3MGA - BACSU - GREMLIN Contacts

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3MGA - DNA-3-methyladenine glycosylase

UniProt:	P37878	Sequences: MTWHEVNDVIVITLPEIFDMNANLGYLTREKNECMYEIENNIITKVIAIGEIRSLVQVSVINNKQMIVQFLNDSRPVEQWKREEIVKYIHEWFDLDNDLTPFYEMAKADPLLKMPARKFYGLRVIGIPDLFEALCWGVLGQQINLAFAYSLKKQFVEAFGDSIEWNGKKYWVFPPYERIARLTPTDLADIKMTVKKSEYIIGIARLMASGELSREKLMKMNFKDAEKNLIKIRGIGPWTANYVLMRCLRFPTAFPIDDVGLIHSIKILRNMNRKPTKDEILEISVPWKEWQSYATFYLWRVLY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	303 (277)
Sequences:	2722 (2083)
Seq/√Len:	125.1

ECOLI - 3MG2
BACSU - 3MGA YFJP
HALSA - Q9HQ94 Q9HQ62

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
161_D	178_R	4.134	1.00
90_H	96_D	4.023	1.00
175_P	178_R	3.914	1.00
150_S	154_Q	3.415	1.00
221_N	224_D	3.405	1.00
226_E	241_N	3.178	1.00
285_V	288_K	3.099	1.00
259_V	263_H	3.087	1.00
228_N	231_K	2.733	1.00
44_T	57_Q	2.717	1.00
134_L	243_V	2.709	1.00
183_T	186_D	2.523	1.00
201_I	205_R	2.471	1.00
138_V	203_I	2.395	1.00
230_I	240_A	2.391	1.00
155_F	179_I	2.363	1.00
144_N	147_F	2.363	1.00
98_D	101_P	2.346	1.00
131_F	176_Y	2.329	1.00
134_L	203_I	2.290	1.00
276_T	279_E	2.254	1.00
42_I	57_Q	2.243	1.00
198_E	202_G	2.186	1.00
230_I	237_P	2.096	1.00
226_E	230_I	2.057	1.00
252_T	291_Q	2.026	1.00
139_L	152_K	2.020	1.00
222_F	250_F	2.016	1.00
158_A	186_D	1.986	1.00
109_D	287_W	1.968	1.00
35_M	156_V	1.910	1.00
48_A	161_D	1.860	1.00
162_S	169_K	1.859	1.00
135_C	200_I	1.837	1.00
91_E	96_D	1.818	1.00
86_V	90_H	1.781	1.00
131_F	204_A	1.761	1.00
226_E	240_A	1.757	1.00
142_Q	147_F	1.749	1.00
57_Q	69_Q	1.742	1.00
153_K	157_E	1.730	1.00
245_M	292_S	1.690	1.00
205_R	209_S	1.674	1.00
135_C	173_F	1.659	1.00
159_F	186_D	1.647	1.00
159_F	182_L	1.642	1.00
94_D	97_N	1.618	1.00
139_L	151_L	1.601	1.00
202_G	206_L	1.601	1.00
202_G	205_R	1.587	1.00
154_Q	191_K	1.580	1.00
226_E	244_L	1.564	1.00
225_A	244_L	1.559	1.00
213_S	216_K	1.556	1.00
253_A	292_S	1.547	1.00
134_L	235_I	1.528	1.00
202_G	232_I	1.522	1.00
151_L	192_M	1.512	1.00
126_G	249_R	1.498	1.00
131_F	135_C	1.492	1.00
206_L	211_E	1.483	1.00
206_L	232_I	1.469	1.00
109_D	269_R	1.462	1.00
184_P	197_S	1.445	1.00
207_M	214_R	1.445	1.00
151_L	154_Q	1.445	1.00
61_I	67_I	1.431	1.00
137_G	242_Y	1.427	1.00
19_D	22_A	1.408	1.00
131_F	207_M	1.405	1.00
180_A	208_A	1.397	1.00
144_N	259_V	1.391	1.00
224_D	227_K	1.387	1.00
68_V	89_I	1.382	1.00
256_I	281_L	1.376	1.00
198_E	233_R	1.359	1.00
261_L	295_T	1.356	1.00
193_T	196_K	1.346	1.00
220_M	224_D	1.334	1.00
147_F	150_S	1.326	1.00
184_P	198_E	1.304	1.00
45_K	132_E	1.294	1.00
177_E	208_A	1.275	1.00
184_P	201_I	1.269	1.00
225_A	248_L	1.268	1.00
180_A	205_R	1.264	1.00
287_W	294_A	1.257	1.00
