RL4 - HALSA - GREMLIN Contacts

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RL4 - 50S ribosomal protein L4

UniProt:	Q9HPD3	Sequences: MQVTVRDLDGDDAGTLDLPRVFEEPVRPDLVKRAVLAAQANRTQEYGADEYAGLRTTAESQGSGRGMAHVPKANGQGARVPQTVGGRKAHPPKAEKDHGLDVNDKERKAAVRAAVAATTDSELVADRGHNFDDDVEFPLVVSDDFEDLVKTQDVVSLLEALGVHADIERADEGRTVRAGQGTLRGRKYQEPTSILFVTASESGPSTAARNLAGVDVATGREVNAEDLAPGAEPGRLTVWTESAVEEVAQR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	250 (246)
Sequences:	444 (269)
Seq/√Len:	17.1

HALSA - RL4
SULSO - RL4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
143_D	242_S	5.125	1.00
38_A	102_V	3.961	1.00
197_V	237_T	3.894	1.00
118_T	237_T	3.513	1.00
157_L	161_L	3.435	1.00
115_V	239_W	3.154	0.99
7_D	11_D	2.880	0.98
141_V	161_L	2.866	0.98
164_H	167_I	2.865	0.98
241_E	245_E	2.841	0.98
77_G	83_T	2.681	0.97
70_V	80_V	2.625	0.97
170_A	211_L	2.482	0.95
43_T	46_Y	2.470	0.95
174_R	190_E	2.455	0.95
61_Q	65_R	2.446	0.95
33_R	37_A	2.407	0.95
163_V	236_L	2.341	0.94
49_D	55_R	2.285	0.93
201_E	204_P	2.202	0.92
14_G	241_E	2.198	0.91
173_G	191_P	2.170	0.91
161_L	238_V	2.164	0.91
31_V	233_P	2.097	0.89
154_V	208_A	2.039	0.88
43_T	98_H	2.013	0.87
176_V	188_Y	1.954	0.86
97_D	100_L	1.855	0.82
148_L	157_L	1.850	0.82
34_A	102_V	1.849	0.82
163_V	166_D	1.845	0.82
32_K	36_L	1.842	0.82
134_D	162_G	1.819	0.81
63_S	69_H	1.813	0.81
35_V	39_Q	1.789	0.80
47_G	92_P	1.789	0.80
220_R	246_E	1.754	0.79
32_K	231_A	1.738	0.78
180_Q	183_L	1.738	0.78
179_G	186_R	1.720	0.77
145_F	157_L	1.702	0.76
155_V	164_H	1.700	0.76
33_R	106_E	1.668	0.75
124_V	137_F	1.665	0.75
26_V	233_P	1.663	0.75
46_Y	92_P	1.631	0.73
146_E	199_A	1.628	0.73
18_L	22_F	1.621	0.73
145_F	240_T	1.571	0.70
77_G	85_G	1.570	0.70
134_D	137_F	1.561	0.70
211_L	214_V	1.554	0.69
83_T	243_A	1.513	0.67
108_K	219_G	1.512	0.67
24_E	112_R	1.470	0.65
57_T	98_H	1.467	0.65
125_A	132_D	1.441	0.63
80_V	83_T	1.428	0.63
46_Y	98_H	1.421	0.62
199_A	242_S	1.404	0.61
122_E	125_A	1.389	0.61
35_V	231_A	1.379	0.60
78_A	85_G	1.354	0.58
163_V	238_V	1.354	0.58
189_Q	215_D	1.300	0.55
174_R	178_A	1.294	0.55
114_A	228_A	1.279	0.54
131_F	196_F	1.275	0.54
37_A	41_N	1.251	0.52
194_I	238_V	1.250	0.52
58_A	78_A	1.245	0.52
146_E	200_S	1.239	0.52
115_V	137_F	1.232	0.51
159_E	164_H	1.228	0.51
142_S	241_E	1.226	0.51
40_A	43_T	1.206	0.50
57_T	78_A	1.202	0.49
143_D	153_D	1.197	0.49
