RL3 - SULSO - GREMLIN Contacts

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RL3 - 50S ribosomal protein L3

UniProt:	Q9UXA8	Sequences: MGHRKLASPRRGSAGLRPRKRSSELLPTPRTWPQINSQNPKLLGFVGYKVGMTHVFMIDDWPNSPTNGKEIYMPVTVLEVPPIIPLALRAYAIDGKGEPNVITEYWSSSSLQFLDITRRIHSISSFLKDDESKKKFDERFNTKLDLIKSNLDRIVYFRLLVSTQPRKIPSLGKKAPDLVEIQIGGGEKKSQLDYALNILGKEITIRDVFKEGQLIDVVGVTKGKGFAGVIKRYSVVELPRWHKHRKGSRKIGTRGPSLGTPSYTPQPGQLGFHRRTEYNKRIIKIGDEPKEINPAGGFVRYGIVRNTYVLLEGSILGSKKRPIFLREPVRPSYVFENPPKITYVNLLSQQG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	351 (330)
Sequences:	397 (238)
Seq/√Len:	13.1

HALSA - RL3
SULSO - RL3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
187_E	190_S	6.881	1.00
277_E	280_K	5.767	1.00
47_G	78_L	4.652	1.00
227_A	231_K	4.617	1.00
151_L	157_F	4.498	1.00
227_A	270_L	4.387	1.00
78_L	315_I	4.359	1.00
230_I	235_V	4.276	1.00
293_N	303_I	4.247	1.00
311_L	315_I	4.073	1.00
219_G	316_L	3.786	0.99
77_V	310_L	3.719	0.99
194_Y	198_I	3.698	0.99
231_K	270_L	3.698	0.99
159_L	195_A	3.655	0.99
59_D	66_T	3.478	0.99
160_L	178_L	3.284	0.98
219_G	323_I	2.953	0.96
83_I	161_V	2.945	0.96
25_L	272_F	2.790	0.95
247_G	250_K	2.680	0.94
14_A	264_T	2.673	0.94
206_R	287_D	2.653	0.93
17_R	233_Y	2.433	0.90
161_V	181_I	2.409	0.89
226_F	267_P	2.377	0.89
47_G	80_V	2.331	0.88
293_N	299_V	2.188	0.84
289_P	293_N	2.185	0.84
14_A	17_R	2.178	0.84
145_D	149_S	2.154	0.83
24_E	30_R	2.148	0.83
226_F	246_K	1.988	0.78
315_I	323_I	1.980	0.77
182_Q	191_Q	1.970	0.77
116_I	160_L	1.911	0.75
159_L	203_I	1.887	0.74
231_K	237_E	1.812	0.71
236_V	246_K	1.746	0.68
151_L	199_L	1.718	0.66
237_E	248_S	1.698	0.65
348_S	351_G	1.685	0.65
233_Y	267_P	1.680	0.64
24_E	28_T	1.647	0.63
243_K	246_K	1.646	0.63
9_P	13_S	1.617	0.61
9_P	12_G	1.598	0.60
43_L	182_Q	1.596	0.60
84_I	202_E	1.589	0.60
42_L	159_L	1.562	0.59
254_R	266_Q	1.552	0.58
88_L	199_L	1.549	0.58
50_V	293_N	1.548	0.58
30_R	218_V	1.504	0.56
22_S	220_V	1.493	0.55
115_D	166_R	1.482	0.55
217_V	315_I	1.437	0.52
293_N	298_F	1.422	0.51
231_K	234_S	1.421	0.51
169_P	305_R	1.420	0.51
156_Y	191_Q	1.412	0.51
308_Y	318_S	1.408	0.51
88_L	159_L	1.405	0.50
115_D	293_N	1.403	0.50
84_I	164_Q	1.382	0.49
213_Q	260_T	1.372	0.49
217_V	323_I	1.362	0.48
92_A	102_I	1.359	0.48
88_L	195_A	1.347	0.47
149_S	153_R	1.344	0.47
35_I	41_K	1.336	0.47
8_S	11_R	1.328	0.46
102_I	155_V	1.326	0.46
24_E	183_I	1.318	0.46
237_E	259_G	1.313	0.46
229_V	247_G	1.304	0.45
78_L	311_L	1.297	0.45
238_L	244_H	1.290	0.44
288_E	308_Y	1.289	0.44
189_K	193_D	1.280	0.44