66_M	93_F	1.256	1.00
199_Y	202_G	1.251	1.00
157_E	171_W	1.251	1.00
224_D	228_N	1.248	1.00
59_S	67_I	1.248	1.00
159_F	179_I	1.246	1.00
127_I	133_A	1.243	1.00
244_L	250_F	1.236	0.99
50_G	84_E	1.233	0.99
222_F	244_L	1.225	0.99
46_V	169_K	1.209	0.99
280_I	284_S	1.208	0.99
275_P	279_E	1.197	0.99
91_E	126_G	1.195	0.99
21_N	41_N	1.195	0.99
222_F	252_T	1.194	0.99
39_E	42_I	1.194	0.99
265_I	280_I	1.193	0.99
140_G	143_I	1.182	0.99
222_F	253_A	1.182	0.99
20_M	60_V	1.181	0.99
176_Y	204_A	1.181	0.99
196_K	236_G	1.179	0.99
288_K	291_Q	1.176	0.99
143_I	238_W	1.167	0.99
255_P	261_L	1.166	0.99
100_T	104_E	1.164	0.99
70_F	85_I	1.162	0.99
18_F	23_N	1.159	0.99
143_I	147_F	1.158	0.99
187_L	200_I	1.156	0.99
216_K	228_N	1.150	0.99
250_F	253_A	1.144	0.99
260_G	264_S	1.136	0.99
136_W	152_K	1.134	0.99
97_N	102_F	1.122	0.99
244_L	248_L	1.116	0.99
142_Q	193_T	1.114	0.99
141_Q	238_W	1.109	0.99
99_L	103_Y	1.086	0.99
46_V	172_V	1.079	0.99
203_I	232_I	1.079	0.99
91_E	249_R	1.074	0.99
114_M	118_K	1.072	0.99
237_P	294_A	1.069	0.99
284_S	287_W	1.069	0.99
282_E	285_V	1.057	0.98
156_V	171_W	1.056	0.98
223_K	227_K	1.048	0.98
148_A	238_W	1.041	0.98
33_E	153_K	1.041	0.98
176_Y	207_M	1.037	0.98
37_E	44_T	1.035	0.98
14_L	18_F	1.032	0.98
255_P	295_T	1.030	0.98
210_G	213_S	1.029	0.98
133_A	247_C	1.019	0.98
30_E	137_G	1.018	0.98
97_N	293_Y	1.016	0.98
49_I	52_I	1.016	0.98
147_F	191_K	1.016	0.98
143_I	148_A	1.014	0.98
84_E	87_K	1.011	0.98
154_Q	157_E	0.998	0.98
225_A	250_F	0.993	0.98
47_I	128_P	0.984	0.97
138_V	199_Y	0.982	0.97
222_F	225_A	0.982	0.97
140_G	242_Y	0.978	0.97
211_E	231_K	0.976	0.97
107_K	117_R	0.974	0.97
194_V	198_E	0.970	0.97
24_L	38_I	0.968	0.97
220_M	228_N	0.965	0.97
261_L	298_L	0.953	0.97
180_A	204_A	0.952	0.97
92_W	128_P	0.951	0.97
164_E	169_K	0.951	0.97
255_P	292_S	0.949	0.97
113_K	117_R	0.948	0.97
132_E	173_F	0.947	0.97
160_G	172_V	0.942	0.97
202_G	233_R	0.941	0.97
165_W	169_K	0.940	0.97
139_L	192_M	0.935	0.97
181_R	201_I	0.930	0.96
185_T	189_D	0.930	0.96
178_R	181_R	0.921	0.96
292_S	295_T	0.914	0.96
220_M	225_A	0.912	0.96
50_G	53_R	0.903	0.96
162_S	171_W	0.900	0.96
242_Y	246_R	0.897	0.96
147_F	151_L	0.894	0.96
184_P	188_A	0.884	0.95
42_I	59_S	0.883	0.95
146_A	149_Y	0.883	0.95
119_F	300_R	0.874	0.95
143_I	239_T	0.872	0.95
262_I	266_K	0.869	0.95
182_L	186_D	0.867	0.95
294_A	298_L	0.865	0.95
263_H	266_K	0.862	0.95
142_Q	238_W	0.861	0.95
55_L	61_I	0.854	0.94
194_V	197_S	0.849	0.94
102_F	293_Y	0.848	0.94
61_I	64_K	0.845	0.94
57_Q	60_V	0.839	0.94
145_L	242_Y	0.827	0.93
192_M	200_I	0.826	0.93
197_S	201_I	0.825	0.93
133_A	136_W	0.824	0.93
115_P	297_Y	0.822	0.93
109_D	294_A	0.820	0.93
254_F	284_S	0.806	0.92
151_L	190_I	0.800	0.92
