3MGH - BACSU - GREMLIN Contacts

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3MGH - Putative 3-methyladenine DNA glycosylase

UniProt:	P94378	Sequences: MTREKNPLPITFYQKTALELAPSLLGCLLVKETDEGTASGYIVETEAYMGAGDRAAHSFNNRRTKRTEIMFAEAGRVYTYVMHTHTLLNVVAAEEDVPQAVLIRAIEPHEGQLLMEERRPGRSPREWTNGPGKLTKALGVTMNDYGRWITEQPLYIESGYTPEAISTGPRIGIDNSGEARDYPWRFWVTGNRYVSR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	196 (182)
Sequences:	1780 (1205)
Seq/√Len:	89.3

BACSU - 3MGH

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
40_G	106_I	3.733	1.00
15_K	23_S	3.494	1.00
69_I	145_Y	3.440	1.00
63_R	68_E	3.369	1.00
168_G	187_W	3.022	1.00
116_E	124_P	2.881	1.00
166_S	189_T	2.620	1.00
25_L	188_V	2.617	1.00
28_L	39_S	2.411	1.00
49_M	184_W	2.347	1.00
20_L	92_A	2.311	1.00
16_T	19_E	2.294	1.00
129_N	133_K	2.168	1.00
179_A	182_Y	2.160	1.00
90_V	156_I	2.102	1.00
27_C	158_S	2.042	1.00
28_L	109_H	2.031	1.00
81_V	84_T	2.016	1.00
18_L	186_F	1.984	1.00
15_K	20_L	1.965	1.00
10_I	148_W	1.963	1.00
86_T	142_M	1.934	1.00
38_A	118_R	1.880	1.00
81_V	132_G	1.819	1.00
33_T	36_G	1.809	1.00
77_V	88_L	1.777	1.00
54_R	179_A	1.758	1.00
41_Y	107_E	1.742	1.00
70_M	100_A	1.715	1.00
87_L	135_T	1.699	1.00
91_V	100_A	1.670	1.00
17_A	99_Q	1.653	1.00
88_L	103_I	1.648	1.00
43_V	191_N	1.633	1.00
123_S	126_E	1.621	1.00
141_T	144_D	1.617	1.00
108_P	115_M	1.580	1.00
126_E	129_N	1.551	1.00
17_A	49_M	1.506	1.00
12_F	15_K	1.500	1.00
187_W	194_V	1.488	1.00
90_V	149_I	1.485	1.00
73_E	95_E	1.466	0.99
164_A	189_T	1.464	0.99
166_S	187_W	1.463	0.99
85_H	136_K	1.435	0.99
20_L	23_S	1.429	0.99
18_L	184_W	1.423	0.99
93_A	99_Q	1.389	0.99
58_S	70_M	1.387	0.99
30_V	39_S	1.351	0.99
13_Y	156_I	1.351	0.99
88_L	140_V	1.343	0.99
58_S	98_P	1.336	0.99
144_D	147_R	1.327	0.99
69_I	146_G	1.280	0.99
31_K	144_D	1.276	0.99
82_M	87_L	1.266	0.98
72_A	76_R	1.251	0.98
17_A	93_A	1.242	0.98
173_I	180_R	1.216	0.98
42_I	103_I	1.211	0.98
65_K	68_E	1.202	0.98
74_A	94_E	1.198	0.98
37_T	110_E	1.190	0.98
22_P	167_T	1.182	0.98
41_Y	109_H	1.182	0.98
43_V	193_Y	1.161	0.97
49_M	99_Q	1.158	0.97
49_M	52_G	1.141	0.97
107_E	191_N	1.140	0.97
57_H	78_Y	1.126	0.97
13_Y	20_L	1.126	0.97
188_V	191_N	1.120	0.97
40_G	108_P	1.116	0.97
82_M	132_G	1.113	0.97
112_Q	124_P	1.102	0.96
32_E	37_T	1.098	0.96
14_Q	74_A	1.091	0.96
39_S	109_H	1.088	0.96
31_K	139_G	1.058	0.95
38_A	114_L	1.050	0.95
66_R	70_M	1.047	0.95
