MSRA - ECOLI - GREMLIN Contacts

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MSRA - Peptide methionine sulfoxide reductase MsrA

UniProt:	P0A744	Sequences: MSLFDKKHLVSPADALPGRNTPMPVATLHAVNGHSMTNVPDGMEIAIFAMGCFWGVERLFWQLPGVYSTAAGYTGGYTPNPTYREVCSGDTGHAEAVRIVYDPSVISYEQLLQVFWENHDPAQGMRQGNDHGTQYRSAIYPLTPEQDAAARASLERFQAAMLAADDDRHITTEIANATPFYYAEDDHQQYLHKNPYGYCGIGGIGVCLPPEA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11433
Length:	212 (165)
Sequences:	3356 (2212)
Seq/√Len:	172.2

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
147_D	151_R	3.642	1.00
46_A	108_Y	3.510	1.00
47_I	142_L	3.407	1.00
116_W	153_S	3.054	1.00
45_I	98_R	3.004	1.00
141_P	147_D	2.730	1.00
70_A	180_F	2.436	1.00
48_F	111_L	2.354	1.00
74_T	96_A	2.323	1.00
49_A	96_A	2.211	1.00
154_L	174_I	2.170	1.00
78_T	85_E	2.161	1.00
44_E	143_T	2.153	1.00
89_G	134_Q	2.125	1.00
124_G	171_T	2.108	1.00
50_M	56_V	2.055	1.00
141_P	176_N	2.017	1.00
63_L	114_V	2.007	1.00
43_M	67_Y	1.997	1.00
75_G	138_A	1.933	1.00
56_V	118_N	1.893	1.00
116_W	154_L	1.865	1.00
109_E	149_A	1.856	1.00
63_L	106_I	1.835	1.00
47_I	98_R	1.785	1.00
53_F	73_Y	1.778	1.00
74_T	177_A	1.776	1.00
64_P	105_V	1.741	1.00
94_A	138_A	1.697	1.00
44_E	146_Q	1.690	1.00
126_R	131_H	1.651	1.00
94_A	136_R	1.649	1.00
139_I	150_A	1.587	1.00
47_I	96_A	1.571	1.00
109_E	152_A	1.571	1.00
44_E	101_Y	1.567	1.00
70_A	98_R	1.554	1.00
47_I	74_T	1.521	1.00
82_T	85_E	1.503	1.00
94_A	175_A	1.489	1.00
119_H	137_S	1.465	1.00
107_S	110_Q	1.465	1.00
70_A	182_Y	1.453	1.00
144_P	147_D	1.446	1.00
155_E	159_A	1.444	1.00
112_L	149_A	1.440	1.00
123_Q	126_R	1.424	1.00
50_M	118_N	1.406	1.00
48_F	60_F	1.394	1.00
84_R	186_D	1.381	1.00
70_A	100_V	1.368	1.00
61_W	69_T	1.345	1.00
148_A	152_A	1.308	1.00
152_A	156_R	1.278	1.00
76_G	93_H	1.242	1.00
138_A	173_E	1.232	1.00
87_C	134_Q	1.230	1.00
48_F	112_L	1.227	1.00
185_D	193_K	1.226	1.00
140_Y	173_E	1.225	1.00
92_G	133_T	1.214	1.00
102_D	105_V	1.200	1.00
71_A	188_Q	1.183	1.00
151_R	154_L	1.156	1.00
48_F	108_Y	1.146	1.00
45_I	100_V	1.113	1.00
55_G	191_L	1.111	1.00
145_E	148_A	1.108	1.00
101_Y	146_Q	1.105	1.00
49_A	138_A	1.094	1.00
43_M	100_V	1.082	1.00
42_G	104_S	1.080	1.00
58_R	202_G	1.057	1.00
136_R	173_E	1.048	0.99
86_V	91_T	1.039	0.99
61_W	192_H	1.035	0.99
137_S	172_T	1.034	0.99
47_I	177_A	1.027	0.99
138_A	175_A	1.019	0.99
142_L	146_Q	1.013	0.99
119_H	172_T	1.011	0.99
151_R	155_E	1.003	0.99
158_Q	170_I	1.003	0.99
110_Q	113_Q	1.002	0.99
59_L	118_N	0.989	0.99
81_P	181_Y	0.986	0.99
61_W	189_Q	0.982	0.99
144_P	148_A	0.982	0.99
74_T	178_T	0.965	0.99
43_M	103_P	0.958	0.99
200_G	203_G	0.942	0.99
66_V	106_I	0.940	0.99
150_A	174_I	0.936	0.99
197_G	200_G	0.934	0.99
73_Y	184_E	0.909	0.99
79_P	179_P	0.902	0.98
133_T	136_R	0.897	0.98
48_F	99_I	0.894	0.98
166_D	169_H	0.894	0.98
123_Q	131_H	0.887	0.98
79_P	181_Y	0.879	0.98
39_V	182_Y	0.872	0.98
123_Q	171_T	0.871	0.98
141_P	174_I	0.866	0.98
148_A	151_R	0.863	0.98
154_L	170_I	0.849	0.98
45_I	142_L	0.844	0.98
74_T	179_P	0.843	0.98
68_S	100_V	0.837	0.97
78_T	81_P	0.834	0.97
40_P	67_Y	0.830	0.97
124_G	133_T	0.828	0.97
77_Y	92_G	0.827	0.97
157_F	170_I	0.826	0.97
175_A	178_T	0.824	0.97
147_D	176_N	0.822	0.97
58_R	191_L	0.822	0.97
112_L	139_I	0.821	0.97
78_T	91_T	0.816	0.97
142_L	177_A	0.814	0.97
49_A	94_A	0.813	0.97
108_Y	150_A	0.806	0.97
125_M	133_T	0.802	0.97
