EcoRI_methylase - PFAM28P - GREMLIN Contacts

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EcoRI_methylase - Adenine-specific methyltransferase EcoRI

PFAM:	PF13651	Sequences: NLHKAKKAKNDEFYTQLSDIEKELKHYKDHFRGKVVLCNCDDPEESNFFKYFALNFEKLGLKKLIATCYKGSPIAGTQLSLEDEDLFSDKDKEKAYKLEITEVKDKNGDGAIDLEDIEWLKKNELTYLKGDGDFRSDECIELLKEADIVVTNPPFSLFREYVAQLVEYDKKFLIIGNQNAITYKEIFPLIKENKLWLGYGFNSGDMEFIVPDDYELYATGRRIDENGKKYIRVGNVCWFTNLDHGKRHEPLILYKKYNPEEYPKYDNYDAIEVPKTDDIPSDYDGVMGVPITFLDKYNPEQFEIIGLTKGKRTGVKGYKLGKKGYKKDGGDKGGYPYINGKRPYARILIRNK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	352 (347)
Sequences:	3369 (2538)
Seq/√Len:	136.3
META:	0.929

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
286_V	348_L	4.632	1.00
243_D	248_H	4.235	1.00
162_V	186_I	3.614	1.00
207_E	222_R	2.967	1.00
24_L	173_L	2.912	1.00
309_K	342_R	2.894	1.00
255_K	261_E	2.766	1.00
284_D	351_N	2.638	1.00
307_L	345_A	2.611	1.00
258_N	261_E	2.563	1.00
332_K	335_Y	2.508	1.00
55_N	58_K	2.401	1.00
331_D	336_P	2.345	1.00
162_V	174_I	2.327	1.00
209_I	228_K	2.309	1.00
109_D	113_D	2.286	1.00
105_D	109_D	2.211	1.00
335_Y	342_R	2.063	1.00
224_D	228_K	2.034	1.00
199_Y	244_H	2.021	1.00
178_Q	292_T	2.002	1.00
51_Y	59_L	1.990	1.00
330_G	334_G	1.982	1.00
333_G	336_P	1.923	1.00
331_D	334_G	1.922	1.00
345_A	348_L	1.914	1.00
335_Y	345_A	1.912	1.00
166_V	189_L	1.884	1.00
141_E	144_K	1.882	1.00
334_G	337_Y	1.854	1.00
32_R	60_G	1.809	1.00
50_K	54_L	1.798	1.00
264_K	269_D	1.795	1.00
328_D	331_D	1.789	1.00
334_G	342_R	1.785	1.00
207_E	230_Y	1.775	1.00
205_D	232_R	1.741	1.00
329_G	332_K	1.737	1.00
331_D	335_Y	1.711	1.00
329_G	334_G	1.706	1.00
326_K	330_G	1.683	1.00
231_I	234_G	1.682	1.00
317_G	321_G	1.671	1.00
63_K	99_E	1.654	1.00
329_G	333_G	1.628	1.00
259_P	263_P	1.626	1.00
330_G	333_G	1.620	1.00
332_K	336_P	1.619	1.00
342_R	345_A	1.611	1.00
186_I	195_L	1.604	1.00
233_V	236_V	1.603	1.00
201_F	206_M	1.598	1.00
337_Y	342_R	1.593	1.00
308_T	342_R	1.582	1.00
163_A	167_E	1.566	1.00
313_T	317_G	1.566	1.00
333_G	342_R	1.563	1.00
325_Y	329_G	1.559	1.00
330_G	336_P	1.558	1.00
310_G	342_R	1.545	1.00
200_G	206_M	1.534	1.00
307_L	310_G	1.528	1.00
332_K	342_R	1.522	1.00
201_F	205_D	1.518	1.00
317_G	320_L	1.514	1.00
308_T	345_A	1.508	1.00
303_E	350_R	1.505	1.00
323_K	326_K	1.501	1.00
337_Y	340_G	1.494	1.00
321_G	324_G	1.487	1.00
321_G	326_K	1.481	1.00
326_K	331_D	1.473	1.00
202_N	205_D	1.468	1.00
206_M	236_V	1.467	1.00
206_M	234_G	1.454	1.00
317_G	324_G	1.452	1.00
326_K	335_Y	1.435	1.00
207_E	221_R	1.428	1.00
335_Y	338_I	1.419	1.00
328_D	335_Y	1.412	1.00
325_Y	331_D	1.408	1.00
329_G	335_Y	1.403	1.00
207_E	232_R	1.402	1.00
315_V	318_Y	1.387	1.00