234_S	270_L	1.278	0.44
214_L	332_S	1.272	0.44
10_R	13_S	1.268	0.43
207_D	224_K	1.252	0.43
277_E	300_R	1.246	0.42
13_S	19_R	1.238	0.42
227_A	234_S	1.238	0.42
293_N	349_Q	1.234	0.42
226_F	230_I	1.229	0.41
105_Y	148_K	1.229	0.41
328_P	331_P	1.227	0.41
79_E	306_N	1.223	0.41
14_A	263_Y	1.222	0.41
232_R	275_R	1.199	0.40
183_I	194_Y	1.198	0.40
144_L	199_L	1.188	0.39
13_S	22_S	1.186	0.39
148_K	196_L	1.181	0.39
239_P	245_R	1.178	0.39
244_H	247_G	1.177	0.39
258_L	307_T	1.171	0.38
239_P	243_K	1.169	0.38
5_K	10_R	1.162	0.38
94_D	346_L	1.162	0.38
194_Y	235_V	1.161	0.38
187_E	286_G	1.153	0.38
286_G	290_K	1.151	0.37
193_D	272_F	1.150	0.37
108_S	197_N	1.149	0.37
139_R	142_T	1.145	0.37
220_V	322_P	1.145	0.37
229_V	235_V	1.136	0.37
212_G	338_P	1.121	0.36
108_S	145_D	1.120	0.36
48_Y	51_G	1.116	0.36
316_L	323_I	1.101	0.35
64_S	106_W	1.094	0.35
26_L	220_V	1.091	0.35
46_V	322_P	1.087	0.34
171_L	323_I	1.083	0.34
162_S	257_S	1.081	0.34
179_V	324_F	1.076	0.34
85_P	145_D	1.070	0.34
239_P	244_H	1.064	0.33
75_V	79_E	1.062	0.33
286_G	309_V	1.055	0.33
108_S	309_V	1.041	0.32
157_F	199_L	1.040	0.32
215_I	282_I	1.039	0.32
213_Q	327_E	1.035	0.32
224_K	231_K	1.027	0.32
259_G	273_H	1.026	0.32
239_P	247_G	1.025	0.31
108_S	215_I	1.022	0.31
29_P	218_V	1.021	0.31
59_D	339_P	1.018	0.31
62_P	284_K	1.017	0.31
34_Q	127_L	1.017	0.31
90_A	154_I	1.013	0.31
167_K	212_G	1.011	0.31
244_H	250_K	1.010	0.31
55_V	69_K	1.008	0.31
89_R	104_E	0.993	0.30
56_F	60_D	0.989	0.30
116_I	122_S	0.987	0.30
165_P	168_I	0.986	0.30
24_E	44_G	0.984	0.30
155_V	222_K	0.983	0.30
79_E	301_Y	0.982	0.30
53_T	75_V	0.970	0.29
88_L	204_T	0.966	0.29
47_G	51_G	0.962	0.29
42_L	203_I	0.959	0.29
265_P	306_N	0.958	0.29
65_P	258_L	0.953	0.28
343_Y	347_L	0.953	0.28
99_P	102_I	0.951	0.28
238_L	243_K	0.951	0.28
60_D	95_G	0.950	0.28
94_D	337_N	0.949	0.28
24_E	27_P	0.943	0.28
34_Q	282_I	0.942	0.28
83_I	179_V	0.939	0.28
240_R	245_R	0.938	0.28
15_G	45_F	0.937	0.28
219_G	320_K	0.935	0.28
243_K	247_G	0.934	0.27
139_R	168_I	0.932	0.27
182_Q	186_G	0.931	0.27
19_R	29_P	0.928	0.27
240_R	243_K	0.925	0.27
183_I	197_N	0.919	0.27
98_E	295_A	0.915	0.27
141_N	145_D	0.914	0.27
102_I	224_K	0.912	0.27
56_F	342_T	0.911	0.27
85_P	205_I	0.908	0.26
293_N	304_V	0.908	0.26
198_I	207_D	0.907	0.26
18_P	21_R	0.905	0.26
88_L	189_K	0.900	0.26
117_T	160_L	0.900	0.26
216_D	255_G	0.898	0.26
80_V	157_F	0.897	0.26
41_K	327_E	0.895	0.26
254_R	261_P	0.893	0.26
86_L	162_S	0.889	0.26
179_V	233_Y	0.888	0.26
237_E	246_K	0.886	0.26
