RSMC - ECOLI - GREMLIN Contacts

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RSMC - Ribosomal RNA small subunit methyltransferase C

UniProt:	P39406	Sequences: MSAFTPASEVLLRHSDDFEQSRILFAGDLQDDLPARLDTAASRAHTQQFHHWQVLSRQMGDNARFSLVATADDVADCDTLIYYWPKNKPEAQFQLMNLLSLLPVGTDIFVVGENRSGVRSAEQMLADYAPLNKVDSARRCGLYFGRLEKQPVFDAEKFWGEYSVDGLTVKTLPGVFSRDGLDVGSQLLLSTLTPHTKGKVLDVGCGAGVLSVAFARHSPKIRLTLCDVSAPAVEASRATLAANGVEGEVFASNVFSEVKGRFDMIISNPPFHDGMQTSLDAAQTLIRGAVRHLNSGGELRIVANAFLPYPDVLDETFGFHEVIAQTGRFKVYRAIMTRQAKKG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12596
Length:	343 (321)
Sequences:	1795 (1230)
Seq/√Len:	68.7

ECOLI - RSMC RLMG

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
214_F	266_I	5.945	1.00
201_L	262_F	5.004	1.00
321_E	333_R	4.517	1.00
200_V	214_F	4.459	1.00
263_D	294_N	3.991	1.00
199_K	222_R	3.976	1.00
298_E	333_R	3.915	1.00
300_R	323_I	3.425	1.00
211_S	225_L	3.280	1.00
14_H	17_D	3.037	1.00
199_K	294_N	2.969	1.00
185_S	210_L	2.955	1.00
222_R	248_E	2.889	1.00
200_V	264_M	2.782	1.00
199_K	224_T	2.766	1.00
322_V	325_Q	2.741	1.00
283_Q	312_V	2.739	1.00
224_T	262_F	2.735	1.00
234_E	237_R	2.725	1.00
224_T	250_F	2.714	1.00
240_L	249_V	2.696	1.00
22_R	78_D	2.675	1.00
310_P	330_K	2.629	1.00
155_A	158_F	2.456	1.00
225_L	236_S	2.430	1.00
205_C	211_S	2.339	1.00
289_A	299_L	2.314	1.00
212_V	239_T	2.281	1.00
187_L	326_T	2.275	1.00
225_L	249_V	2.263	1.00
183_V	328_R	2.218	1.00
14_H	18_F	2.042	1.00
205_C	227_D	1.995	1.00
237_R	241_A	1.975	1.00
171_T	178_R	1.968	1.00
85_P	91_A	1.897	1.00
160_G	164_V	1.896	1.00
136_S	140_C	1.893	1.00
198_G	263_D	1.891	1.00
252_S	257_E	1.877	1.00
102_L	106_T	1.871	1.00
191_T	324_A	1.837	1.00
267_S	301_I	1.834	1.00
49_F	53_Q	1.823	1.00
300_R	333_R	1.821	1.00
282_A	286_I	1.759	1.00
153_F	157_K	1.744	1.00
190_S	326_T	1.738	1.00
237_R	249_V	1.737	1.00
153_F	159_W	1.716	1.00
203_V	254_V	1.716	1.00
308_P	311_D	1.698	1.00
271_F	304_N	1.694	1.00
44_A	55_L	1.656	0.99
114_N	117_G	1.624	0.99
159_W	162_Y	1.621	0.99
154_D	157_K	1.585	0.99
140_C	143_Y	1.578	0.99
153_F	158_F	1.572	0.99
187_L	324_A	1.566	0.99
233_V	249_V	1.546	0.99
185_S	189_L	1.543	0.99
34_P	44_A	1.540	0.99
238_A	242_A	1.538	0.99
159_W	164_V	1.508	0.99
169_V	239_T	1.493	0.99
224_T	248_E	1.492	0.99
113_E	140_C	1.490	0.99
167_L	212_V	1.483	0.99
236_S	249_V	1.461	0.99
134_V	141_G	1.447	0.98
155_A	159_W	1.446	0.98
169_V	207_A	1.414	0.98
114_N	136_S	1.412	0.98
135_D	138_R	1.412	0.98
134_V	144_F	1.394	0.98