328_D	333_G	1.382	1.00
336_P	343_P	1.378	1.00
336_P	342_R	1.371	1.00
330_G	335_Y	1.359	1.00
325_Y	333_G	1.357	1.00
325_Y	335_Y	1.347	1.00
230_Y	234_G	1.346	1.00
205_D	233_V	1.334	1.00
329_G	336_P	1.334	1.00
325_Y	342_R	1.333	1.00
326_K	332_K	1.328	1.00
314_G	317_G	1.324	1.00
18_S	21_E	1.323	1.00
205_D	234_G	1.316	1.00
207_E	234_G	1.313	1.00
331_D	342_R	1.310	1.00
307_L	342_R	1.308	1.00
316_K	319_K	1.307	1.00
201_F	204_G	1.294	1.00
180_A	183_Y	1.290	1.00
326_K	333_G	1.289	1.00
216_L	231_I	1.289	1.00
333_G	337_Y	1.276	1.00
318_Y	321_G	1.274	1.00
326_K	342_R	1.273	1.00
201_F	207_E	1.273	1.00
206_M	233_V	1.265	1.00
323_K	327_K	1.236	1.00
315_V	319_K	1.230	1.00
70_K	131_D	1.225	1.00
320_L	342_R	1.223	1.00
328_D	334_G	1.215	1.00
216_L	221_R	1.213	1.00
316_K	320_L	1.210	1.00
319_K	323_K	1.205	1.00
328_D	336_P	1.195	1.00
293_F	297_Y	1.195	1.00
333_G	345_A	1.193	1.00
306_G	309_K	1.188	1.00
182_T	345_A	1.179	0.99
321_G	325_Y	1.178	0.99
218_A	234_G	1.177	0.99
232_R	235_N	1.175	0.99
137_D	141_E	1.175	0.99
105_D	116_D	1.167	0.99
317_G	323_K	1.162	0.99
329_G	342_R	1.159	0.99
322_K	325_Y	1.158	0.99
209_I	230_Y	1.151	0.99
313_T	316_K	1.151	0.99
311_K	314_G	1.149	0.99
336_P	340_G	1.149	0.99
218_A	231_I	1.148	0.99
313_T	321_G	1.148	0.99
327_K	335_Y	1.144	0.99
94_K	127_Y	1.141	0.99
313_T	320_L	1.140	0.99
317_G	325_Y	1.134	0.99
309_K	345_A	1.131	0.99
314_G	318_Y	1.130	0.99
314_G	319_K	1.127	0.99
107_N	113_D	1.124	0.99
330_G	337_Y	1.124	0.99
325_Y	332_K	1.124	0.99
248_H	300_E	1.114	0.99
50_K	53_A	1.112	0.99
318_Y	323_K	1.112	0.99
200_G	205_D	1.108	0.99
220_G	232_R	1.105	0.99
328_D	332_K	1.105	0.99
210_V	214_Y	1.103	0.99
308_T	343_P	1.098	0.99
109_D	116_D	1.097	0.99
317_G	334_G	1.095	0.99
258_N	263_P	1.094	0.99
326_K	329_G	1.091	0.99
275_K	278_D	1.084	0.99
319_K	325_Y	1.082	0.99
327_K	342_R	1.082	0.99
200_G	236_V	1.075	0.99
324_G	328_D	1.075	0.99
203_S	207_E	1.075	0.99
331_D	337_Y	1.071	0.99
221_R	224_D	1.070	0.99
201_F	237_C	1.069	0.99
216_L	234_G	1.066	0.99
207_E	231_I	1.061	0.99
199_Y	202_N	1.061	0.99
308_T	335_Y	1.055	0.99
206_M	237_C	1.055	0.99
318_Y	342_R	1.049	0.99
286_V	305_I	1.045	0.99
313_T	318_Y	1.042	0.99
324_G	335_Y	1.038	0.99
212_D	229_K	1.038	0.99
202_N	207_E	1.035	0.99
207_E	237_C	1.030	0.99
218_A	221_R	1.027	0.99
212_D	228_K	1.020	0.98
324_G	327_K	1.019	0.98
320_L	323_K	1.016	0.98
318_Y	322_K	1.012	0.98
324_G	334_G	1.005	0.98
67_T	128_L	1.003	0.98
336_P	345_A	1.001	0.98
190_I	294_L	1.001	0.98
308_T	334_G	1.001	0.98
334_G	345_A	0.995	0.98
310_G	345_A	0.991	0.98
327_K	331_D	0.991	0.98
217_Y	221_R	0.988	0.98
140_I	144_K	0.984	0.98
309_K	334_G	0.977	0.98
30_H	242_L	0.977	0.98
