RRP4 - SULSO - GREMLIN Contacts

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RRP4 - Exosome complex component Rrp4

UniProt:	Q9UXC4	Sequences: MNMSQSQKIVLQPRSIVVPGELLAEGEFQIPWSPYILKINSKYYSTVVGLFDVKDTQFEVIPLEGSFYYPKINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLLGRSINVGEDLRRYLDVGDYVIARIENFDRSIDPVLSVKGKDLGRVSNGIVIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVANNGRIWATCPSRFSEEILIEAIRKIENESHIKGLTDRIKQFIEEKLGERNASSGETKTNS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	249 (212)
Sequences:	760 (515)
Seq/√Len:	35.4

SULSO - RRP4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
80_V	90_V	5.405	1.00
78_G	90_V	5.093	1.00
17_V	60_V	5.075	1.00
92_I	98_A	4.790	1.00
128_A	141_L	4.759	1.00
31_P	35_Y	4.709	1.00
31_P	34_P	4.414	1.00
131_E	142_S	2.821	1.00
32_W	35_Y	2.710	1.00
213_K	217_E	2.422	1.00
124_D	150_R	2.390	1.00
70_P	139_P	2.331	0.99
221_K	224_T	2.226	0.99
81_E	97_K	2.187	0.99
19_P	48_V	2.178	0.99
108_R	116_L	2.167	0.99
35_Y	46_T	2.122	0.99
158_D	193_R	2.084	0.99
211_I	215_E	2.049	0.99
74_D	186_I	2.046	0.99
76_V	156_V	2.024	0.98
75_I	148_L	1.987	0.98
115_D	118_R	1.882	0.97
76_V	80_V	1.875	0.97
17_V	44_Y	1.870	0.97
88_W	117_R	1.800	0.97
125_Y	156_V	1.745	0.96
22_L	42_K	1.728	0.96
228_K	231_I	1.709	0.95
211_I	214_I	1.655	0.95
161_P	183_G	1.646	0.94
69_Y	162_V	1.583	0.93
105_L	167_V	1.578	0.93
197_T	204_E	1.565	0.93
221_K	229_Q	1.561	0.93
77_I	151_V	1.553	0.93
226_R	230_F	1.552	0.92
87_G	102_A	1.534	0.92
160_M	215_E	1.490	0.91
31_P	36_I	1.489	0.91
54_K	58_F	1.480	0.91
214_I	217_E	1.474	0.90
80_V	120_L	1.466	0.90
132_N	138_D	1.463	0.90
226_R	229_Q	1.450	0.90
221_K	225_D	1.441	0.89
23_L	36_I	1.436	0.89
224_T	229_Q	1.433	0.89
167_V	174_M	1.427	0.89
120_L	123_G	1.413	0.88
33_S	151_V	1.405	0.88
218_S	222_G	1.382	0.87
120_L	185_S	1.376	0.87
221_K	230_F	1.364	0.87
43_Y	126_V	1.353	0.86
74_D	130_I	1.350	0.86
141_L	188_V	1.338	0.85
47_V	62_P	1.323	0.85
149_G	167_V	1.311	0.84
90_V	126_V	1.306	0.84
101_P	133_F	1.296	0.84
105_L	108_R	1.278	0.83
19_P	100_L	1.254	0.81
98_A	128_A	1.246	0.81
32_W	43_Y	1.230	0.80
63_L	124_D	1.221	0.80
75_I	127_I	1.207	0.79
214_I	218_S	1.202	0.79
147_D	153_N	1.202	0.79
217_E	226_R	1.195	0.78
156_V	159_I	1.193	0.78
22_L	44_Y	1.186	0.78
178_L	207_L	1.174	0.77
52_D	61_I	1.143	0.75
184_C	188_V	1.140	0.75
219_H	223_L	1.133	0.74
88_W	163_K	1.122	0.74
210_A	214_I	1.101	0.72
106_L	145_G	1.100	0.72
105_L	143_V	1.073	0.70
154_G	178_L	1.062	0.69
46_T	132_N	1.062	0.69
74_D	182_S	1.057	0.69
184_C	227_I	1.051	0.69
73_N	124_D	1.048	0.68
50_L	186_I	1.045	0.68
43_Y	127_I	1.038	0.68
139_P	190_N	1.036	0.67
196_A	208_I	1.034	0.67
207_L	210_A	1.029	0.67
84_E	89_V	1.027	0.67
174_M	206_I	1.022	0.66
140_V	143_V	1.002	0.65
34_P	144_K	0.989	0.64
36_I	160_M	0.981	0.63
