RLMC - ECOLI - GREMLIN Contacts

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RLMC - 23S rRNA (uracil(747)-C(5))-methyltransferase RlmC

UniProt:	P75817	Sequences: MQCALYDAGRCRSCQWIMQPIPEQLSAKTADLKNLLADFPVEEWCAPVSGPEQGFRNKAKMVVSGSVEKPLLGMLHRDGTPEDLCDCPLYPASFAPVFAALKPFIARAGLTPYNVARKRGELKYILLTESQSDGGMMLRFVLRSDTKLAQLRKALPWLHEQLPQLKVITVNIQPVHMAIMEGETEIYLTEQQALAERFNDVPLWIRPQSFFQTNPAVASQLYATARDWVRQLPVKHMWDLFCGVGGFGLHCATPDMQLTGIEIASEAIACAKQSAAELGLTRLQFQALDSTQFATAQGDVPELVLVNPPRRGIGKPLCDYLSTMAPRFIIYSSCNAQTMAKDIRELPGFRIERVQLFDMFPHTAHYEVLTLLVKQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13427
Length:	375 (362)
Sequences:	4837 (3549)
Seq/√Len:	186.5

ECOLI - RLMC RLMD TRMA
BACSU - YFJO RLMCD

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
352_E	373_V	3.786	1.00
343_I	372_L	3.581	1.00
23_E	26_S	3.495	1.00
45_C	353_R	3.317	1.00
29_T	33_K	3.285	1.00
257_Q	284_Q	3.230	1.00
76_H	79_G	3.116	1.00
224_T	227_D	2.997	1.00
304_V	321_L	2.977	1.00
142_L	170_V	2.888	1.00
251_C	305_L	2.832	1.00
91_P	129_E	2.638	1.00
24_Q	362_H	2.597	1.00
228_W	353_R	2.408	1.00
195_A	202_P	2.373	1.00
83_D	102_K	2.369	1.00
197_R	202_P	2.303	1.00
351_I	370_T	2.284	1.00
30_A	34_N	2.281	1.00
236_H	257_Q	2.192	1.00
321_L	329_I	2.181	1.00
29_T	46_A	2.169	1.00
204_W	273_Q	2.153	1.00
306_V	313_I	2.147	1.00
70_P	74_M	2.104	1.00
288_L	293_F	2.093	1.00
322_S	347_P	2.088	1.00
225_A	332_S	2.081	1.00
70_P	73_G	2.077	1.00
187_Y	192_Q	2.076	1.00
242_C	260_G	2.045	1.00
197_R	200_D	2.026	1.00
206_R	270_C	2.017	1.00
262_E	268_I	1.928	1.00
202_P	277_E	1.903	1.00
302_E	327_R	1.894	1.00
29_T	47_P	1.891	1.00
238_W	301_P	1.881	1.00
318_C	346_L	1.869	1.00
21_I	25_L	1.852	1.00
54_G	92_A	1.850	1.00
289_D	292_Q	1.842	1.00
242_C	268_I	1.833	1.00
25_L	49_S	1.822	1.00
318_C	345_E	1.809	1.00
273_Q	276_A	1.803	1.00
193_A	204_W	1.797	1.00
221_L	357_F	1.789	1.00
339_M	368_V	1.777	1.00
315_K	319_D	1.771	1.00
223_A	227_D	1.745	1.00
130_S	133_D	1.729	1.00
313_I	318_C	1.727	1.00
92_A	96_P	1.708	1.00
167_V	192_Q	1.674	1.00
280_L	283_L	1.672	1.00
93_S	129_E	1.670	1.00
48_V	357_F	1.667	1.00
74_M	79_G	1.642	1.00
97_V	136_M	1.624	1.00
339_M	370_T	1.601	1.00
226_R	254_P	1.583	1.00
11_C	14_C	1.579	1.00
36_L	354_V	1.574	1.00
63_V	125_I	1.572	1.00
169_T	187_Y	1.572	1.00
