RLMM - ECOLI - GREMLIN Contacts

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RLMM - Ribosomal RNA large subunit methyltransferase M

UniProt:	P0ADR6	Sequences: MNKVVLLCRPGFEKECAAEITDKAGQREIFGFARVKENAGYVIYECYQPDDGDKLIRELPFSSLIFARQWFVVGELLQHLPPEDRITPIVGMLQGVVEKGGELRVEVADTNESKELLKFCRKFTVPLRAALRDAGVLANYETPKRPVVHVFFIAPGCCYTGYSYSNNNSPFYMGIPRLKFPADAPSRSTLKLEEAFHVFIPADEWDERLANGMWAVDLGACPGGWTYQLVKRNMWVYSVDNGPMAQSLMDTGQVTWLREDGFKFRPTRSNISWMVCDMVEKPAKVAALMAQWLVNGWCRETIFNLKLPMKKRYEEVSHNLAYIQAQLDEHGINAQIQARQLYHDREEVTVHVRRIWAAVGGRRDER	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11794
Length:	366 (347)
Sequences:	451 (273)
Seq/√Len:	14.6

ECOLI - RLMM

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
338_A	348_V	7.000	1.00
246_Q	250_D	5.012	1.00
300_E	351_H	4.918	1.00
119_F	123_F	4.522	1.00
208_R	300_E	4.512	1.00
6_L	20_I	4.010	1.00
171_F	340_Q	3.528	0.99
107_V	113_S	3.510	0.99
201_P	205_W	3.391	0.99
208_R	351_H	3.171	0.98
101_G	146_P	3.153	0.98
216_V	271_I	2.972	0.98
237_Y	257_L	2.941	0.97
93_L	96_V	2.821	0.97
243_P	258_R	2.795	0.96
226_T	230_V	2.707	0.96
335_Q	353_R	2.699	0.96
31_G	44_Y	2.654	0.95
104_R	147_V	2.624	0.95
315_E	318_H	2.519	0.94
125_V	128_R	2.484	0.93
239_V	264_F	2.431	0.92
200_I	205_W	2.413	0.92
265_R	297_W	2.242	0.89
202_A	205_W	2.229	0.88
211_N	233_N	2.196	0.88
107_V	173_M	2.195	0.88
171_F	176_P	2.191	0.87
323_I	352_V	2.145	0.86
111_N	114_K	2.101	0.85
197_H	205_W	2.100	0.85
14_K	37_E	2.096	0.85
32_F	45_E	2.079	0.84
163_S	168_N	2.071	0.84
16_C	21_T	2.063	0.84
152_F	158_C	2.060	0.84
123_F	152_F	2.057	0.84
196_F	278_M	2.047	0.84
10_P	40_G	2.011	0.82
53_D	164_Y	1.930	0.80
205_W	210_A	1.925	0.79
280_E	288_L	1.886	0.78
65_I	313_Y	1.843	0.76
261_G	278_M	1.814	0.75
338_A	350_V	1.789	0.74
199_F	300_E	1.773	0.73
147_V	168_N	1.767	0.73
16_C	67_A	1.721	0.71
12_F	346_E	1.703	0.70
71_F	161_G	1.700	0.70
244_M	249_M	1.667	0.69
119_F	155_P	1.664	0.68
124_T	128_R	1.620	0.66
262_F	285_V	1.619	0.66
86_I	123_F	1.610	0.66
104_R	169_S	1.602	0.65
320_L	338_A	1.564	0.63
189_T	228_Q	1.560	0.63
230_V	251_T	1.544	0.62
123_F	330_H	1.543	0.62
105_V	120_C	1.533	0.62
41_Y	239_V	1.527	0.61
93_L	239_V	1.522	0.61
286_A	290_A	1.516	0.61
47_Y	221_C	1.515	0.61
320_L	350_V	1.506	0.60
336_I	352_V	1.465	0.58
185_P	292_W	1.458	0.58
227_Y	280_E	1.458	0.58
276_C	346_E	1.458	0.58
311_K	314_E	1.437	0.57
3_K	43_I	1.437	0.57
14_K	20_I	1.434	0.56
274_M	301_T	1.433	0.56
110_T	115_E	1.400	0.55
193_E	205_W	1.395	0.54
176_P	340_Q	1.383	0.54
46_C	52_G	1.378	0.53
201_P	206_D	1.373	0.53
217_D	349_T	1.371	0.53
221_C	227_Y	1.359	0.52
7_L	114_K	1.357	0.52
201_P	210_A	1.351	0.52