54_R	60_N	1.027	0.95
28_L	41_Y	1.025	0.95
55_A	175_N	1.023	0.94
126_E	133_K	1.015	0.94
39_S	110_E	1.004	0.94
77_V	148_W	0.996	0.94
56_A	100_A	0.992	0.94
54_R	175_N	0.977	0.93
120_P	123_S	0.977	0.93
73_E	76_R	0.974	0.93
22_P	186_F	0.967	0.93
44_E	102_L	0.958	0.92
79_T	86_T	0.957	0.92
16_T	49_M	0.953	0.92
54_R	174_D	0.946	0.92
55_A	181_D	0.945	0.92
40_G	115_M	0.943	0.92
111_G	115_M	0.939	0.92
128_T	137_A	0.932	0.91
77_V	154_L	0.929	0.91
82_M	85_H	0.926	0.91
10_I	73_E	0.925	0.91
41_Y	159_G	0.918	0.91
106_I	138_L	0.917	0.91
115_M	127_W	0.916	0.90
12_F	23_S	0.911	0.90
50_G	98_P	0.910	0.90
169_P	187_W	0.905	0.90
55_A	179_A	0.900	0.90
30_V	155_Y	0.900	0.90
118_R	139_G	0.889	0.89
179_A	184_W	0.884	0.89
108_P	128_T	0.859	0.87
43_V	105_A	0.857	0.87
40_G	138_L	0.856	0.87
58_S	100_A	0.856	0.87
114_L	117_E	0.855	0.87
122_R	126_E	0.854	0.87
53_D	182_Y	0.851	0.87
40_G	43_V	0.848	0.87
25_L	165_I	0.846	0.87
10_I	150_T	0.835	0.86
10_I	76_R	0.834	0.86
63_R	96_D	0.826	0.85
79_T	140_V	0.820	0.85
66_R	84_T	0.813	0.84
17_A	22_P	0.812	0.84
68_E	72_A	0.809	0.84
159_G	163_E	0.808	0.84
106_I	128_T	0.806	0.84
114_L	118_R	0.803	0.84
28_L	157_E	0.802	0.84
81_V	86_T	0.797	0.83
149_I	156_I	0.789	0.83
147_R	153_P	0.783	0.82
55_A	173_I	0.781	0.82
174_D	180_R	0.779	0.82
39_S	157_E	0.776	0.82
27_C	159_G	0.775	0.81
15_K	19_E	0.774	0.81
69_I	76_R	0.773	0.81
175_N	180_R	0.772	0.81
56_A	99_Q	0.771	0.81
33_T	114_L	0.771	0.81
12_F	20_L	0.767	0.81
31_K	38_A	0.765	0.81
17_A	92_A	0.757	0.80
103_I	134_L	0.755	0.80
79_T	142_M	0.754	0.80
132_G	135_T	0.754	0.80
111_G	119_R	0.754	0.80
36_G	114_L	0.753	0.80
142_M	145_Y	0.752	0.79
43_V	108_P	0.750	0.79
76_R	100_A	0.749	0.79
54_R	59_F	0.747	0.79
35_E	114_L	0.743	0.79
86_T	141_T	0.733	0.78
175_N	179_A	0.731	0.78
108_P	193_Y	0.731	0.78
116_E	121_G	0.727	0.77
120_P	136_K	0.720	0.76
119_R	136_K	0.720	0.76
13_Y	150_T	0.719	0.76
144_D	153_P	0.716	0.76
31_K	154_L	0.713	0.76
45_T	87_L	0.711	0.76
119_R	137_A	0.709	0.75
86_T	135_T	0.708	0.75
165_I	189_T	0.706	0.75
108_P	137_A	0.702	0.75
74_A	93_A	0.700	0.74
81_V	135_T	0.698	0.74
107_E	195_S	0.698	0.74
121_G	129_N	0.697	0.74
148_W	151_E	0.697	0.74
33_T	38_A	0.697	0.74
115_M	128_T	0.695	0.74
38_A	138_L	0.695	0.74
100_A	135_T	0.673	0.72
134_L	138_L	0.672	0.71
57_H	66_R	0.670	0.71
94_E	97_V	0.670	0.71
77_V	90_V	0.670	0.71
40_G	171_I	0.670	0.71
82_M	175_N	0.668	0.71
161_T	164_A	0.668	0.71