177_S	180_G	1.391	0.98
137_A	140_C	1.362	0.98
68_V	71_A	1.343	0.98
52_W	56_S	1.340	0.97
191_T	331_V	1.336	0.97
15_S	18_F	1.330	0.97
35_A	39_T	1.324	0.97
74_V	77_C	1.323	0.97
47_Q	229_S	1.320	0.97
79_T	107_D	1.294	0.97
170_K	238_A	1.291	0.97
152_V	157_K	1.277	0.97
313_L	320_H	1.271	0.97
156_E	159_W	1.262	0.96
151_P	155_A	1.258	0.96
307_L	313_L	1.252	0.96
136_S	141_G	1.249	0.96
133_K	137_A	1.245	0.96
177_S	236_S	1.244	0.96
229_S	272_H	1.212	0.95
200_V	221_I	1.207	0.95
288_G	291_R	1.207	0.95
125_L	145_G	1.201	0.95
153_F	156_E	1.196	0.95
106_T	132_N	1.189	0.95
261_R	294_N	1.183	0.95
147_L	150_Q	1.182	0.95
253_N	256_S	1.178	0.95
175_V	207_A	1.178	0.95
201_L	292_H	1.166	0.94
280_D	284_T	1.148	0.94
160_G	163_S	1.147	0.94
114_N	119_R	1.144	0.94
215_A	245_V	1.142	0.94
293_L	297_G	1.140	0.94
138_R	143_Y	1.123	0.93
152_V	155_A	1.117	0.93
186_Q	190_S	1.111	0.93
267_S	299_L	1.110	0.93
272_H	302_V	1.102	0.92
102_L	134_V	1.094	0.92
154_D	158_F	1.090	0.92
303_A	307_L	1.089	0.92
305_A	325_Q	1.087	0.92
213_A	216_R	1.074	0.91
325_Q	332_Y	1.072	0.91
79_T	109_F	1.065	0.91
271_F	307_L	1.065	0.91
161_E	164_V	1.063	0.91
26_A	94_Q	1.062	0.91
189_L	213_A	1.060	0.91
283_Q	287_R	1.058	0.91
234_E	238_A	1.055	0.91
137_A	142_L	1.049	0.90
197_K	200_V	1.046	0.90
320_H	332_Y	1.043	0.90
199_K	221_I	1.042	0.90
156_E	163_S	1.038	0.90
213_A	217_H	1.037	0.90
305_A	308_P	1.032	0.90
158_F	162_Y	1.031	0.90
199_K	263_D	1.030	0.90
303_A	308_P	1.029	0.90
187_L	190_S	1.028	0.90
298_E	335_I	1.026	0.89
131_L	143_Y	1.023	0.89
182_D	185_S	1.022	0.89
175_V	235_A	1.019	0.89
199_K	261_R	1.014	0.89
210_L	216_R	1.013	0.89
157_K	164_V	1.011	0.89
197_K	218_S	1.004	0.88
136_S	139_R	1.002	0.88
171_T	177_S	0.996	0.88
191_T	323_I	0.990	0.88
148_E	151_P	0.990	0.88
261_R	292_H	0.989	0.88
93_F	97_N	0.973	0.87
37_L	42_S	0.971	0.87
184_G	187_L	0.970	0.87
137_A	143_Y	0.969	0.87
49_F	257_E	0.969	0.87
174_G	231_P	0.965	0.86
239_T	243_N	0.964	0.86
119_R	123_Q	0.964	0.86
206_G	268_N	0.963	0.86
121_A	125_L	0.963	0.86
262_F	265_I	0.956	0.86
145_G	148_E	0.951	0.86
260_G	295_S	0.951	0.86
98_L	102_L	0.949	0.85
27_G	90_E	0.942	0.85
325_Q	330_K	0.938	0.85
136_S	144_F	0.934	0.85
35_A	59_M	0.929	0.84
123_Q	146_R	0.926	0.84
136_S	143_Y	0.926	0.84
137_A	141_G	0.924	0.84
23_I	79_T	0.918	0.84
215_A	240_L	0.918	0.84
122_E	143_Y	0.917	0.83
157_K	162_Y	0.915	0.83
212_V	245_V	0.905	0.83
215_A	244_G	0.904	0.83
189_L	210_L	0.893	0.82
86_K	275_M	0.890	0.82
