T	91_T	0.545	0.94
144_Y	148_K	0.545	0.94
31_Y	45_C	0.537	0.93
16_A	153_C	0.536	0.93
46_T	49_T	0.535	0.93
45_C	87_N	0.531	0.93
14_T	73_F	0.530	0.93
78_D	84_R	0.529	0.93
82_L	91_T	0.526	0.93
156_V	160_K	0.526	0.93
44_V	47_D	0.524	0.92
52_A	95_S	0.523	0.92
40_T	45_C	0.519	0.92
24_V	27_V	0.519	0.92
6_L	97_I	0.518	0.92
87_N	154_R	0.518	0.92
17_V	156_V	0.518	0.92
150_N	155_L	0.517	0.92
31_Y	136_A	0.515	0.92
41_Y	137_E	0.514	0.92
14_T	29_P	0.511	0.92
13_C	29_P	0.502	0.91
143_F	147_H	0.500	0.91
26_S	56_Q	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	0.9096	100	0.032	Contact Map
1ff3A	5	0.9266	100	0.043	Contact Map
1fvgA	1	0.8588	100	0.05	Contact Map
4d7lA	3	0.9322	100	0.051	Contact Map
3e0mA	4	0.9831	100	0.051	Contact Map
2j89A	1	0.9492	100	0.053	Contact Map
3pimA	2	0.8644	100	0.073	Contact Map
1nwaA	1	0.8814	100	0.084	Contact Map
4gwbA	2	0.9153	100	0.091	Contact Map
4lwlA	1	0.9492	100	0.155	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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