176_V	206_T	1.192	0.49
35_V	225_E	1.179	0.48
7_D	142_S	1.175	0.48
84_V	148_L	1.173	0.48
118_T	239_W	1.169	0.47
167_I	211_L	1.164	0.47
92_P	169_R	1.161	0.47
54_L	87_R	1.158	0.47
200_S	203_G	1.158	0.47
72_K	102_V	1.153	0.47
56_T	85_G	1.148	0.46
22_F	115_V	1.145	0.46
172_E	211_L	1.131	0.45
115_V	119_T	1.119	0.44
179_G	184_R	1.116	0.44
84_V	96_K	1.116	0.44
6_R	141_V	1.111	0.44
85_G	136_E	1.109	0.44
33_R	100_L	1.101	0.43
133_D	165_A	1.095	0.43
58_A	63_S	1.093	0.43
63_S	76_Q	1.092	0.43
141_V	242_S	1.092	0.43
60_S	78_A	1.082	0.42
39_Q	226_D	1.080	0.42
56_T	77_G	1.076	0.42
81_P	88_K	1.071	0.42
167_I	214_V	1.067	0.41
164_H	171_D	1.061	0.41
47_G	137_F	1.059	0.41
56_T	79_R	1.057	0.41
131_F	193_S	1.049	0.40
165_A	168_E	1.045	0.40
145_F	160_A	1.043	0.40
101_D	215_D	1.041	0.40
63_S	75_G	1.026	0.39
81_P	84_V	1.013	0.38
181_G	187_K	1.006	0.38
225_E	231_A	1.003	0.38
4_T	12_D	0.998	0.37
239_W	244_V	0.993	0.37
60_S	63_S	0.991	0.37
195_L	215_D	0.987	0.37
31_V	113_A	0.982	0.37
181_G	184_R	0.979	0.36
78_A	107_R	0.978	0.36
149_V	201_E	0.961	0.35
60_S	140_V	0.956	0.35
157_L	196_F	0.956	0.35
144_D	147_D	0.953	0.35
151_T	211_L	0.949	0.35
32_K	187_K	0.948	0.35
41_N	46_Y	0.948	0.35
152_Q	240_T	0.945	0.35
219_G	239_W	0.945	0.35
30_L	189_Q	0.942	0.34
20_R	109_A	0.940	0.34
127_R	215_D	0.939	0.34
173_G	190_E	0.934	0.34
223_N	226_D	0.932	0.34
160_A	242_S	0.930	0.34
40_A	46_Y	0.929	0.34
113_A	166_D	0.921	0.33
108_K	194_I	0.913	0.33
54_L	79_R	0.908	0.33
127_R	233_P	0.906	0.32
156_S	160_A	0.898	0.32
193_S	211_L	0.897	0.32
11_D	180_Q	0.888	0.32
81_P	87_R	0.887	0.31
24_E	90_H	0.884	0.31
56_T	60_S	0.883	0.31
48_A	94_A	0.883	0.31
26_V	120_D	0.883	0.31
181_G	186_R	0.882	0.31
54_L	194_I	0.875	0.31
150_K	153_D	0.874	0.31
70_V	82_Q	0.869	0.31
77_G	133_D	0.869	0.31
59_E	79_R	0.867	0.30
73_A	78_A	0.867	0.30
38_A	107_R	0.865	0.30
11_D	169_R	0.865	0.30
228_A	235_R	0.859	0.30
161_L	200_S	0.852	0.30
188_Y	192_T	0.849	0.30
49_D	54_L	0.848	0.29
61_Q	210_N	0.848	0.29
10_G	146_E	0.844	0.29
24_E	187_K	0.834	0.29
166_D	193_S	0.834	0.29
146_E	207_A	0.832	0.29
170_A	190_E	0.829	0.29
196_F	248_A	0.829	0.29
26_V	118_T	0.828	0.28
50_E	54_L	0.828	0.28
16_L	199_A	0.825	0.28
57_T	61_Q	0.822	0.28
179_G	230_G	0.822	0.28
143_D	241_E	0.817	0.28
183_L	231_A	0.813	0.28
197_V	214_V	0.810	0.28
149_V	153_D	0.810	0.28
111_V	224_A	0.800	0.27