54_K	117_R	0.966	0.62
22_L	43_Y	0.964	0.62
73_N	231_I	0.962	0.62
43_Y	199_P	0.956	0.61
98_A	103_S	0.954	0.61
153_N	198_C	0.939	0.60
27_E	159_I	0.936	0.59
83_V	87_G	0.932	0.59
27_E	80_V	0.931	0.59
73_N	129_R	0.930	0.59
118_R	185_S	0.927	0.59
147_D	185_S	0.927	0.59
185_S	199_P	0.922	0.58
30_I	181_K	0.921	0.58
77_I	104_N	0.919	0.58
60_V	158_D	0.914	0.58
148_L	166_R	0.908	0.57
225_D	228_K	0.908	0.57
81_E	202_F	0.907	0.57
109_S	143_V	0.902	0.57
209_E	215_E	0.892	0.56
88_W	116_L	0.891	0.56
217_E	229_Q	0.890	0.56
104_N	133_F	0.889	0.56
224_T	227_I	0.886	0.55
133_F	139_P	0.884	0.55
70_P	209_E	0.884	0.55
66_S	189_A	0.882	0.55
151_V	195_W	0.876	0.54
120_L	130_I	0.874	0.54
78_G	91_D	0.865	0.53
13_P	39_I	0.865	0.53
105_L	116_L	0.859	0.53
210_A	227_I	0.857	0.53
70_P	198_C	0.853	0.52
89_V	222_G	0.850	0.52
60_V	129_R	0.850	0.52
212_R	228_K	0.847	0.52
21_E	160_M	0.843	0.52
53_V	58_F	0.841	0.51
93_K	98_A	0.835	0.51
52_D	183_G	0.830	0.50
213_K	230_F	0.829	0.50
58_F	121_D	0.828	0.50
90_V	98_A	0.826	0.50
21_E	197_T	0.825	0.50
107_G	116_L	0.820	0.50
105_L	114_E	0.817	0.49
72_I	132_N	0.813	0.49
83_V	150_R	0.810	0.49
134_D	137_I	0.808	0.49
44_Y	85_I	0.802	0.48
223_L	226_R	0.801	0.48
214_I	223_L	0.796	0.48
106_L	143_V	0.793	0.47
120_L	126_V	0.788	0.47
45_S	91_D	0.787	0.47
108_R	114_E	0.786	0.47
83_V	102_A	0.784	0.46
209_E	216_N	0.782	0.46
47_V	64_E	0.782	0.46
76_V	201_R	0.778	0.46
224_T	230_F	0.775	0.46
196_A	205_E	0.771	0.45
129_R	144_K	0.769	0.45
21_E	59_E	0.766	0.45
23_L	79_L	0.763	0.45
84_E	196_A	0.763	0.45
106_L	109_S	0.759	0.44
221_K	228_K	0.758	0.44
88_W	114_E	0.757	0.44
105_L	118_R	0.753	0.44
51_F	98_A	0.752	0.44
79_L	129_R	0.752	0.44
135_R	153_N	0.752	0.44
101_P	140_V	0.751	0.44
217_E	222_G	0.743	0.43
44_Y	69_Y	0.743	0.43
66_S	125_Y	0.742	0.43
40_N	50_L	0.742	0.43
42_K	205_E	0.741	0.43
84_E	117_R	0.740	0.43
17_V	23_L	0.737	0.42
20_G	123_G	0.730	0.42
186_I	194_I	0.727	0.42
156_V	164_V	0.725	0.41
102_A	116_L	0.722	0.41
143_V	149_G	0.722	0.41
33_S	140_V	0.720	0.41
24_A	48_V	0.719	0.41
127_I	185_S	0.718	0.41
104_N	126_V	0.708	0.40
46_T	55_D	0.705	0.40
157_I	216_N	0.703	0.40
73_N	125_Y	0.703	0.40
88_W	120_L	0.701	0.39
125_Y	162_V	0.695	0.39
73_N	86_Y	0.691	0.39
109_S	127_I	0.687	0.38
221_K	226_R	0.687	0.38
223_L	227_I	0.684	0.38
120_L	128_A	0.683	0.38
108_R	118_R	0.681	0.38
209_E	217_E	0.680	0.38
33_S	66_S	0.679	0.38
177_T	185_S	0.678	0.38
102_A	124_D	0.674	0.37
53_V	193_R	0.671	0.37
62_P	100_L	0.671	0.37
162_V	174_M	0.667	0.37
217_E	223_L	0.664	0.36
105_L	120_L	0.663	0.36
216_N	228_K	0.658	0.36
36_I	41_S	0.658	0.36
224_T	228_K	0.655	0.36
103_S	127_I	0.654	0.36
77_I	158_D	0.653	0.36
77_I	214_I	0.652	0.36
32_W	36_I	0.651	0.35
225_D	230_F	0.649	0.35
131_E	144_K	0.646	0.35
137_I	179_T	0.644	0.35
62_P	170_K	0.644	0.35