57_N	215_P	1.565	1.00
137_M	167_V	1.563	1.00
107_R	157_W	1.558	1.00
48_V	220_Q	1.541	1.00
32_L	356_L	1.537	1.00
328_F	373_V	1.526	1.00
20_P	23_E	1.524	1.00
339_M	343_I	1.522	1.00
219_S	223_A	1.518	1.00
237_M	255_D	1.513	1.00
26_S	29_T	1.487	1.00
322_S	348_G	1.484	1.00
224_T	355_Q	1.484	1.00
45_C	355_Q	1.483	1.00
265_S	269_A	1.482	1.00
41_V	344_R	1.480	1.00
32_L	366_Y	1.475	1.00
70_P	106_A	1.455	1.00
94_F	127_L	1.453	1.00
100_A	161_Q	1.448	1.00
235_K	302_E	1.440	1.00
158_L	165_L	1.438	1.00
118_K	176_H	1.437	1.00
36_L	343_I	1.434	1.00
234_V	256_M	1.429	1.00
5_L	84_L	1.422	1.00
350_R	373_V	1.417	1.00
304_V	326_P	1.417	1.00
248_G	258_L	1.415	1.00
159_H	189_T	1.413	1.00
232_L	235_K	1.408	1.00
260_G	271_A	1.401	1.00
148_L	151_L	1.396	1.00
14_C	87_C	1.392	1.00
11_C	87_C	1.389	1.00
30_A	33_K	1.386	1.00
105_I	122_L	1.378	1.00
126_L	139_R	1.367	1.00
201_V	253_T	1.361	1.00
73_G	79_G	1.355	1.00
135_G	166_K	1.341	1.00
86_D	95_A	1.336	1.00
201_V	249_L	1.315	1.00
19_Q	23_E	1.311	1.00
199_N	250_H	1.308	1.00
6_Y	9_G	1.300	1.00
166_K	191_Q	1.290	1.00
77_R	80_T	1.282	1.00
269_A	272_K	1.281	1.00
100_A	162_L	1.279	1.00
71_L	74_M	1.269	1.00
64_S	81_P	1.265	1.00
26_S	30_A	1.252	1.00
229_V	303_L	1.246	1.00
260_G	285_F	1.244	1.00
271_A	285_F	1.231	1.00
152_R	156_P	1.231	1.00
3_C	11_C	1.221	1.00
335_N	338_T	1.217	1.00
195_A	204_W	1.216	1.00
275_A	285_F	1.208	1.00
54_G	88_P	1.203	1.00
135_G	191_Q	1.200	1.00
224_T	228_W	1.197	1.00
249_L	275_A	1.193	1.00
228_W	371_L	1.193	1.00
96_P	164_Q	1.180	1.00
185_E	208_Q	1.179	1.00
6_Y	18_M	1.175	1.00
66_S	70_P	1.174	1.00
156_P	160_E	1.167	1.00
319_D	323_T	1.166	1.00
260_G	283_L	1.166	1.00
236_H	259_T	1.162	1.00
352_E	371_L	1.150	1.00
55_F	363_T	1.149	1.00
73_G	76_H	1.149	1.00
132_S	197_R	1.141	1.00
249_L	283_L	1.140	1.00
121_E	144_S	1.135	1.00
93_S	96_P	1.131	1.00
74_M	78_D	1.131	1.00
315_K	345_E	1.127	1.00
36_L	339_M	1.126	1.00
255_D	282_R	1.120	1.00
204_W	277_E	1.102	1.00
368_V	372_L	1.099	1.00
224_T	369_L	1.095	1.00
145_D	184_T	1.087	1.00
343_I	351_I	1.087	1.00
33_K	37_A	1.085	1.00
16_W	27_A	1.085	1.00
252_A	280_L	1.082	1.00
59_A	90_Y	1.077	1.00
19_Q	27_A	1.076	1.00
248_G	283_L	1.070	1.00
93_S	136_M	1.063	1.00
231_Q	237_M	1.061	1.00
353_R	371_L	1.059	1.00
154_A	157_W	1.056	1.00
151_L	155_L	1.055	1.00