38_D	41_A	0.888	0.81
254_V	284_T	0.887	0.81
103_P	106_T	0.887	0.81
215_A	223_L	0.886	0.81
83_Y	111_V	0.883	0.81
262_F	292_H	0.879	0.81
161_E	168_T	0.878	0.81
95_L	331_V	0.873	0.80
253_N	284_T	0.871	0.80
259_K	291_R	0.868	0.80
152_V	156_E	0.867	0.80
312_V	316_T	0.863	0.80
88_K	120_S	0.850	0.79
141_G	145_G	0.846	0.78
214_F	221_I	0.845	0.78
187_L	191_T	0.843	0.78
186_Q	213_A	0.842	0.78
133_K	204_G	0.841	0.78
135_D	141_G	0.841	0.78
53_Q	56_S	0.839	0.78
46_T	52_W	0.837	0.77
138_R	141_G	0.832	0.77
133_K	144_F	0.832	0.77
117_G	143_Y	0.823	0.76
228_V	272_H	0.821	0.76
41_A	53_Q	0.821	0.76
181_L	209_V	0.818	0.76
313_L	334_A	0.816	0.76
233_V	237_R	0.815	0.76
87_N	174_G	0.814	0.75
210_L	266_I	0.811	0.75
110_V	125_L	0.811	0.75
186_Q	210_L	0.797	0.74
179_D	183_V	0.796	0.74
310_P	332_Y	0.794	0.74
217_H	301_I	0.792	0.73
202_D	206_G	0.791	0.73
102_L	108_I	0.789	0.73
185_S	188_L	0.789	0.73
114_N	262_F	0.787	0.73
223_L	240_L	0.784	0.73
109_F	134_V	0.782	0.72
59_M	62_N	0.782	0.72
153_F	162_Y	0.776	0.72
131_L	145_G	0.775	0.72
286_I	299_L	0.775	0.72
114_N	122_E	0.774	0.72
211_S	223_L	0.774	0.72
276_Q	285_L	0.772	0.72
323_I	333_R	0.772	0.72
305_A	330_K	0.771	0.71
56_S	66_S	0.771	0.71
239_T	242_A	0.769	0.71
258_V	324_A	0.767	0.71
230_A	251_A	0.766	0.71
47_Q	58_Q	0.765	0.71
138_R	181_L	0.764	0.71
80_L	229_S	0.761	0.70
118_V	121_A	0.760	0.70
86_K	110_V	0.758	0.70
119_R	122_E	0.758	0.70
167_L	216_R	0.756	0.70
202_D	268_N	0.755	0.70
158_F	164_V	0.751	0.69
56_S	61_D	0.751	0.69
171_T	179_D	0.749	0.69
133_K	141_G	0.746	0.69
200_V	219_P	0.745	0.69
92_Q	96_M	0.745	0.69
76_D	79_T	0.744	0.69
192_L	214_F	0.743	0.69
77_C	106_T	0.742	0.69
306_F	309_Y	0.742	0.69
171_T	174_G	0.741	0.68
64_R	67_L	0.741	0.68
28_D	51_H	0.741	0.68
51_H	54_V	0.739	0.68
304_N	309_Y	0.738	0.68
84_W	121_A	0.736	0.68
321_E	325_Q	0.734	0.68
208_G	268_N	0.731	0.67
73_D	76_D	0.726	0.67
148_E	152_V	0.723	0.66
267_S	286_I	0.722	0.66
304_N	307_L	0.721	0.66
155_A	160_G	0.721	0.66
199_K	295_S	0.720	0.66
90_E	229_S	0.720	0.66
185_S	209_V	0.720	0.66
52_W	55_L	0.717	0.66
186_Q	189_L	0.716	0.66
320_H	334_A	0.715	0.66
188_L	210_L	0.711	0.65
81_I	111_V	0.709	0.65
250_F	258_V	0.709	0.65
204_G	226_C	0.708	0.65
138_R	142_L	0.707	0.65
29_L	83_Y	0.707	0.65
139_R	143_Y	0.707	0.65
287_R	316_T	0.703	0.64
222_R	246_E	0.703	0.64
154_D	159_W	0.701	0.64
134_V	138_R	0.701	0.64
28_D	34_P	0.701	0.64
125_L	142_L	0.700	0.64
182_D	272_H	0.699	0.64
312_V	315_E	0.698	0.64
237_R	248_E	0.698	0.64