94_D	293_Y	0.795	0.92
276_T	280_I	0.791	0.92
216_K	220_M	0.788	0.91
120_Y	252_T	0.787	0.91
14_L	20_M	0.786	0.91
206_L	209_S	0.782	0.91
141_Q	239_T	0.771	0.91
143_I	196_K	0.763	0.90
81_K	84_E	0.757	0.90
103_Y	116_A	0.749	0.89
133_A	137_G	0.749	0.89
278_D	282_E	0.746	0.89
134_L	232_I	0.746	0.89
106_A	113_K	0.740	0.89
14_L	60_V	0.738	0.89
192_M	197_S	0.738	0.89
60_V	64_K	0.737	0.89
260_G	297_Y	0.733	0.88
140_G	299_W	0.732	0.88
147_F	196_K	0.730	0.88
102_F	106_A	0.728	0.88
94_D	251_P	0.725	0.88
256_I	295_T	0.722	0.87
148_A	239_T	0.720	0.87
82_R	86_V	0.720	0.87
142_Q	259_V	0.720	0.87
222_F	226_E	0.719	0.87
242_Y	255_P	0.719	0.87
83_E	87_K	0.717	0.87
58_V	68_V	0.715	0.87
140_G	148_A	0.715	0.87
143_I	192_M	0.714	0.87
48_A	53_R	0.713	0.87
238_W	258_D	0.713	0.87
118_K	219_K	0.711	0.87
30_E	242_Y	0.710	0.87
154_Q	190_I	0.708	0.86
90_H	95_L	0.704	0.86
245_M	255_P	0.703	0.86
47_I	173_F	0.702	0.86
280_I	283_I	0.700	0.86
277_K	281_L	0.695	0.85
143_I	151_L	0.691	0.85
45_K	48_A	0.690	0.85
151_L	191_K	0.688	0.85
241_N	255_P	0.686	0.85
244_L	247_C	0.684	0.85
245_M	295_T	0.680	0.84
296_F	300_R	0.680	0.84
212_L	232_I	0.679	0.84
30_E	145_L	0.676	0.84
185_T	194_V	0.675	0.84
133_A	249_R	0.674	0.84
223_K	281_L	0.674	0.84
180_A	201_I	0.673	0.84
142_Q	151_L	0.673	0.84
24_L	294_A	0.671	0.83
166_N	170_Y	0.670	0.83
142_Q	260_G	0.667	0.83
43_I	54_S	0.664	0.83
166_N	169_K	0.664	0.83
260_G	263_H	0.662	0.83
161_D	172_V	0.662	0.83
244_L	253_A	0.661	0.82
238_W	242_Y	0.660	0.82
151_L	197_S	0.660	0.82
54_S	60_V	0.658	0.82
134_L	138_V	0.656	0.82
101_P	290_W	0.655	0.82
283_I	286_P	0.655	0.82
188_A	197_S	0.654	0.82
21_N	61_I	0.654	0.82
130_L	247_C	0.651	0.82
58_V	66_M	0.650	0.81
140_G	238_W	0.649	0.81
60_V	63_N	0.649	0.81
56_V	68_V	0.640	0.80
247_C	254_F	0.639	0.80
222_F	241_N	0.639	0.80
26_Y	296_F	0.637	0.80
206_L	212_L	0.635	0.80
209_S	216_K	0.635	0.80
97_N	249_R	0.634	0.80
29_R	146_A	0.633	0.80
73_D	80_W	0.633	0.80
46_V	170_Y	0.632	0.80
143_I	259_V	0.631	0.79
240_A	244_L	0.629	0.79
55_L	68_V	0.628	0.79
179_I	204_A	0.628	0.79
186_D	189_D	0.628	0.79
295_T	299_W	0.627	0.79
237_P	241_N	0.623	0.79
251_P	293_Y	0.623	0.79
279_E	282_E	0.622	0.79
243_V	247_C	0.620	0.78
140_G	145_L	0.619	0.78
254_F	257_D	0.618	0.78
25_G	29_R	0.616	0.78
230_I	241_N	0.614	0.78
142_Q	194_V	0.614	0.78
235_I	243_V	0.609	0.77
160_G	178_R	0.607	0.77
138_V	151_L	0.606	0.77
156_V	174_P	0.605	0.77
58_V	89_I	0.603	0.76
25_G	28_T	0.600	0.76
48_A	51_E	0.599	0.76
53_R	161_D	0.594	0.75
238_W	260_G	0.591	0.75
31_K	149_Y	0.591	0.75
39_E	43_I	0.590	0.75
183_T	188_A	0.590	0.75
14_L	63_N	0.590	0.75
119_F	297_Y	0.590	0.75
30_E	43_I	0.588	0.75
137_G	239_T	0.587	0.74