314_G	321_G	0.974	0.98
201_F	234_G	0.973	0.98
307_L	348_L	0.973	0.98
306_G	310_G	0.972	0.98
325_Y	334_G	0.969	0.98
205_D	236_V	0.968	0.98
105_D	113_D	0.967	0.98
326_K	336_P	0.961	0.98
110_G	116_D	0.960	0.98
332_K	345_A	0.951	0.98
323_K	342_R	0.949	0.98
318_Y	324_G	0.949	0.98
322_K	326_K	0.947	0.98
173_L	242_L	0.945	0.98
310_G	333_G	0.945	0.98
310_G	334_G	0.944	0.97
316_K	321_G	0.944	0.97
324_G	342_R	0.941	0.97
334_G	343_P	0.941	0.97
28_K	58_K	0.940	0.97
178_Q	202_N	0.937	0.97
204_G	207_E	0.937	0.97
207_E	233_V	0.936	0.97
222_R	232_R	0.931	0.97
216_L	223_I	0.930	0.97
219_T	231_I	0.927	0.97
326_K	334_G	0.922	0.97
255_K	281_S	0.921	0.97
323_K	335_Y	0.920	0.97
232_R	236_V	0.920	0.97
196_W	247_R	0.919	0.97
207_E	216_L	0.919	0.97
326_K	345_A	0.910	0.97
334_G	338_I	0.910	0.97
202_N	237_C	0.908	0.97
202_N	232_R	0.908	0.97
204_G	236_V	0.908	0.97
135_R	160_E	0.907	0.97
178_Q	237_C	0.903	0.97
219_T	224_D	0.898	0.97
309_K	336_P	0.897	0.97
200_G	203_S	0.893	0.96
201_F	231_I	0.886	0.96
325_Y	328_D	0.885	0.96
203_S	237_C	0.884	0.96
318_Y	325_Y	0.880	0.96
203_S	206_M	0.879	0.96
315_V	324_G	0.876	0.96
216_L	220_G	0.875	0.96
232_R	237_C	0.875	0.96
217_Y	231_I	0.874	0.96
250_P	298_N	0.873	0.96
4_K	7_K	0.872	0.96
206_M	231_I	0.872	0.96
218_A	222_R	0.871	0.96
36_V	61_L	0.870	0.96
268_Y	286_V	0.869	0.96
309_K	343_P	0.869	0.96
36_V	150_V	0.868	0.96
329_G	337_Y	0.868	0.96
3_H	6_K	0.867	0.96
308_T	317_G	0.867	0.96
312_R	317_G	0.866	0.96
323_K	333_G	0.863	0.96
21_E	51_Y	0.862	0.96
327_K	333_G	0.862	0.96
257_Y	277_D	0.861	0.96
320_L	326_K	0.856	0.96
323_K	334_G	0.854	0.95
63_K	145_E	0.853	0.95
201_F	229_K	0.850	0.95
307_L	335_Y	0.849	0.95
337_Y	345_A	0.846	0.95
327_K	330_G	0.844	0.95
220_G	231_I	0.843	0.95
317_G	342_R	0.840	0.95
178_Q	197_L	0.836	0.95
18_S	22_K	0.834	0.95
207_E	228_K	0.832	0.95
178_Q	234_G	0.832	0.95
324_G	333_G	0.831	0.95
140_I	168_Y	0.831	0.95
318_Y	334_G	0.829	0.95
317_G	326_K	0.826	0.95
343_P	348_L	0.826	0.95
319_K	335_Y	0.824	0.95
200_G	237_C	0.823	0.94
228_K	231_I	0.821	0.94
216_L	230_Y	0.820	0.94
182_T	291_I	0.820	0.94
308_T	332_K	0.819	0.94
201_F	236_V	0.818	0.94
214_Y	231_I	0.818	0.94
224_D	230_Y	0.817	0.94
315_V	320_L	0.815	0.94
321_G	330_G	0.814	0.94
221_R	231_I	0.812	0.94
324_G	332_K	0.811	0.94
207_E	220_G	0.804	0.94
313_T	323_K	0.803	0.94
320_L	324_G	0.803	0.94
178_Q	201_F	0.800	0.94
309_K	335_Y	0.798	0.94
335_Y	339_N	0.797	0.93
229_K	234_G	0.792	0.93
178_Q	232_R	0.790	0.93
325_Y	330_G	0.788	0.93
314_G	323_K	0.786	0.93
205_D	218_A	0.786	0.93
31_F	150_V	0.786	0.93
327_K	336_P	0.783	0.93
318_Y	335_Y	0.779	0.93
335_Y	340_G	0.779	0.93
210_V	229_K	0.777	0.93
220_G	234_G	0.776	0.93