135_D	140_C	0.696	0.64
265_I	289_A	0.695	0.63
184_G	272_H	0.692	0.63
195_H	218_S	0.692	0.63
177_S	235_A	0.690	0.63
206_G	232_A	0.689	0.63
217_H	265_I	0.688	0.63
57_R	61_D	0.687	0.63
204_G	268_N	0.684	0.62
152_V	159_W	0.683	0.62
172_L	274_G	0.681	0.62
57_R	237_R	0.679	0.62
273_D	276_Q	0.678	0.62
145_G	152_V	0.678	0.62
255_F	292_H	0.677	0.61
243_N	278_S	0.676	0.61
313_L	317_F	0.675	0.61
224_T	258_V	0.675	0.61
141_G	144_F	0.673	0.61
153_F	164_V	0.673	0.61
196_T	263_D	0.672	0.61
272_H	304_N	0.672	0.61
240_L	245_V	0.671	0.61
139_R	203_V	0.667	0.60
88_K	92_Q	0.667	0.60
20_Q	53_Q	0.665	0.60
33_L	272_H	0.664	0.60
165_D	217_H	0.664	0.60
18_F	29_L	0.662	0.60
306_F	310_P	0.662	0.60
26_A	42_S	0.661	0.60
322_V	332_Y	0.654	0.59
158_F	161_E	0.653	0.59
289_A	317_F	0.651	0.58
183_V	326_T	0.650	0.58
212_V	243_N	0.649	0.58
232_A	268_N	0.649	0.58
109_F	144_F	0.649	0.58
307_L	310_P	0.647	0.58
314_D	320_H	0.646	0.58
267_S	285_L	0.644	0.58
56_S	67_L	0.644	0.58
102_L	132_N	0.643	0.57
118_V	122_E	0.641	0.57
113_E	117_G	0.639	0.57
114_N	139_R	0.639	0.57
182_D	302_V	0.638	0.57
25_F	30_Q	0.638	0.57
184_G	192_L	0.637	0.57
188_L	266_I	0.636	0.57
181_L	184_G	0.636	0.57
22_R	39_T	0.635	0.57
32_D	58_Q	0.632	0.56
215_A	242_A	0.632	0.56
204_G	255_F	0.630	0.56
271_F	303_A	0.627	0.56
229_S	328_R	0.625	0.55
133_K	136_S	0.622	0.55
96_M	128_Y	0.621	0.55
135_D	139_R	0.618	0.55
40_A	45_H	0.618	0.55
149_K	177_S	0.617	0.54
22_R	42_S	0.616	0.54
181_L	185_S	0.616	0.54
151_P	159_W	0.616	0.54
330_K	333_R	0.616	0.54
109_F	265_I	0.615	0.54
135_D	143_Y	0.614	0.54
47_Q	50_H	0.611	0.54
273_D	278_S	0.607	0.53
86_K	304_N	0.604	0.53
95_L	121_A	0.602	0.53
155_A	165_D	0.601	0.52
101_L	110_V	0.595	0.52
267_S	282_A	0.595	0.52
156_E	162_Y	0.595	0.52
137_A	144_F	0.594	0.52
157_K	161_E	0.593	0.52
201_L	258_V	0.592	0.51
220_K	324_A	0.592	0.51
22_R	75_A	0.591	0.51
26_A	30_Q	0.591	0.51
95_L	173_P	0.588	0.51
157_K	160_G	0.587	0.51
185_S	254_V	0.586	0.51
27_G	48_Q	0.586	0.51
78_D	105_G	0.585	0.51
314_D	318_G	0.585	0.51
177_S	307_L	0.584	0.50
47_Q	55_L	0.584	0.50
97_N	101_L	0.583	0.50
129_A	145_G	0.582	0.50
252_S	256_S	0.582	0.50
148_E	163_S	0.581	0.50
200_V	223_L	0.581	0.50
259_K	327_G	0.580	0.50
254_V	281_A	0.579	0.50
157_K	165_D	0.578	0.50
93_F	172_L	0.577	0.50
20_Q	56_S	0.577	0.50
56_S	60_G	0.576	0.49
103_P	250_F	0.575	0.49
213_A	265_I	0.575	0.49
90_E	174_G	0.573	0.49
235_A	273_D	0.572	0.49
279_L	283_Q	0.571	0.49
202_D	208_G	0.569	0.49