58_A	65_R	0.800	0.27
63_S	88_K	0.794	0.27
14_G	147_D	0.790	0.27
156_S	178_A	0.788	0.27
196_F	208_A	0.788	0.27
50_E	245_E	0.787	0.27
76_Q	139_L	0.787	0.27
140_V	158_L	0.781	0.26
39_Q	215_D	0.781	0.26
114_A	197_V	0.777	0.26
199_A	202_S	0.771	0.26
48_A	98_H	0.766	0.26
41_N	98_H	0.765	0.26
135_V	139_L	0.764	0.25
68_A	147_D	0.760	0.25
162_G	169_R	0.754	0.25
58_A	91_P	0.753	0.25
80_V	166_D	0.753	0.25
172_E	176_V	0.751	0.25
30_L	106_E	0.750	0.25
121_S	147_D	0.748	0.25
15_T	18_L	0.740	0.24
11_D	143_D	0.737	0.24
30_L	196_F	0.732	0.24
181_G	234_G	0.730	0.24
18_L	44_Q	0.730	0.24
11_D	15_T	0.729	0.24
163_V	167_I	0.726	0.24
43_T	56_T	0.725	0.24
45_E	182_T	0.724	0.24
69_H	84_V	0.723	0.24
71_P	80_V	0.722	0.24
111_V	115_V	0.720	0.24
135_V	162_G	0.719	0.23
94_A	137_F	0.718	0.23
32_K	106_E	0.717	0.23
10_G	160_A	0.715	0.23
175_T	189_Q	0.715	0.23
208_A	225_E	0.712	0.23
214_V	247_V	0.708	0.23
57_T	247_V	0.708	0.23
93_K	219_G	0.707	0.23
46_Y	101_D	0.706	0.23
115_V	214_V	0.704	0.23
42_R	51_Y	0.703	0.23
157_L	160_A	0.703	0.23
34_A	105_K	0.701	0.23
75_G	226_D	0.697	0.23
105_K	137_F	0.695	0.22
170_A	193_S	0.692	0.22
228_A	240_T	0.691	0.22
60_S	128_G	0.689	0.22
68_A	214_V	0.688	0.22
18_L	26_V	0.685	0.22
16_L	244_V	0.685	0.22
45_E	245_E	0.680	0.22
118_T	185_G	0.678	0.22
114_A	177_R	0.677	0.22
125_A	141_V	0.672	0.22
61_Q	67_M	0.668	0.21
67_M	82_Q	0.664	0.21
16_L	119_T	0.662	0.21
142_S	207_A	0.662	0.21
124_V	169_R	0.662	0.21
147_D	152_Q	0.658	0.21
3_V	212_A	0.657	0.21
4_T	157_L	0.656	0.21
22_F	217_A	0.654	0.21
174_R	189_Q	0.653	0.21
5_V	136_E	0.652	0.21
30_L	200_S	0.652	0.21
26_V	231_A	0.651	0.21
38_A	112_R	0.649	0.21
196_F	214_V	0.647	0.21
166_D	212_A	0.647	0.21
39_Q	225_E	0.646	0.20
188_Y	197_V	0.642	0.20
68_A	155_V	0.641	0.20
45_E	171_D	0.640	0.20
179_G	197_V	0.640	0.20
64_G	79_R	0.639	0.20
19_P	27_R	0.639	0.20
93_K	103_N	0.635	0.20
45_E	187_K	0.632	0.20
28_P	242_S	0.629	0.20
37_A	40_A	0.627	0.20
224_A	231_A	0.624	0.20
13_A	142_S	0.623	0.20
66_G	92_P	0.621	0.20
94_A	130_N	0.620	0.19
16_L	220_R	0.620	0.19
45_E	180_Q	0.620	0.19
63_S	79_R	0.620	0.19
215_D	237_T	0.620	0.19
111_V	217_A	0.618	0.19
61_Q	222_V	0.616	0.19
9_D	12_D	0.614	0.19
8_L	240_T	0.613	0.19
43_T	57_T	0.613	0.19
229_P	243_A	0.608	0.19
132_D	147_D	0.605	0.19
77_G	105_K	0.602	0.19
101_D	104_D	0.602	0.19
189_Q	192_T	0.601	0.19