238_L	250_K	0.885	0.25
16_L	160_L	0.882	0.25
205_I	285_I	0.876	0.25
54_H	75_V	0.875	0.25
230_I	246_K	0.874	0.25
93_I	272_F	0.871	0.25
233_Y	274_R	0.869	0.25
50_V	289_P	0.868	0.25
209_F	282_I	0.863	0.25
62_P	293_N	0.859	0.24
97_G	348_S	0.859	0.24
167_K	202_E	0.857	0.24
97_G	296_G	0.852	0.24
31_T	329_V	0.851	0.24
215_I	219_G	0.850	0.24
304_V	323_I	0.840	0.24
48_Y	163_T	0.837	0.24
88_L	307_T	0.837	0.24
140_F	230_I	0.833	0.23
244_H	248_S	0.830	0.23
251_I	254_R	0.828	0.23
178_L	272_F	0.828	0.23
54_H	79_E	0.819	0.23
101_V	203_I	0.819	0.23
193_D	196_L	0.816	0.23
87_A	177_D	0.814	0.23
48_Y	52_M	0.813	0.23
259_G	334_V	0.813	0.23
272_F	340_K	0.812	0.23
342_T	345_N	0.812	0.23
197_N	201_K	0.809	0.23
147_I	199_L	0.807	0.23
15_G	238_L	0.803	0.22
160_L	311_L	0.803	0.22
102_I	154_I	0.802	0.22
7_A	246_K	0.799	0.22
50_V	62_P	0.799	0.22
140_F	147_I	0.799	0.22
240_R	246_K	0.793	0.22
86_L	160_L	0.790	0.22
30_R	144_L	0.790	0.22
230_I	282_I	0.787	0.22
83_I	328_P	0.783	0.22
283_I	341_I	0.783	0.22
22_S	308_Y	0.779	0.21
140_F	199_L	0.773	0.21
213_Q	328_P	0.773	0.21
55_V	126_F	0.773	0.21
46_V	163_T	0.771	0.21
237_E	254_R	0.766	0.21
161_V	179_V	0.763	0.21
24_E	218_V	0.760	0.21
298_F	349_Q	0.757	0.21
217_V	311_L	0.757	0.21
44_G	324_F	0.756	0.21
25_L	217_V	0.755	0.21
275_R	321_R	0.754	0.21
8_S	230_I	0.751	0.21
139_R	171_L	0.749	0.20
22_S	314_S	0.747	0.20
215_I	325_L	0.747	0.20
14_A	175_A	0.745	0.20
16_L	186_G	0.741	0.20
161_V	178_L	0.741	0.20
146_L	149_S	0.741	0.20
237_E	244_H	0.740	0.20
85_P	215_I	0.739	0.20
5_K	11_R	0.738	0.20
16_L	80_V	0.737	0.20
183_I	235_V	0.735	0.20
15_G	219_G	0.733	0.20
116_I	227_A	0.731	0.20
64_S	67_N	0.730	0.20
165_P	330_R	0.730	0.20
251_I	266_Q	0.730	0.20
204_T	307_T	0.729	0.20
191_Q	274_R	0.726	0.20
19_R	322_P	0.725	0.20
115_D	118_R	0.721	0.20
25_L	44_G	0.720	0.19
151_L	272_F	0.720	0.19
82_P	315_I	0.720	0.19
190_S	286_G	0.714	0.19
108_S	144_L	0.714	0.19
74_P	266_Q	0.714	0.19
31_T	203_I	0.714	0.19
35_I	50_V	0.711	0.19
313_G	317_G	0.710	0.19
5_K	12_G	0.710	0.19
16_L	260_T	0.708	0.19
85_P	208_V	0.708	0.19
299_V	309_V	0.707	0.19
111_L	162_S	0.706	0.19
81_P	268_G	0.704	0.19
59_D	71_I	0.703	0.19
216_D	326_R	0.703	0.19
295_A	347_L	0.703	0.19
80_V	233_Y	0.701	0.19
90_A	157_F	0.700	0.19
77_V	273_H	0.700	0.19
143_K	215_I	0.700	0.19
249_R	275_R	0.698	0.19
46_V	179_V	0.697	0.19
48_Y	206_R	0.694	0.19
273_H	340_K	0.692	0.19
83_I	178_L	0.690	0.19
334_V	341_I	0.689	0.18
243_K	250_K	0.684	0.18
291_E	318_S	0.683	0.18
6_L	45_F	0.681	0.18