157_W	161_Q	1.051	1.00
192_Q	196_E	1.051	1.00
225_A	330_I	1.047	1.00
121_E	143_R	1.046	1.00
220_Q	223_A	1.044	1.00
261_I	293_F	1.039	1.00
51_P	220_Q	1.038	1.00
85_C	99_A	1.037	1.00
200_D	253_T	1.036	1.00
273_Q	277_E	1.035	1.00
25_L	47_P	1.033	1.00
169_T	207_P	1.031	1.00
133_D	197_R	1.028	1.00
265_S	287_A	1.028	1.00
35_L	336_A	1.025	1.00
151_L	158_L	1.024	1.00
3_C	14_C	1.024	1.00
199_N	219_S	1.018	1.00
269_A	273_Q	1.012	1.00
220_Q	357_F	1.011	1.00
329_I	349_F	1.010	0.99
103_P	106_A	1.009	0.99
44_W	356_L	1.002	0.99
215_P	218_A	1.001	0.99
53_Q	362_H	0.997	0.99
97_V	162_L	0.990	0.99
224_T	353_R	0.989	0.99
240_L	317_L	0.989	0.99
54_G	86_D	0.988	0.99
48_V	355_Q	0.986	0.99
138_L	165_L	0.981	0.99
33_K	44_W	0.980	0.99
209_S	270_C	0.979	0.99
150_Q	153_K	0.978	0.99
319_D	345_E	0.978	0.99
242_C	271_A	0.977	0.99
242_C	285_F	0.975	0.99
274_S	278_L	0.973	0.99
329_I	346_L	0.973	0.99
209_S	267_A	0.970	0.99
231_Q	235_K	0.966	0.99
15_Q	364_A	0.963	0.99
272_K	284_Q	0.962	0.99
201_V	252_A	0.961	0.99
343_I	370_T	0.960	0.99
52_E	362_H	0.956	0.99
36_L	340_A	0.955	0.99
172_I	186_I	0.950	0.99
185_E	207_P	0.949	0.99
139_R	207_P	0.947	0.99
301_P	304_V	0.945	0.99
326_P	349_F	0.940	0.99
155_L	159_H	0.938	0.99
45_C	228_W	0.938	0.99
97_V	100_A	0.925	0.99
249_L	280_L	0.925	0.99
4_A	86_D	0.924	0.99
54_G	95_A	0.922	0.99
199_N	223_A	0.921	0.99
259_T	301_P	0.920	0.99
156_P	159_H	0.916	0.99
229_V	330_I	0.916	0.99
224_T	357_F	0.915	0.99
129_E	136_M	0.913	0.99
3_C	87_C	0.910	0.99
237_M	303_L	0.910	0.99
290_S	294_A	0.909	0.99
259_T	286_Q	0.907	0.99
195_A	277_E	0.904	0.99
369_L	373_V	0.903	0.99
43_E	353_R	0.901	0.99
73_G	78_D	0.901	0.99
201_V	280_L	0.901	0.99
216_A	219_S	0.901	0.99
230_R	328_F	0.899	0.99
276_A	281_T	0.899	0.99
231_Q	255_D	0.898	0.99
325_A	374_K	0.893	0.99
218_A	246_G	0.890	0.99
226_R	253_T	0.889	0.99
102_K	106_A	0.888	0.99
135_G	195_A	0.884	0.99
328_F	371_L	0.879	0.99
217_V	359_M	0.876	0.99
231_Q	303_L	0.875	0.99
40_P	340_A	0.868	0.98
93_S	164_Q	0.867	0.98
263_I	289_D	0.867	0.98
226_R	250_H	0.866	0.98
213_T	359_M	0.864	0.98
140_F	143_R	0.861	0.98
157_W	160_E	0.858	0.98
268_I	287_A	0.855	0.98
190_E	196_E	0.852	0.98
259_T	299_D	0.852	0.98
165_L	168_I	0.847	0.98
48_V	224_T	0.842	0.98
190_E	198_F	0.841	0.98
228_W	355_Q	0.836	0.98