106_I	110_Q	0.796	0.97
58_R	203_G	0.796	0.97
113_Q	117_E	0.791	0.96
114_V	117_E	0.787	0.96
35_S	38_N	0.787	0.96
156_R	159_A	0.784	0.96
195_P	198_Y	0.779	0.96
58_R	199_C	0.776	0.96
115_F	137_S	0.776	0.96
98_R	142_L	0.773	0.96
71_A	189_Q	0.768	0.96
48_F	139_I	0.762	0.96
156_R	160_A	0.756	0.95
161_M	166_D	0.755	0.95
157_F	161_M	0.750	0.95
94_A	140_Y	0.750	0.95
56_V	59_L	0.744	0.95
57_E	69_T	0.738	0.95
113_Q	153_S	0.737	0.95
149_A	152_A	0.735	0.95
116_W	174_I	0.734	0.95
108_Y	146_Q	0.729	0.94
196_Y	200_G	0.721	0.94
154_L	158_Q	0.717	0.94
109_E	156_R	0.716	0.94
80_N	85_E	0.715	0.94
44_E	103_P	0.707	0.94
63_L	66_V	0.704	0.93
189_Q	192_H	0.703	0.93
158_Q	169_H	0.702	0.93
55_G	71_A	0.696	0.93
53_F	184_E	0.694	0.93
67_Y	70_A	0.691	0.93
75_G	140_Y	0.690	0.93
56_V	71_A	0.690	0.93
186_D	194_N	0.689	0.93
145_E	149_A	0.688	0.93
86_V	134_Q	0.680	0.92
60_F	99_I	0.673	0.92
78_T	93_H	0.669	0.92
85_E	91_T	0.666	0.91
96_A	140_Y	0.660	0.91
153_S	157_F	0.657	0.91
85_E	90_D	0.648	0.90
197_G	201_I	0.646	0.90
59_L	62_Q	0.646	0.90
40_P	43_M	0.637	0.89
59_L	202_G	0.637	0.89
109_E	153_S	0.634	0.89
129_N	201_I	0.634	0.89
88_S	91_T	0.633	0.89
58_R	61_W	0.632	0.89
91_T	133_T	0.632	0.89
194_N	198_Y	0.629	0.89
39_V	43_M	0.628	0.89
55_G	200_G	0.625	0.89
59_L	114_V	0.624	0.88
89_G	133_T	0.623	0.88
112_L	153_S	0.614	0.88
75_G	175_A	0.611	0.87
151_R	174_I	0.611	0.87
189_Q	193_K	0.610	0.87
75_G	93_H	0.606	0.87
109_E	113_Q	0.598	0.86
94_A	137_S	0.596	0.86
58_R	62_Q	0.596	0.86
149_A	153_S	0.595	0.86
78_T	82_T	0.594	0.86
129_N	196_Y	0.593	0.86
125_M	131_H	0.592	0.86
44_E	145_E	0.592	0.86
115_F	119_H	0.589	0.85
56_V	115_F	0.589	0.85
157_F	160_A	0.589	0.85
144_P	176_N	0.587	0.85
74_T	138_A	0.586	0.85
118_N	201_I	0.584	0.85
119_H	123_Q	0.580	0.85
69_T	97_V	0.580	0.85
152_A	155_E	0.579	0.84
62_Q	192_H	0.573	0.84
86_V	89_G	0.570	0.84
129_N	200_G	0.568	0.83
66_V	99_I	0.567	0.83
114_V	118_N	0.564	0.83
122_A	171_T	0.560	0.82
118_N	202_G	0.559	0.82
80_N	181_Y	0.555	0.82
112_L	116_W	0.555	0.82
140_Y	175_A	0.553	0.82
44_E	142_L	0.552	0.82
122_A	168_R	0.550	0.81
81_P	85_E	0.550	0.81
141_P	150_A	0.545	0.81
68_S	182_Y	0.545	0.81
190_Y	197_G	0.544	0.81
87_C	129_N	0.542	0.80
141_P	177_A	0.541	0.80
120_D	126_R	0.538	0.80
58_R	200_G	0.538	0.80
94_A	125_M	0.538	0.80
128_G	197_G	0.537	0.80
43_M	102_D	0.536	0.80
127_Q	136_R	0.534	0.79
190_Y	194_N	0.533	0.79
196_Y	201_I	0.532	0.79
123_Q	128_G	0.526	0.78
61_W	191_L	0.526	0.78
49_A	74_T	0.524	0.78
128_G	199_C	0.524	0.78
49_A	140_Y	0.520	0.78
194_N	197_G	0.520	0.78
39_V	68_S	0.520	0.78
153_S	156_R	0.519	0.77
63_L	110_Q	0.514	0.77
55_G	58_R	0.514	0.77
42_G	103_P	0.510	0.76
41_D	104_S	0.508	0.76
94_A	126_R	0.508	0.76
122_A	170_I	0.508	0.76
120_D	168_R	0.506	0.76
46_A	111_L	0.502	0.75
64_P	106_I	0.501	0.75
125_M	137_S	0.501	0.75
69_T	99_I	0.500	0.75

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
1ff3A	5	0.9906	100	0.051	Contact Map
4d7lA	3	0.9623	100	0.054	Contact Map
1fvgA	1	0.9009	100	0.105	Contact Map
3bqhA	1	0.7642	100	0.155	Contact Map
2j89A	1	0.8443	100	0.159	Contact Map
3e0mA	4	0.7736	100	0.17	Contact Map
3pimA	2	0.8066	100	0.177	Contact Map
1nwaA	1	0.7877	100	0.208	Contact Map
4gwbA	2	0.7689	100	0.221	Contact Map
4lwlA	1	0.7406	100	0.273	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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