292_I	305_R	0.679	0.18
32_W	43_L	0.675	0.18
182_Q	345_N	0.673	0.18
8_S	236_V	0.672	0.18
79_E	343_Y	0.669	0.18
167_K	227_A	0.669	0.18
80_V	273_H	0.666	0.18
311_L	338_P	0.664	0.18
64_S	341_I	0.664	0.18
15_G	278_Y	0.663	0.18
192_L	310_L	0.662	0.18
9_P	20_K	0.662	0.18
317_G	321_R	0.661	0.18
172_G	318_S	0.661	0.18
78_L	208_V	0.660	0.18
116_I	178_L	0.658	0.18
239_P	246_K	0.656	0.17
257_S	260_T	0.655	0.17
46_V	83_I	0.655	0.17
103_T	150_N	0.654	0.17
183_I	193_D	0.654	0.17
60_D	306_N	0.653	0.17
297_G	302_G	0.653	0.17
330_R	350_Q	0.651	0.17
235_V	264_T	0.651	0.17
226_F	336_E	0.650	0.17
62_P	285_I	0.650	0.17
253_T	346_L	0.649	0.17
14_A	234_S	0.647	0.17
55_V	219_G	0.647	0.17
83_I	107_S	0.645	0.17
168_I	272_F	0.645	0.17
62_P	303_I	0.642	0.17
185_G	232_R	0.641	0.17
25_L	220_V	0.640	0.17
95_G	102_I	0.639	0.17
141_N	149_S	0.639	0.17
140_F	151_L	0.638	0.17
298_F	303_I	0.638	0.17
246_K	263_Y	0.637	0.17
194_Y	197_N	0.636	0.17
208_V	285_I	0.635	0.17
110_S	293_N	0.635	0.17
250_K	258_L	0.631	0.17
33_P	235_V	0.631	0.17
282_I	309_V	0.631	0.17
23_S	196_L	0.629	0.17
288_E	300_R	0.629	0.17
151_L	204_T	0.629	0.17
187_E	305_R	0.627	0.17
13_S	263_Y	0.625	0.17
230_I	331_P	0.625	0.17
151_L	336_E	0.624	0.17
186_G	238_L	0.621	0.16
77_V	341_I	0.620	0.16
226_F	265_P	0.620	0.16
94_D	97_G	0.618	0.16
153_R	175_A	0.618	0.16
139_R	224_K	0.618	0.16
230_I	273_H	0.617	0.16
244_H	312_E	0.617	0.16
234_S	265_P	0.617	0.16
155_V	168_I	0.617	0.16
48_Y	165_P	0.616	0.16
56_F	72_Y	0.613	0.16
108_S	141_N	0.612	0.16
146_L	282_I	0.611	0.16
246_K	277_E	0.610	0.16
97_G	294_P	0.609	0.16
227_A	330_R	0.609	0.16
169_P	306_N	0.607	0.16
106_W	163_T	0.606	0.16
235_V	304_V	0.606	0.16
107_S	144_L	0.600	0.16
30_R	61_W	0.599	0.16
165_P	235_V	0.597	0.16
8_S	163_T	0.593	0.16
149_S	187_E	0.592	0.16
253_T	266_Q	0.591	0.16
142_T	311_L	0.591	0.16
14_A	171_L	0.590	0.16
307_T	344_V	0.589	0.16
230_I	234_S	0.588	0.15
194_Y	203_I	0.586	0.15
196_L	236_V	0.585	0.15
24_E	258_L	0.585	0.15
202_E	262_S	0.582	0.15
80_V	88_L	0.581	0.15
175_A	213_Q	0.581	0.15
52_M	70_E	0.580	0.15
60_D	282_I	0.580	0.15
17_R	263_Y	0.580	0.15
168_I	171_L	0.579	0.15
244_H	260_T	0.579	0.15
55_V	196_L	0.577	0.15
239_P	248_S	0.576	0.15
225_G	275_R	0.575	0.15
280_K	311_L	0.572	0.15
199_L	330_R	0.572	0.15
55_V	276_T	0.571	0.15
268_G	313_G	0.571	0.15
270_L	330_R	0.568	0.15
248_S	282_I	0.567	0.15
166_R	206_R	0.566	0.15
183_I	198_I	0.565	0.15
93_I	155_V	0.565	0.15
278_Y	311_L	0.565	0.15
172_G	322_P	0.564	0.15
139_R	202_E	0.563	0.15