5_V	71_F	1.344	0.52
26_Q	50_D	1.342	0.51
123_F	348_V	1.342	0.51
177_R	345_R	1.335	0.51
286_A	336_I	1.324	0.50
183_D	289_M	1.322	0.50
214_W	270_N	1.322	0.50
291_Q	326_Q	1.320	0.50
63_S	340_Q	1.308	0.50
187_R	341_L	1.302	0.49
283_A	322_Y	1.298	0.49
315_E	319_N	1.297	0.49
202_A	334_A	1.295	0.49
29_I	54_K	1.291	0.49
40_G	319_N	1.266	0.47
286_A	323_I	1.264	0.47
251_T	337_Q	1.263	0.47
84_D	87_T	1.263	0.47
46_C	51_D	1.262	0.47
290_A	322_Y	1.250	0.46
181_P	189_T	1.248	0.46
220_A	343_H	1.247	0.46
22_D	313_Y	1.234	0.45
9_R	13_E	1.233	0.45
189_T	227_Y	1.221	0.45
239_V	257_L	1.216	0.44
235_W	253_Q	1.214	0.44
234_M	253_Q	1.206	0.44
80_L	121_R	1.203	0.44
94_Q	134_A	1.203	0.44
177_R	343_H	1.186	0.43
192_L	278_M	1.179	0.42
25_G	31_G	1.178	0.42
107_V	354_R	1.176	0.42
243_P	256_W	1.165	0.42
34_R	45_E	1.165	0.42
232_R	287_A	1.162	0.42
52_G	160_T	1.160	0.41
266_P	292_W	1.160	0.41
201_P	351_H	1.160	0.41
21_T	25_G	1.158	0.41
260_D	292_W	1.150	0.41
293_L	352_V	1.147	0.41
227_Y	251_T	1.144	0.41
29_I	46_C	1.140	0.40
100_G	202_A	1.135	0.40
33_A	211_N	1.131	0.40
66_F	345_R	1.126	0.40
52_G	55_L	1.125	0.40
76_L	159_Y	1.124	0.39
290_A	338_A	1.120	0.39
196_F	280_E	1.118	0.39
68_R	345_R	1.116	0.39
226_T	229_L	1.106	0.39
253_Q	272_S	1.104	0.38
76_L	157_C	1.090	0.38
16_C	196_F	1.086	0.37
278_M	281_K	1.081	0.37
270_N	296_G	1.079	0.37
324_Q	328_D	1.075	0.37
100_G	148_V	1.068	0.37
119_F	122_K	1.063	0.36
6_L	16_C	1.059	0.36
181_P	228_Q	1.059	0.36
327_L	334_A	1.055	0.36
156_G	239_V	1.052	0.36
55_L	59_L	1.047	0.35
218_L	305_L	1.018	0.34
33_A	132_R	1.015	0.34
276_C	280_E	1.004	0.33
227_Y	231_K	1.000	0.33
320_L	336_I	0.999	0.33
150_V	158_C	0.991	0.33
86_I	179_K	0.985	0.32
158_C	221_C	0.984	0.32
178_L	193_E	0.981	0.32
3_K	76_L	0.974	0.32
293_L	298_C	0.973	0.32
14_K	18_A	0.973	0.32
260_D	284_K	0.971	0.32
100_G	136_V	0.970	0.32
111_N	201_P	0.970	0.32
286_A	352_V	0.968	0.32
38_N	183_D	0.967	0.32
211_N	234_M	0.966	0.31
20_I	24_A	0.965	0.31
200_I	206_D	0.964	0.31
122_K	313_Y	0.959	0.31
213_M	300_E	0.952	0.31
285_V	350_V	0.942	0.30
154_A	157_C	0.939	0.30
7_L	173_M	0.936	0.30
201_P	208_R	0.932	0.30
185_P	266_P	0.931	0.30
69_Q	106_E	0.928	0.30
227_Y	279_V	0.928	0.30
9_R	292_W	0.924	0.30
188_S	338_A	0.921	0.29
241_N	253_Q	0.919	0.29
69_Q	114_K	0.916	0.29
101_G	141_E	0.916	0.29
175_I	178_L	0.914	0.29
11_G	276_C	0.912	0.29
48_Q	51_D	0.910	0.29
10_P	256_W	0.908	0.29
205_W	234_M	0.898	0.28
195_A	345_R	0.897	0.28
20_I	38_N	0.891	0.28
279_V	344_D	0.890	0.28
249_M	252_G	0.884	0.28
180_F	189_T	0.878	0.27
133_D	336_I	0.878	0.27
208_R	353_R	0.876	0.27
139_N	239_V	0.873	0.27
248_L	254_V	0.863	0.27