92_W	261_L	0.586	0.74
142_Q	237_P	0.586	0.74
281_L	284_S	0.585	0.74
103_Y	297_Y	0.584	0.74
251_P	290_W	0.584	0.74
141_Q	199_Y	0.584	0.74
176_Y	201_I	0.582	0.74
152_K	173_F	0.582	0.74
212_L	215_E	0.582	0.74
46_V	49_I	0.581	0.74
141_Q	236_G	0.579	0.73
106_A	116_A	0.579	0.73
58_V	62_N	0.579	0.73
215_E	219_K	0.578	0.73
238_W	259_V	0.574	0.73
135_C	179_I	0.574	0.73
247_C	296_F	0.573	0.73
135_C	203_I	0.572	0.73
103_Y	119_F	0.570	0.72
26_Y	137_G	0.569	0.72
141_Q	151_L	0.568	0.72
27_L	31_K	0.566	0.72
29_R	32_N	0.565	0.72
22_A	29_R	0.563	0.71
145_L	196_K	0.562	0.71
241_N	256_I	0.560	0.71
187_L	192_M	0.560	0.71
131_F	197_S	0.559	0.71
144_N	190_I	0.558	0.71
261_L	264_S	0.555	0.70
28_T	40_N	0.554	0.70
232_I	235_I	0.550	0.70
283_I	287_W	0.550	0.70
255_P	262_I	0.547	0.69
208_A	232_I	0.547	0.69
144_N	151_L	0.546	0.69
155_F	158_A	0.545	0.69
85_I	93_F	0.544	0.69
26_Y	242_Y	0.543	0.69
27_L	32_N	0.543	0.69
49_I	56_V	0.542	0.69
239_T	299_W	0.540	0.68
132_E	137_G	0.539	0.68
54_S	57_Q	0.539	0.68
44_T	55_L	0.538	0.68
196_K	258_D	0.538	0.68
145_L	236_G	0.538	0.68
49_I	54_S	0.538	0.68
57_Q	67_I	0.538	0.68
206_L	231_K	0.538	0.68
180_A	187_L	0.535	0.68
104_E	107_K	0.535	0.68
99_L	248_L	0.535	0.68
58_V	93_F	0.535	0.68
88_Y	91_E	0.535	0.68
182_L	189_D	0.533	0.67
82_R	90_H	0.529	0.67
24_L	28_T	0.528	0.67
66_M	72_N	0.528	0.67
292_S	299_W	0.527	0.66
52_I	81_K	0.527	0.66
122_L	160_G	0.527	0.66
122_L	296_F	0.527	0.66
264_S	298_L	0.527	0.66
215_E	220_M	0.526	0.66
26_Y	148_A	0.526	0.66
99_L	290_W	0.525	0.66
50_G	55_L	0.525	0.66
45_K	49_I	0.524	0.66
94_D	99_L	0.524	0.66
179_I	183_T	0.523	0.66
90_H	100_T	0.522	0.66
142_Q	239_T	0.521	0.65
293_Y	296_F	0.521	0.65
26_Y	246_R	0.520	0.65
106_A	294_A	0.519	0.65
16_E	23_N	0.518	0.65
252_T	289_E	0.517	0.65
142_Q	264_S	0.515	0.65
270_N	275_P	0.513	0.64
188_A	192_M	0.511	0.64
136_W	148_A	0.510	0.64
144_N	193_T	0.510	0.64
56_V	287_W	0.508	0.64
44_T	47_I	0.507	0.63
148_A	259_V	0.507	0.63
83_E	86_V	0.507	0.63
198_E	201_I	0.505	0.63
140_G	239_T	0.504	0.63
101_P	180_A	0.504	0.63
227_K	230_I	0.504	0.63
120_Y	289_E	0.504	0.63
192_M	196_K	0.502	0.63
199_Y	239_T	0.501	0.63
112_L	254_F	0.500	0.62

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
2jhnA	1	0.934	100	0.258	Contact Map
3i0wA	1	0.9307	100	0.268	Contact Map
4ejyA	1	0.9307	100	0.27	Contact Map
1mpgA	1	0.9076	100	0.276	Contact Map
2xhiA	1	0.9538	100	0.288	Contact Map
4b21A	2	0.6667	100	0.396	Contact Map
2yg9A	1	0.6502	100	0.442	Contact Map
2h56A	1	0.6667	100	0.443	Contact Map
3s6iA	1	0.6436	100	0.463	Contact Map
3fhgA	2	0.6205	100	0.611	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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