144_K	168_Y	0.775	0.93
165_L	168_Y	0.775	0.93
308_T	333_G	0.771	0.92
215_E	218_A	0.771	0.92
327_K	334_G	0.770	0.92
308_T	336_P	0.768	0.92
216_L	219_T	0.765	0.92
332_K	337_Y	0.765	0.92
37_L	139_C	0.764	0.92
197_L	202_N	0.763	0.92
181_I	197_L	0.761	0.92
312_R	316_K	0.761	0.92
221_R	229_K	0.760	0.92
321_G	333_G	0.759	0.92
328_D	342_R	0.757	0.92
327_K	332_K	0.753	0.91
210_V	213_D	0.753	0.91
17_L	21_E	0.753	0.91
205_D	237_C	0.752	0.91
325_Y	336_P	0.748	0.91
205_D	231_I	0.747	0.91
207_E	236_V	0.744	0.91
332_K	340_G	0.742	0.91
205_D	230_Y	0.741	0.91
222_R	228_K	0.740	0.91
317_G	322_K	0.738	0.91
221_R	234_G	0.738	0.91
313_T	319_K	0.734	0.90
317_G	332_K	0.732	0.90
218_A	232_R	0.732	0.90
335_Y	343_P	0.730	0.90
330_G	342_R	0.729	0.90
318_Y	330_G	0.724	0.90
29_D	32_R	0.721	0.90
332_K	338_I	0.721	0.90
321_G	335_Y	0.717	0.89
161_Y	164_Q	0.716	0.89
231_I	235_N	0.713	0.89
86_L	89_D	0.711	0.89
323_K	330_G	0.711	0.89
310_G	330_G	0.711	0.89
323_K	332_K	0.710	0.89
331_D	345_A	0.710	0.89
315_V	321_G	0.709	0.89
308_T	331_D	0.708	0.89
200_G	207_E	0.707	0.89
337_Y	343_P	0.706	0.89
318_Y	326_K	0.701	0.88
215_E	222_R	0.700	0.88
70_K	95_A	0.700	0.88
222_R	231_I	0.697	0.88
234_G	237_C	0.697	0.88
76_G	80_S	0.697	0.88
316_K	342_R	0.696	0.88
217_Y	222_R	0.695	0.88
338_I	341_K	0.693	0.88
323_K	345_A	0.692	0.88
314_G	320_L	0.690	0.87
324_G	329_G	0.689	0.87
215_E	219_T	0.688	0.87
322_K	335_Y	0.685	0.87
97_K	100_I	0.685	0.87
319_K	324_G	0.683	0.87
323_K	329_G	0.683	0.87
200_G	232_R	0.679	0.87
321_G	342_R	0.679	0.87
220_G	223_I	0.675	0.86
317_G	333_G	0.674	0.86
264_K	283_Y	0.673	0.86
206_M	229_K	0.666	0.86
171_K	241_N	0.666	0.86
319_K	322_K	0.663	0.85
328_D	337_Y	0.662	0.85
206_M	220_G	0.662	0.85
205_D	221_R	0.662	0.85
219_T	223_I	0.656	0.85
203_S	216_L	0.656	0.85
318_Y	327_K	0.655	0.85
332_K	343_P	0.654	0.84
200_G	231_I	0.651	0.84
333_G	338_I	0.649	0.84
320_L	325_Y	0.643	0.83
311_K	316_K	0.643	0.83
140_I	164_Q	0.643	0.83
315_V	326_K	0.639	0.83
218_A	223_I	0.639	0.83
337_Y	348_L	0.637	0.83
199_Y	246_K	0.637	0.83
222_R	230_Y	0.637	0.83
309_K	317_G	0.636	0.83
200_G	204_G	0.635	0.83
206_M	232_R	0.633	0.83
324_G	330_G	0.633	0.83
207_E	218_A	0.631	0.82
216_L	229_K	0.631	0.82
321_G	327_K	0.631	0.82
201_F	218_A	0.630	0.82
313_T	324_G	0.629	0.82
309_K	333_G	0.629	0.82
112_I	116_D	0.628	0.82
316_K	322_K	0.626	0.82
202_N	234_G	0.626	0.82
321_G	328_D	0.626	0.82
324_G	331_D	0.626	0.82
193_N	297_Y	0.624	0.82
105_D	110_G	0.623	0.82
336_P	339_N	0.622	0.81
201_F	222_R	0.619	0.81
311_K	317_G	0.617	0.81
204_G	233_V	0.615	0.81
201_F	233_V	0.615	0.81
312_R	318_Y	0.614	0.81
319_K	327_K	0.611	0.80
325_Y	345_A	0.611	0.80
207_E	235_N	0.607	0.80