263_K	278_M	0.862	0.27
145_R	165_S	0.862	0.27
24_A	55_L	0.862	0.27
29_I	58_E	0.856	0.26
179_K	233_N	0.853	0.26
8_C	13_E	0.851	0.26
213_M	272_S	0.850	0.26
262_F	284_K	0.849	0.26
304_N	344_D	0.847	0.26
289_M	301_T	0.846	0.26
128_R	245_A	0.845	0.26
196_F	234_M	0.841	0.26
293_L	336_I	0.837	0.26
32_F	37_E	0.833	0.25
276_C	307_L	0.832	0.25
302_I	339_R	0.832	0.25
217_D	225_W	0.829	0.25
307_L	345_R	0.828	0.25
316_V	348_V	0.827	0.25
174_G	345_R	0.822	0.25
52_G	239_V	0.821	0.25
206_D	210_A	0.819	0.25
298_C	313_Y	0.819	0.25
205_W	281_K	0.818	0.25
203_D	332_I	0.817	0.25
212_G	253_Q	0.814	0.25
89_I	152_F	0.810	0.25
286_A	322_Y	0.809	0.24
218_L	292_W	0.808	0.24
26_Q	42_V	0.806	0.24
201_P	244_M	0.805	0.24
177_R	346_E	0.801	0.24
52_G	72_V	0.801	0.24
45_E	205_W	0.796	0.24
206_D	233_N	0.794	0.24
10_P	25_G	0.790	0.24
193_E	231_K	0.789	0.24
161_G	345_R	0.785	0.24
74_G	159_Y	0.781	0.23
68_R	177_R	0.780	0.23
289_M	318_H	0.778	0.23
202_A	299_R	0.776	0.23
150_V	289_M	0.774	0.23
45_E	147_V	0.773	0.23
226_T	340_Q	0.772	0.23
86_I	202_A	0.770	0.23
201_P	234_M	0.770	0.23
199_F	337_Q	0.767	0.23
101_G	138_A	0.765	0.23
107_V	151_F	0.761	0.23
193_E	315_E	0.761	0.23
188_S	350_V	0.760	0.23
99_K	198_V	0.758	0.22
199_F	208_R	0.758	0.22
15_E	350_V	0.757	0.22
68_R	307_L	0.756	0.22
20_I	29_I	0.752	0.22
113_S	155_P	0.746	0.22
272_S	319_N	0.743	0.22
185_P	304_N	0.743	0.22
108_A	151_F	0.742	0.22
191_K	219_G	0.742	0.22
191_K	222_P	0.742	0.22
191_K	306_K	0.742	0.22
191_K	223_G	0.742	0.22
191_K	224_G	0.742	0.22
191_K	240_D	0.742	0.22
277_D	347_E	0.742	0.22
191_K	277_D	0.742	0.22
306_K	347_E	0.742	0.22
191_K	347_E	0.742	0.22
240_D	347_E	0.742	0.22
222_P	306_K	0.742	0.22
222_P	277_D	0.742	0.22
222_P	240_D	0.742	0.22
219_G	306_K	0.742	0.22
219_G	277_D	0.742	0.22
219_G	240_D	0.742	0.22
219_G	347_E	0.742	0.22
219_G	224_G	0.742	0.22
219_G	223_G	0.742	0.22
222_P	347_E	0.742	0.22
223_G	240_D	0.742	0.22
240_D	306_K	0.742	0.22
240_D	277_D	0.742	0.22
224_G	347_E	0.742	0.22
224_G	306_K	0.742	0.22
224_G	277_D	0.742	0.22
224_G	240_D	0.742	0.22
223_G	347_E	0.742	0.22
223_G	306_K	0.742	0.22
223_G	277_D	0.742	0.22
219_G	222_P	0.742	0.22
277_D	306_K	0.742	0.22
226_T	274_M	0.739	0.22
47_Y	172_Y	0.738	0.22
95_G	206_D	0.738	0.22
57_R	302_I	0.737	0.22
81_P	86_I	0.735	0.22
40_G	144_K	0.734	0.22
9_R	266_P	0.733	0.22
51_D	54_K	0.733	0.22
29_I	78_Q	0.733	0.22
199_F	351_H	0.730	0.21
80_L	85_R	0.728	0.21
62_S	337_Q	0.728	0.21
27_R	339_R	0.725	0.21
181_P	238_S	0.725	0.21
69_Q	149_H	0.724	0.21
56_I	70_W	0.723	0.21
43_I	330_H	0.723	0.21
123_F	130_A	0.722	0.21
265_R	288_L	0.721	0.21
43_I	159_Y	0.721	0.21
4_V	95_G	0.721	0.21