217_V	220_Q	0.834	0.98
100_A	103_P	0.831	0.98
154_A	158_L	0.829	0.98
370_T	373_V	0.827	0.98
69_K	73_G	0.825	0.98
63_V	73_G	0.825	0.98
351_I	372_L	0.824	0.98
237_M	251_C	0.821	0.98
140_F	144_S	0.820	0.98
241_F	291_T	0.818	0.98
238_W	294_A	0.815	0.98
21_I	49_S	0.811	0.98
193_A	196_E	0.810	0.98
239_D	260_G	0.808	0.98
286_Q	293_F	0.808	0.98
175_V	183_E	0.807	0.98
170_V	188_L	0.806	0.98
354_V	370_T	0.806	0.98
90_Y	94_F	0.800	0.97
330_I	369_L	0.799	0.97
143_R	174_P	0.798	0.97
306_V	321_L	0.796	0.97
108_A	157_W	0.794	0.97
75_L	79_G	0.792	0.97
171_N	182_G	0.788	0.97
236_H	256_M	0.787	0.97
122_L	140_F	0.786	0.97
327_R	373_V	0.785	0.97
226_R	251_C	0.782	0.97
70_P	75_L	0.781	0.97
35_L	340_A	0.780	0.97
22_P	26_S	0.776	0.97
237_M	258_L	0.776	0.97
104_F	108_A	0.775	0.97
28_K	358_D	0.773	0.97
272_K	276_A	0.773	0.97
6_Y	15_Q	0.772	0.97
210_F	334_C	0.771	0.97
21_I	52_E	0.770	0.97
225_A	305_L	0.770	0.97
322_S	345_E	0.769	0.97
205_I	211_F	0.762	0.97
51_P	216_A	0.762	0.97
351_I	354_V	0.760	0.96
169_T	185_E	0.760	0.96
235_K	255_D	0.760	0.96
132_S	219_S	0.756	0.96
334_C	367_E	0.755	0.96
266_E	269_A	0.755	0.96
97_V	138_L	0.754	0.96
204_W	270_C	0.754	0.96
158_L	162_L	0.754	0.96
330_I	371_L	0.754	0.96
47_P	356_L	0.752	0.96
221_L	359_M	0.750	0.96
103_P	161_Q	0.748	0.96
69_K	74_M	0.745	0.96
67_V	70_P	0.744	0.96
291_T	314_G	0.744	0.96
213_T	339_M	0.743	0.96
248_G	285_F	0.741	0.96
38_D	42_E	0.741	0.96
327_R	349_F	0.741	0.96
222_Y	247_F	0.739	0.96
169_T	172_I	0.737	0.96
59_A	94_F	0.736	0.96
70_P	76_H	0.732	0.96
17_I	53_Q	0.731	0.96
108_A	150_Q	0.731	0.96
70_P	79_G	0.730	0.96
194_L	197_R	0.730	0.96
236_H	299_D	0.730	0.96
194_L	198_F	0.729	0.96
171_N	174_P	0.727	0.95
242_C	262_E	0.722	0.95
99_A	103_P	0.721	0.95
63_V	105_I	0.720	0.95
50_G	216_A	0.714	0.95
90_Y	95_A	0.713	0.95
151_L	186_I	0.711	0.95
91_P	95_A	0.706	0.95
268_I	272_K	0.706	0.95
196_E	211_F	0.704	0.95
101_L	125_I	0.703	0.95
153_K	157_W	0.702	0.95
147_K	150_Q	0.701	0.95
189_T	192_Q	0.699	0.94
35_L	39_F	0.698	0.94
368_V	373_V	0.694	0.94
187_Y	190_E	0.693	0.94
63_V	122_L	0.692	0.94
257_Q	299_D	0.692	0.94
29_T	44_W	0.692	0.94
11_C	17_I	0.690	0.94
147_K	151_L	0.689	0.94
71_L	106_A	0.688	0.94
288_L	294_A	0.687	0.94
173_Q	177_M	0.686	0.94
57_N	211_F	0.684	0.94
325_A	348_G	0.684	0.94