201_F	232_R	0.607	0.80
322_K	342_R	0.606	0.80
221_R	230_Y	0.606	0.80
206_M	219_T	0.606	0.80
309_K	332_K	0.605	0.80
323_K	328_D	0.604	0.80
256_K	281_S	0.604	0.80
199_Y	230_Y	0.602	0.79
317_G	328_D	0.602	0.79
200_G	233_V	0.600	0.79
216_L	222_R	0.598	0.79
310_G	329_G	0.597	0.79
202_N	220_G	0.596	0.79
311_K	334_G	0.594	0.78
166_V	169_D	0.591	0.78
200_G	234_G	0.591	0.78
24_L	36_V	0.589	0.78
326_K	337_Y	0.589	0.78
310_G	321_G	0.588	0.78
204_G	234_G	0.587	0.78
309_K	316_K	0.587	0.78
257_Y	263_P	0.585	0.77
202_N	231_I	0.584	0.77
137_D	140_I	0.582	0.77
265_Y	272_E	0.576	0.76
312_R	321_G	0.576	0.76
331_D	343_P	0.575	0.76
219_T	234_G	0.574	0.76
320_L	329_G	0.571	0.76
317_G	329_G	0.571	0.76
223_I	228_K	0.564	0.75
209_I	234_G	0.563	0.75
310_G	335_Y	0.563	0.75
172_F	195_L	0.563	0.75
205_D	210_V	0.562	0.75
318_Y	333_G	0.561	0.74
203_S	220_G	0.561	0.74
202_N	206_M	0.560	0.74
309_K	326_K	0.560	0.74
225_E	228_K	0.559	0.74
219_T	232_R	0.557	0.74
308_T	337_Y	0.552	0.73
219_T	222_R	0.551	0.73
206_M	235_N	0.550	0.73
158_F	180_A	0.550	0.73
16_Q	19_D	0.550	0.73
215_E	234_G	0.549	0.73
314_G	322_K	0.549	0.73
319_K	336_P	0.547	0.73
223_I	226_N	0.543	0.72
311_K	315_V	0.541	0.72
117_I	120_L	0.537	0.71
305_I	308_T	0.537	0.71
204_G	232_R	0.536	0.71
316_K	323_K	0.534	0.71
316_K	333_G	0.533	0.71
77_T	80_S	0.533	0.71
317_G	336_P	0.529	0.70
230_Y	233_V	0.529	0.70
220_G	224_D	0.527	0.70
222_R	234_G	0.526	0.70
320_L	330_G	0.525	0.69
314_G	342_R	0.525	0.69
306_G	335_Y	0.524	0.69
338_I	343_P	0.524	0.69
316_K	335_Y	0.524	0.69
204_G	237_C	0.521	0.69
319_K	333_G	0.521	0.69
313_T	326_K	0.521	0.69
312_R	320_L	0.519	0.69
315_V	325_Y	0.517	0.68
328_D	345_A	0.517	0.68
228_K	234_G	0.514	0.68
311_K	335_Y	0.514	0.68
201_F	216_L	0.513	0.68
308_T	311_K	0.513	0.68
318_Y	331_D	0.513	0.68
203_S	231_I	0.512	0.68
316_K	330_G	0.512	0.68
213_D	229_K	0.512	0.68
320_L	335_Y	0.511	0.67
309_K	318_Y	0.510	0.67
209_I	222_R	0.509	0.67
312_R	319_K	0.509	0.67
334_G	348_L	0.506	0.67
217_Y	220_G	0.506	0.67
308_T	324_G	0.505	0.67
243_D	247_R	0.505	0.67
70_K	93_E	0.505	0.67
207_E	219_T	0.503	0.66
310_G	317_G	0.502	0.66
312_R	315_V	0.500	0.66

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
2f8lA	1	0.5994	51	0.974	Contact Map
2okcA	1	0.7188	36	0.977	Contact Map
2kz2A	1	0.2642	25.9	0.978	Contact Map
3ufbA	1	0.6932	25.9	0.978	Contact Map
2m1uA	1	0.2614	14	0.981	Contact Map
4bzjA	2	0	12.1	0.981	Contact Map
2m8uA	1	0.2188	9.5	0.982	Contact Map
2ml9A	1	0.1648	9.4	0.982	Contact Map
2b1uA	1	0.1989	9.2	0.982	Contact Map
4g3bA	3	0.0653	8.8	0.982	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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