134_V	137_A	0.569	0.49
171_T	207_A	0.569	0.49
90_E	175_V	0.567	0.48
49_F	56_S	0.562	0.48
136_S	142_L	0.561	0.48
299_L	309_Y	0.560	0.48
112_G	118_V	0.558	0.47
286_I	301_I	0.556	0.47
112_G	272_H	0.556	0.47
124_M	127_D	0.556	0.47
198_G	221_I	0.555	0.47
134_V	142_L	0.552	0.47
24_L	43_R	0.552	0.47
201_L	226_C	0.552	0.47
151_P	154_D	0.550	0.46
148_E	157_K	0.549	0.46
72_D	76_D	0.549	0.46
280_D	283_Q	0.547	0.46
172_L	234_E	0.547	0.46
210_L	267_S	0.545	0.46
24_L	77_C	0.544	0.46
22_R	43_R	0.543	0.46
15_S	40_A	0.542	0.45
188_L	206_G	0.542	0.45
89_P	150_Q	0.541	0.45
40_A	43_R	0.540	0.45
303_A	309_Y	0.540	0.45
92_Q	124_M	0.539	0.45
184_G	302_V	0.539	0.45
181_L	266_I	0.539	0.45
170_K	242_A	0.538	0.45
279_L	303_A	0.537	0.45
184_G	271_F	0.536	0.45
39_T	42_S	0.536	0.45
266_I	300_R	0.532	0.44
31_D	54_V	0.532	0.44
25_F	34_P	0.531	0.44
219_P	263_D	0.529	0.44
189_L	209_V	0.528	0.44
222_R	287_R	0.527	0.44
308_P	314_D	0.527	0.44
301_I	332_Y	0.527	0.44
203_V	273_D	0.527	0.44
83_Y	113_E	0.522	0.43
286_I	316_T	0.522	0.43
55_L	66_S	0.522	0.43
140_C	144_F	0.521	0.43
16_D	20_Q	0.521	0.43
231_P	282_A	0.521	0.43
211_S	240_L	0.520	0.43
271_F	309_Y	0.519	0.43
44_A	57_R	0.518	0.43
187_L	331_V	0.517	0.42
88_K	114_N	0.516	0.42
22_R	77_C	0.515	0.42
283_Q	316_T	0.514	0.42
67_L	72_D	0.514	0.42
148_E	210_L	0.513	0.42
133_K	140_C	0.513	0.42
116_S	125_L	0.512	0.42
303_A	312_V	0.512	0.42
143_Y	176_F	0.510	0.42
95_L	135_D	0.510	0.42
85_P	306_F	0.510	0.42
28_D	32_D	0.510	0.42
240_L	247_G	0.509	0.42
286_I	305_A	0.508	0.41
116_S	275_M	0.507	0.41
105_G	108_I	0.506	0.41
202_D	272_H	0.505	0.41
169_V	174_G	0.504	0.41
76_D	248_E	0.504	0.41
205_C	236_S	0.503	0.41
212_V	215_A	0.503	0.41
201_L	252_S	0.502	0.41
115_R	235_A	0.502	0.41
79_T	102_L	0.501	0.41
214_F	218_S	0.501	0.41
255_F	281_A	0.501	0.41
86_K	277_T	0.501	0.41
288_G	292_H	0.501	0.41
177_S	207_A	0.501	0.41
110_V	118_V	0.501	0.41
16_D	22_R	0.500	0.40
47_Q	51_H	0.500	0.40

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
2pjdA	1	0.9738	100	0.34	Contact Map
4dcmA	1	0.9534	100	0.37	Contact Map
3dmgA	1	0.9592	100	0.444	Contact Map
2b3tA	1	0.7114	100	0.684	Contact Map
1nv8A	1	0.6939	100	0.7	Contact Map
1dusA	1	0.5452	100	0.704	Contact Map
3evzA	1	0.5423	99.9	0.743	Contact Map
4mtlA	4	0.5569	99.9	0.748	Contact Map
3lpmA	2	0.5277	99.9	0.749	Contact Map
2ozvA	2	0.4461	99.9	0.754	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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