46_A	356_L	0.682	0.94
252_A	258_L	0.682	0.94
190_E	194_L	0.682	0.94
228_W	369_L	0.677	0.93
4_A	85_C	0.675	0.93
71_L	105_I	0.674	0.93
153_K	156_P	0.673	0.93
171_N	185_E	0.670	0.93
123_K	173_Q	0.668	0.93
151_L	154_A	0.664	0.93
91_P	94_F	0.664	0.93
6_Y	53_Q	0.664	0.93
4_A	88_P	0.664	0.93
69_K	106_A	0.663	0.93
126_L	141_V	0.663	0.93
222_Y	250_H	0.659	0.93
331_Y	339_M	0.656	0.92
144_S	174_P	0.655	0.92
314_G	318_C	0.654	0.92
226_R	248_G	0.651	0.92
34_N	37_A	0.651	0.92
35_L	337_Q	0.647	0.92
39_F	42_E	0.647	0.92
27_A	31_D	0.646	0.92
159_H	162_L	0.646	0.92
105_I	110_L	0.642	0.92
145_D	174_P	0.640	0.91
44_W	354_V	0.639	0.91
259_T	284_Q	0.639	0.91
74_M	77_R	0.639	0.91
228_W	330_I	0.637	0.91
220_Q	224_T	0.636	0.91
35_L	38_D	0.636	0.91
62_V	124_Y	0.633	0.91
104_F	154_A	0.627	0.91
162_L	165_L	0.627	0.91
21_I	358_D	0.627	0.91
173_Q	178_A	0.627	0.91
137_M	141_V	0.626	0.90
191_Q	195_A	0.624	0.90
332_S	369_L	0.624	0.90
317_L	321_L	0.622	0.90
62_V	81_P	0.620	0.90
103_P	107_R	0.620	0.90
334_C	360_F	0.619	0.90
150_Q	157_W	0.617	0.90
212_Q	334_C	0.617	0.90
23_E	27_A	0.616	0.90
292_Q	295_T	0.615	0.90
208_Q	266_E	0.614	0.90
230_R	254_P	0.614	0.90
322_S	346_L	0.613	0.90
69_K	75_L	0.611	0.89
291_T	316_P	0.611	0.89
32_L	368_V	0.610	0.89
97_V	165_L	0.609	0.89
10_R	77_R	0.608	0.89
24_Q	358_D	0.608	0.89
85_C	102_K	0.605	0.89
356_L	366_Y	0.603	0.89
196_E	199_N	0.601	0.89
357_F	369_L	0.601	0.89
120_G	123_K	0.600	0.89
14_C	17_I	0.600	0.89
221_L	369_L	0.600	0.89
42_E	343_I	0.599	0.88
360_F	367_E	0.599	0.88
201_V	250_H	0.599	0.88
38_D	337_Q	0.597	0.88
241_F	290_S	0.596	0.88
61_M	94_F	0.591	0.88
167_V	171_N	0.591	0.88
61_M	240_L	0.589	0.88
198_F	218_A	0.589	0.88
61_M	98_F	0.589	0.88
137_M	140_F	0.588	0.88
168_I	189_T	0.587	0.87
316_P	319_D	0.587	0.87
21_I	50_G	0.586	0.87
289_D	293_F	0.581	0.87
210_F	367_E	0.581	0.87
265_S	272_K	0.581	0.87
337_Q	341_K	0.581	0.87
217_V	357_F	0.580	0.87
240_L	304_V	0.578	0.87
171_N	178_A	0.578	0.87
247_F	305_L	0.577	0.87
71_L	75_L	0.576	0.86
69_K	76_H	0.574	0.86
44_W	47_P	0.572	0.86
268_I	285_F	0.570	0.86
148_L	152_R	0.570	0.86
211_F	244_V	0.569	0.86
39_F	341_K	0.568	0.86
210_F	360_F	0.567	0.86
333_S	338_T	0.564	0.85
159_H	163_P	0.563	0.85
221_L	332_S	0.561	0.85
203_L	244_V	0.559	0.85
137_M	205_I	0.559	0.85