101_V	167_K	0.563	0.15
12_G	21_R	0.562	0.15
7_A	199_L	0.562	0.15
240_R	244_H	0.561	0.15
90_A	155_V	0.560	0.15
104_E	266_Q	0.560	0.15
253_T	328_P	0.558	0.15
34_Q	290_K	0.557	0.15
98_E	156_Y	0.557	0.15
155_V	264_T	0.556	0.15
47_G	316_L	0.554	0.15
33_P	40_P	0.553	0.15
197_N	236_V	0.553	0.15
33_P	326_R	0.553	0.15
337_N	349_Q	0.552	0.15
33_P	44_G	0.551	0.15
74_P	77_V	0.549	0.14
105_Y	217_V	0.549	0.14
235_V	246_K	0.549	0.14
76_T	118_R	0.549	0.14
167_K	287_D	0.549	0.14
240_R	247_G	0.549	0.14
160_L	214_L	0.549	0.14
191_Q	312_E	0.548	0.14
73_M	124_S	0.548	0.14
57_M	71_I	0.547	0.14
299_V	319_K	0.544	0.14
77_V	175_A	0.542	0.14
17_R	252_G	0.542	0.14
143_K	178_L	0.542	0.14
345_N	349_Q	0.541	0.14
48_Y	173_K	0.539	0.14
297_G	326_R	0.538	0.14
61_W	203_I	0.536	0.14
77_V	210_K	0.536	0.14
252_G	266_Q	0.533	0.14
231_K	350_Q	0.533	0.14
236_V	334_V	0.529	0.14
226_F	239_P	0.529	0.14
297_G	321_R	0.528	0.14
13_S	24_E	0.527	0.14
22_S	46_V	0.527	0.14
90_A	94_D	0.527	0.14
280_K	300_R	0.526	0.14
176_P	252_G	0.525	0.14
94_D	99_P	0.524	0.14
250_K	345_N	0.522	0.14
192_L	346_L	0.521	0.14
207_D	309_V	0.520	0.14
142_T	168_I	0.520	0.14
27_P	274_R	0.519	0.14
67_N	244_H	0.519	0.14
91_Y	232_R	0.518	0.14
54_H	299_V	0.518	0.14
17_R	244_H	0.517	0.14
116_I	140_F	0.517	0.14
143_K	165_P	0.517	0.14
103_T	151_L	0.516	0.14
22_S	25_L	0.515	0.14
203_I	282_I	0.515	0.14
192_L	329_V	0.514	0.14
150_N	234_S	0.514	0.14
208_V	247_G	0.514	0.14
19_R	265_P	0.513	0.14
124_S	127_L	0.513	0.14
22_S	318_S	0.513	0.14
143_K	169_P	0.511	0.13
86_L	199_L	0.509	0.13
179_V	311_L	0.508	0.13
290_K	344_V	0.507	0.13
220_V	274_R	0.506	0.13
191_Q	250_K	0.506	0.13
165_P	211_E	0.506	0.13
194_Y	230_I	0.505	0.13
54_H	280_K	0.505	0.13
249_R	321_R	0.504	0.13
230_I	319_K	0.504	0.13
87_A	213_Q	0.503	0.13
231_K	308_Y	0.503	0.13
125_S	323_I	0.503	0.13
6_L	253_T	0.503	0.13
191_Q	327_E	0.502	0.13
181_I	239_P	0.501	0.13
119_R	175_A	0.501	0.13
160_L	277_E	0.501	0.13
99_P	346_L	0.500	0.13
86_L	115_D	0.500	0.13

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
4ujqE	1	0.9772	100	0.202	Contact Map
3zf7f	1	0.9801	100	0.207	Contact Map
3j61B	1	0.9829	100	0.208	Contact Map
1vx7E	1	0.9772	100	0.208	Contact Map
4a17B	1	0.9772	100	0.213	Contact Map
4w20B	1	0.9772	100	0.216	Contact Map
3j21C	1	0.9601	100	0.27	Contact Map
1vq8B	1	0.9487	100	0.297	Contact Map
1vw3C	1	0.6923	100	0.596	Contact Map
4tp9D	1	0.584	100	0.646	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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