217_E	221_K	0.642	0.35
38_K	41_S	0.641	0.35
25_E	52_D	0.641	0.35
74_D	159_I	0.636	0.34
144_K	147_D	0.630	0.34
86_Y	187_F	0.629	0.34
23_L	230_F	0.628	0.34
24_A	72_I	0.628	0.34
92_I	173_S	0.626	0.34
158_D	176_E	0.625	0.33
105_L	127_I	0.623	0.33
169_G	174_M	0.623	0.33
107_G	194_I	0.619	0.33
48_V	66_S	0.617	0.33
95_P	127_I	0.617	0.33
218_S	229_Q	0.615	0.33
83_V	119_Y	0.613	0.33
92_I	133_F	0.609	0.32
44_Y	101_P	0.607	0.32
69_Y	95_P	0.607	0.32
130_I	166_R	0.605	0.32
131_E	143_V	0.602	0.32
120_L	184_C	0.602	0.32
41_S	134_D	0.599	0.31
155_I	208_I	0.598	0.31
79_L	163_K	0.592	0.31
19_P	123_G	0.588	0.31
93_K	155_I	0.587	0.31
14_R	44_Y	0.582	0.30
87_G	99_Y	0.582	0.30
216_N	223_L	0.581	0.30
100_L	126_V	0.581	0.30
24_A	27_E	0.581	0.30
52_D	178_L	0.580	0.30
148_L	151_V	0.577	0.30
98_A	132_N	0.573	0.30
86_Y	118_R	0.571	0.29
114_E	127_I	0.570	0.29
52_D	75_I	0.569	0.29
139_P	171_N	0.569	0.29
134_D	194_I	0.566	0.29
40_N	202_F	0.566	0.29
80_V	83_V	0.565	0.29
54_K	127_I	0.564	0.29
222_G	226_R	0.564	0.29
115_D	198_C	0.562	0.29
58_F	62_P	0.561	0.29
60_V	155_I	0.558	0.28
222_G	231_I	0.557	0.28
81_E	92_I	0.555	0.28
65_G	156_V	0.554	0.28
207_L	211_I	0.553	0.28
21_E	50_L	0.553	0.28
101_P	172_K	0.552	0.28
28_F	43_Y	0.552	0.28
44_Y	196_A	0.551	0.28
86_Y	104_N	0.548	0.28
139_P	153_N	0.547	0.28
171_N	212_R	0.547	0.28
80_V	124_D	0.546	0.28
144_K	229_Q	0.545	0.28
120_L	150_R	0.545	0.28
97_K	175_Y	0.542	0.27
148_L	164_V	0.541	0.27
27_E	224_T	0.540	0.27
63_L	147_D	0.539	0.27
77_I	173_S	0.537	0.27
137_I	140_V	0.537	0.27
58_F	177_T	0.536	0.27
57_Q	145_G	0.533	0.27
31_P	76_V	0.533	0.27
91_D	94_A	0.533	0.27
206_I	211_I	0.532	0.27
205_E	208_I	0.529	0.26
90_V	205_E	0.529	0.26
124_D	129_R	0.528	0.26
14_R	157_I	0.528	0.26
106_L	147_D	0.525	0.26
125_Y	143_V	0.522	0.26
211_I	219_H	0.521	0.26
61_I	183_G	0.519	0.26
30_I	59_E	0.518	0.26
127_I	142_S	0.518	0.26
96_Y	101_P	0.517	0.26
121_D	124_D	0.517	0.26
18_V	108_R	0.514	0.26
133_F	137_I	0.512	0.25
105_L	187_F	0.512	0.25
34_P	137_I	0.510	0.25
57_Q	129_R	0.509	0.25
219_H	222_G	0.509	0.25
49_G	78_G	0.508	0.25
35_Y	185_S	0.507	0.25
21_E	66_S	0.506	0.25
16_I	20_G	0.505	0.25
135_R	138_D	0.504	0.25
118_R	121_D	0.503	0.25
120_L	142_S	0.502	0.25
132_N	135_R	0.501	0.25
17_V	159_I	0.500	0.25

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
2nn6G	1	0.8394	100	0.297	Contact Map
4ifdG	1	0.8755	100	0.301	Contact Map
2je6I	3	0.8233	100	0.315	Contact Map
2z0sA	1	0.6988	100	0.356	Contact Map
2ba0A	1	0.8715	100	0.368	Contact Map
4ifdH	1	0.8795	100	0.43	Contact Map
2nn6H	1	0.8594	100	0.449	Contact Map
2ja9A	2	0.6667	100	0.481	Contact Map
2nn6I	1	0.6305	99.9	0.65	Contact Map
3m7nA	1	0.6506	99.9	0.668	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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