149_A	152_R	0.558	0.85
321_L	324_M	0.557	0.85
50_G	214_N	0.556	0.85
166_K	194_L	0.555	0.84
261_I	290_S	0.554	0.84
368_V	371_L	0.553	0.84
366_Y	371_L	0.553	0.84
5_L	10_R	0.553	0.84
150_Q	154_A	0.549	0.84
16_W	19_Q	0.548	0.84
73_G	102_K	0.545	0.83
291_T	295_T	0.545	0.83
366_Y	372_L	0.544	0.83
319_D	347_P	0.543	0.83
66_S	72_L	0.543	0.83
194_L	199_N	0.543	0.83
192_Q	198_F	0.542	0.83
104_F	158_L	0.541	0.83
314_G	317_L	0.540	0.83
75_L	78_D	0.539	0.83
271_A	283_L	0.538	0.83
51_P	217_V	0.538	0.83
101_L	140_F	0.537	0.82
362_H	365_H	0.533	0.82
198_F	219_S	0.531	0.82
210_F	308_P	0.531	0.82
129_E	134_G	0.531	0.82
237_M	256_M	0.531	0.82
126_L	181_E	0.529	0.82
310_R	334_C	0.529	0.82
42_E	351_I	0.529	0.82
173_Q	176_H	0.527	0.81
39_F	340_A	0.526	0.81
227_D	353_R	0.526	0.81
173_Q	180_M	0.525	0.81
336_A	366_Y	0.525	0.81
62_V	76_H	0.524	0.81
31_D	337_Q	0.524	0.81
262_E	267_A	0.522	0.81
172_I	184_T	0.522	0.81
178_A	311_R	0.522	0.81
306_V	331_Y	0.522	0.81
303_L	330_I	0.521	0.81
104_F	161_Q	0.520	0.80
101_L	105_I	0.518	0.80
166_K	171_N	0.517	0.80
5_L	85_C	0.515	0.80
53_Q	88_P	0.515	0.80
167_V	172_I	0.514	0.80
290_S	317_L	0.513	0.80
58_K	222_Y	0.513	0.80
29_T	355_Q	0.512	0.79
142_L	145_D	0.512	0.79
141_V	145_D	0.511	0.79
97_V	127_L	0.511	0.79
321_L	326_P	0.511	0.79
342_D	345_E	0.510	0.79
50_G	217_V	0.509	0.79
292_Q	316_P	0.507	0.79
313_I	345_E	0.507	0.79
72_L	76_H	0.506	0.79
5_L	88_P	0.506	0.79
244_V	248_G	0.505	0.78
76_H	80_T	0.505	0.78
327_R	350_R	0.505	0.78
222_Y	246_G	0.505	0.78
55_F	213_T	0.504	0.78
34_N	38_D	0.504	0.78
151_L	170_V	0.504	0.78
235_K	303_L	0.503	0.78
96_P	100_A	0.503	0.78
201_V	278_L	0.502	0.78
167_V	187_Y	0.501	0.78
29_T	356_L	0.501	0.78
62_V	178_A	0.501	0.78
226_R	237_M	0.500	0.78
308_P	334_C	0.500	0.78

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
2jjqA	1	0.8827	100	0.264	Contact Map
1uwvA	1	0.92	100	0.309	Contact Map
3bt7A	1	0.9227	100	0.342	Contact Map
3vseA	1	0.88	100	0.643	Contact Map
4dmgA	2	0.8693	100	0.668	Contact Map
2b78A	1	0.872	100	0.674	Contact Map
1wxxA	2	0.8667	100	0.68	Contact Map
3c0kA	2	0.8747	100	0.689	Contact Map
3k6rA	1	0.6507	100	0.716	Contact Map
2as0A	2	0.88	100	0.719	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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