67_T	71_F	0.668	0.71
31_K	118_R	0.668	0.71
27_C	160_Y	0.667	0.71
32_E	155_Y	0.665	0.71
25_L	187_W	0.664	0.71
175_N	182_Y	0.655	0.69
42_I	45_T	0.652	0.69
83_H	142_M	0.651	0.69
32_E	153_P	0.650	0.69
41_Y	160_Y	0.648	0.69
111_G	137_A	0.642	0.68
18_L	182_Y	0.639	0.68
18_L	49_M	0.632	0.67
82_M	86_T	0.629	0.66
14_Q	94_E	0.616	0.65
55_A	180_R	0.612	0.64
162_P	188_V	0.611	0.64
124_P	193_Y	0.606	0.63
128_T	193_Y	0.605	0.63
112_Q	127_W	0.603	0.63
125_R	192_R	0.601	0.63
51_A	97_V	0.598	0.62
81_V	142_M	0.594	0.62
67_T	145_Y	0.594	0.62
72_A	91_V	0.593	0.62
42_I	90_V	0.593	0.62
112_Q	115_M	0.592	0.62
43_V	107_E	0.589	0.61
82_M	135_T	0.589	0.61
56_A	70_M	0.589	0.61
78_Y	89_N	0.586	0.61
51_A	184_W	0.584	0.61
72_A	95_E	0.583	0.61
25_L	191_N	0.582	0.60
51_A	98_P	0.578	0.60
57_H	64_T	0.577	0.60
85_H	132_G	0.577	0.60
77_V	149_I	0.569	0.59
115_M	137_A	0.569	0.59
49_M	182_Y	0.567	0.58
53_D	70_M	0.566	0.58
85_H	91_V	0.566	0.58
147_R	151_E	0.559	0.57
168_G	183_P	0.558	0.57
13_Y	149_I	0.557	0.57
108_P	191_N	0.553	0.57
57_H	71_F	0.553	0.57
51_A	61_N	0.549	0.56
116_E	127_W	0.548	0.56
52_G	59_F	0.545	0.55
67_T	174_D	0.543	0.55
54_R	87_L	0.542	0.55
31_K	153_P	0.542	0.55
79_T	85_H	0.542	0.55
157_E	160_Y	0.539	0.55
104_R	131_P	0.537	0.54
80_Y	100_A	0.536	0.54
19_E	23_S	0.536	0.54
113_L	116_E	0.532	0.54
43_V	55_A	0.528	0.53
74_A	172_G	0.525	0.53
161_T	190_G	0.524	0.53
163_E	188_V	0.524	0.53
45_T	56_A	0.523	0.52
106_I	115_M	0.521	0.52
76_R	145_Y	0.519	0.52
43_V	106_I	0.518	0.52
125_R	129_N	0.517	0.52
49_M	93_A	0.517	0.52
85_H	135_T	0.514	0.51
108_P	112_Q	0.513	0.51
55_A	182_Y	0.512	0.51
111_G	118_R	0.510	0.51
41_Y	188_V	0.510	0.51
88_L	144_D	0.507	0.50
22_P	55_A	0.505	0.50
67_T	128_T	0.505	0.50
187_W	195_S	0.505	0.50
51_A	58_S	0.503	0.50
100_A	149_I	0.503	0.50
79_T	83_H	0.501	0.49
113_L	161_T	0.501	0.49
107_E	193_Y	0.500	0.49

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
3ubyA	1	0.9745	100	0.074	Contact Map
3hi7A	2	0.3163	7	0.97	Contact Map
1hymB	1	0.1224	4.5	0.972	Contact Map
2fmlA	2	0.2959	4.1	0.973	Contact Map
1syqB	1	0.1173	4	0.973	Contact Map
1vqzA	1	0.3112	3.3	0.974	Contact Map
3dlmA	1	0.3214	2.9	0.975	Contact Map
4yn1A	2	0.5867	2.8	0.975	Contact Map
1w7cA	2	0.3316	2.8	0.975	Contact Map
2hw4A	1	0.1786	2.7	0.975	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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