22_D	26_Q	0.718	0.21
32_F	70_W	0.717	0.21
113_S	285_V	0.716	0.21
7_L	71_F	0.716	0.21
308_P	312_R	0.714	0.21
279_V	292_W	0.714	0.21
229_L	275_V	0.713	0.21
290_A	326_Q	0.709	0.21
146_P	165_S	0.708	0.21
290_A	323_I	0.708	0.21
41_Y	51_D	0.708	0.21
185_P	218_L	0.707	0.21
27_R	46_C	0.705	0.20
105_V	128_R	0.704	0.20
12_F	259_E	0.704	0.20
179_K	214_W	0.703	0.20
85_R	309_M	0.697	0.20
156_G	214_W	0.696	0.20
17_A	42_V	0.695	0.20
185_P	190_L	0.694	0.20
218_L	266_P	0.690	0.20
172_Y	314_E	0.690	0.20
205_W	334_A	0.689	0.20
106_E	163_S	0.689	0.20
283_A	319_N	0.688	0.20
328_D	332_I	0.687	0.20
74_G	339_R	0.685	0.20
89_I	202_A	0.685	0.20
197_H	206_D	0.684	0.20
119_F	265_R	0.683	0.20
303_F	308_P	0.682	0.20
39_A	153_I	0.681	0.20
40_G	198_V	0.680	0.20
199_F	205_W	0.679	0.20
249_M	253_Q	0.676	0.19
34_R	41_Y	0.674	0.19
263_K	280_E	0.671	0.19
161_G	248_L	0.662	0.19
289_M	350_V	0.662	0.19
301_T	352_V	0.661	0.19
85_R	118_K	0.659	0.19
116_L	121_R	0.658	0.19
178_L	275_V	0.656	0.19
194_E	224_G	0.655	0.19
191_K	194_E	0.655	0.19
194_E	277_D	0.655	0.19
194_E	219_G	0.655	0.19
194_E	222_P	0.655	0.19
194_E	240_D	0.655	0.19
194_E	223_G	0.655	0.19
194_E	347_E	0.655	0.19
194_E	306_K	0.655	0.19
314_E	317_S	0.654	0.19
12_F	221_C	0.653	0.19
176_P	198_V	0.652	0.19
196_F	255_T	0.652	0.19
70_W	155_P	0.651	0.19
68_R	308_P	0.651	0.19
330_H	334_A	0.650	0.19
76_L	160_T	0.650	0.19
25_G	32_F	0.648	0.18
111_N	115_E	0.647	0.18
72_V	102_E	0.645	0.18
177_R	276_C	0.644	0.18
180_F	305_L	0.642	0.18
59_L	321_A	0.641	0.18
266_P	304_N	0.640	0.18
225_W	349_T	0.640	0.18
93_L	160_T	0.639	0.18
193_E	342_Y	0.638	0.18
293_L	327_L	0.638	0.18
149_H	218_L	0.637	0.18
174_G	177_R	0.636	0.18
66_F	177_R	0.635	0.18
114_K	152_F	0.634	0.18
109_D	113_S	0.632	0.18
63_S	302_I	0.632	0.18
216_V	313_Y	0.630	0.18
279_V	315_E	0.629	0.18
68_R	276_C	0.628	0.18
25_G	170_P	0.624	0.18
43_I	73_V	0.624	0.18
65_I	348_V	0.623	0.18
108_A	114_K	0.623	0.18
260_D	279_V	0.622	0.18
199_F	248_L	0.620	0.18
217_D	220_A	0.620	0.18
49_P	57_R	0.618	0.18
79_H	258_R	0.617	0.17
180_F	188_S	0.616	0.17
121_R	125_V	0.616	0.17
67_A	171_F	0.615	0.17
323_I	350_V	0.614	0.17
193_E	197_H	0.614	0.17
262_F	304_N	0.613	0.17
226_T	275_V	0.613	0.17
17_A	31_G	0.610	0.17
104_R	353_R	0.609	0.17
241_N	258_R	0.609	0.17
196_F	210_A	0.608	0.17
221_C	271_I	0.606	0.17
235_W	267_T	0.604	0.17
227_Y	260_D	0.604	0.17
6_L	14_K	0.601	0.17
34_R	154_A	0.599	0.17
266_P	308_P	0.599	0.17
35_V	231_K	0.598	0.17
83_E	183_D	0.598	0.17
128_R	141_E	0.597	0.17
319_N	322_Y	0.596	0.17
57_R	326_Q	0.595	0.17
76_L	79_H	0.593	0.17
239_V	340_Q	0.592	0.17
22_D	302_I	0.592	0.17
35_V	239_V	0.592	0.17