220_R	239_W	0.600	0.19
10_G	157_L	0.598	0.19
152_Q	165_A	0.598	0.19
14_G	140_V	0.598	0.19
16_L	105_K	0.596	0.19
192_T	195_L	0.594	0.19
32_K	175_T	0.593	0.18
22_F	152_Q	0.592	0.18
33_R	144_D	0.591	0.18
50_E	125_A	0.589	0.18
170_A	242_S	0.588	0.18
169_R	173_G	0.587	0.18
190_E	203_G	0.586	0.18
24_E	109_A	0.584	0.18
133_D	141_V	0.582	0.18
132_D	153_D	0.580	0.18
224_A	233_P	0.578	0.18
31_V	224_A	0.577	0.18
152_Q	200_S	0.576	0.18
191_P	236_L	0.576	0.18
74_N	247_V	0.576	0.18
132_D	165_A	0.572	0.18
70_V	166_D	0.572	0.18
169_R	236_L	0.571	0.18
8_L	145_F	0.569	0.18
119_T	245_E	0.569	0.18
63_S	81_P	0.566	0.18
149_V	203_G	0.565	0.17
108_K	232_E	0.563	0.17
23_E	94_A	0.562	0.17
130_N	147_D	0.561	0.17
23_E	172_E	0.559	0.17
56_T	73_A	0.557	0.17
149_V	162_G	0.556	0.17
79_R	82_Q	0.554	0.17
10_G	52_A	0.550	0.17
115_V	231_A	0.550	0.17
37_A	100_L	0.548	0.17
4_T	31_V	0.546	0.17
21_V	117_A	0.543	0.17
147_D	160_A	0.542	0.17
148_L	245_E	0.541	0.17
152_Q	243_A	0.540	0.17
63_S	83_T	0.539	0.17
216_V	221_E	0.534	0.16
62_G	210_N	0.533	0.16
43_T	108_K	0.533	0.16
141_V	145_F	0.533	0.16
148_L	154_V	0.531	0.16
159_E	166_D	0.531	0.16
46_Y	49_D	0.530	0.16
97_D	120_D	0.529	0.16
61_Q	101_D	0.527	0.16
66_G	81_P	0.527	0.16
181_G	188_Y	0.526	0.16
103_N	106_E	0.525	0.16
81_P	210_N	0.524	0.16
18_L	146_E	0.523	0.16
43_T	73_A	0.521	0.16
97_D	109_A	0.520	0.16
61_Q	84_V	0.519	0.16
21_V	112_R	0.518	0.16
137_F	239_W	0.518	0.16
153_D	156_S	0.517	0.16
22_F	27_R	0.517	0.16
6_R	161_L	0.516	0.16
162_G	217_A	0.514	0.16
122_E	149_V	0.513	0.16
38_A	41_N	0.513	0.16
141_V	157_L	0.513	0.16
9_D	171_D	0.512	0.16
199_A	246_E	0.512	0.16
115_V	142_S	0.511	0.16
96_K	140_V	0.510	0.16
58_A	80_V	0.507	0.16
8_L	148_L	0.505	0.16
4_T	142_S	0.505	0.16
149_V	204_P	0.503	0.15
43_T	49_D	0.503	0.15
107_R	180_Q	0.503	0.15
101_D	223_N	0.502	0.15
65_R	140_V	0.501	0.15
30_L	128_G	0.500	0.15

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
3j21D	1	1	100	0.289	Contact Map
1vx7F	1	1	100	0.293	Contact Map
4ujqF	1	1	100	0.294	Contact Map
4a17C	1	1	100	0.3	Contact Map
3j39C	1	1	100	0.303	Contact Map
3zf7r	1	0.996	100	0.305	Contact Map
3j3bC	1	1	100	0.309	Contact Map
4w20C	1	1	100	0.309	Contact Map
3j61C	1	1	100	0.309	Contact Map
1vq8C	1	0.984	100	0.309	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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