34_R	333_N	0.590	0.17
104_R	270_N	0.589	0.17
92_M	95_G	0.588	0.17
67_A	149_H	0.588	0.17
113_S	117_L	0.588	0.17
110_T	159_Y	0.587	0.17
83_E	96_V	0.585	0.16
215_A	314_E	0.585	0.16
201_P	300_E	0.585	0.16
65_I	129_A	0.581	0.16
221_C	243_P	0.581	0.16
229_L	256_W	0.580	0.16
35_V	204_E	0.580	0.16
221_C	279_V	0.580	0.16
161_G	215_A	0.577	0.16
184_A	220_A	0.576	0.16
127_L	255_T	0.576	0.16
102_E	202_A	0.575	0.16
152_F	278_M	0.575	0.16
149_H	303_F	0.575	0.16
279_V	346_E	0.573	0.16
185_P	262_F	0.571	0.16
189_T	276_C	0.570	0.16
260_D	312_R	0.569	0.16
16_C	36_K	0.567	0.16
66_F	349_T	0.566	0.16
73_V	156_G	0.565	0.16
138_A	141_E	0.564	0.16
72_V	161_G	0.564	0.16
62_S	94_Q	0.561	0.16
237_Y	271_I	0.559	0.16
151_F	173_M	0.559	0.16
39_A	130_A	0.556	0.16
20_I	132_R	0.555	0.16
101_G	145_R	0.555	0.16
108_A	188_S	0.554	0.16
100_G	165_S	0.554	0.16
299_R	334_A	0.549	0.15
227_Y	278_M	0.549	0.15
218_L	284_K	0.548	0.15
188_S	279_V	0.548	0.15
262_F	266_P	0.547	0.15
72_V	94_Q	0.545	0.15
119_F	288_L	0.541	0.15
200_I	300_E	0.540	0.15
63_S	91_G	0.540	0.15
126_P	316_V	0.539	0.15
317_S	320_L	0.538	0.15
7_L	161_G	0.537	0.15
200_I	210_A	0.536	0.15
204_E	247_S	0.536	0.15
94_Q	321_A	0.534	0.15
141_E	145_R	0.534	0.15
73_V	338_A	0.534	0.15
256_W	279_V	0.532	0.15
110_T	151_F	0.532	0.15
120_C	152_F	0.531	0.15
58_E	154_A	0.530	0.15
5_V	323_I	0.530	0.15
77_L	88_P	0.530	0.15
202_A	207_E	0.529	0.15
26_Q	153_I	0.528	0.15
174_G	186_S	0.526	0.15
323_I	334_A	0.526	0.15
292_W	298_C	0.523	0.15
284_K	312_R	0.522	0.15
96_V	144_K	0.521	0.15
112_E	115_E	0.520	0.15
204_E	290_A	0.519	0.15
87_T	325_A	0.519	0.15
262_F	308_P	0.517	0.15
34_R	257_L	0.517	0.15
321_A	325_A	0.517	0.15
147_V	150_V	0.515	0.14
292_W	304_N	0.512	0.14
101_G	152_F	0.512	0.14
105_V	169_S	0.511	0.14
66_F	341_L	0.511	0.14
86_I	130_A	0.510	0.14
149_H	163_S	0.510	0.14
184_A	342_Y	0.510	0.14
119_F	152_F	0.508	0.14
85_R	242_G	0.508	0.14
51_D	239_V	0.507	0.14
258_R	322_Y	0.507	0.14
122_K	271_I	0.507	0.14
301_T	340_Q	0.506	0.14
102_E	128_R	0.504	0.14
304_N	309_M	0.503	0.14
228_Q	232_R	0.502	0.14
41_Y	340_Q	0.502	0.14
167_N	199_F	0.500	0.14

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
4aukA	2	0.9754	100	0.493	Contact Map
4v0qA	2	0.5656	99.8	0.844	Contact Map
4k6mA	2	0.571	99.7	0.859	Contact Map
3lkzA	1	0.582	99.7	0.861	Contact Map
3tm4A	1	0.8825	99.7	0.862	Contact Map
4r8rA	1	0.571	99.6	0.867	Contact Map
2px2A	1	0.5492	99.6	0.87	Contact Map
3tmaA	2	0.8443	99.6	0.873	Contact Map
2oxtA	1	0.582	99.5	0.874	Contact Map
2wa2A	1	0.5902	99.5	0.876	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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