RS4E - HALSA - GREMLIN Contacts

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RS4E - 30S ribosomal protein S4e

UniProt:	Q9HPC2	Sequences: MTNHQKRLSVPKSWPVERKTETFTAKAGAGPHGESGVPLVVVLRDVLEYVDDTSEAQYAINTDGVLVNGDSVGDVNRPIGMFDILAFPDRDEYYRVFPDEGGRLGLTEIDADAAGSKLNKVTDKTTVSGGRTQLNFHDGSNLALDEDAYAGGDSVVVDTDTNEIVAHFQYEEGALVTAVAGQHAGDIGEIAEINVQPGSASNTVRVDDENGGFETIAEYVVVIDENFVEEDDE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	233 (223)
Sequences:	454 (297)
Seq/√Len:	19.9

HALSA - RS4E
SULSO - RS4E

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
176_V	206_V	4.633	1.00
68_N	117_K	4.167	1.00
86_A	93_Y	4.011	1.00
42_V	106_L	3.856	1.00
134_L	164_I	3.442	1.00
60_I	65_V	3.440	1.00
65_V	87_F	3.438	1.00
66_L	88_P	3.399	1.00
119_N	157_V	3.267	1.00
116_S	156_V	2.940	0.99
121_V	149_Y	2.916	0.99
96_V	106_L	2.727	0.98
152_G	217_A	2.682	0.98
28_G	74_D	2.630	0.98
92_E	108_E	2.555	0.98
123_D	135_N	2.455	0.97
63_D	73_G	2.442	0.97
176_V	190_I	2.266	0.95
64_G	89_D	2.217	0.94
91_D	175_L	2.166	0.94
54_S	58_Y	2.021	0.91
140_S	162_N	1.920	0.89
166_A	225_E	1.902	0.88
9_S	26_K	1.882	0.88
57_Q	75_V	1.851	0.87
158_D	161_T	1.849	0.87
117_K	140_S	1.743	0.83
174_A	222_V	1.722	0.83
5_Q	27_A	1.704	0.82
23_F	58_Y	1.675	0.81
97_F	107_T	1.665	0.80
52_D	60_I	1.642	0.79
29_A	139_G	1.596	0.77
49_Y	92_E	1.562	0.76
31_P	78_P	1.490	0.72
68_N	160_D	1.482	0.72
68_N	138_D	1.457	0.71
50_V	59_A	1.456	0.71
26_K	29_A	1.444	0.70
82_F	140_S	1.392	0.67
68_N	82_F	1.392	0.67
174_A	226_N	1.384	0.67
44_R	68_N	1.374	0.66
115_G	160_D	1.373	0.66
194_N	203_T	1.369	0.66
117_K	138_D	1.356	0.65
164_I	167_H	1.347	0.64
180_A	221_V	1.345	0.64
216_I	219_Y	1.312	0.62
130_G	133_Q	1.311	0.62
5_Q	14_W	1.299	0.61
199_S	206_V	1.293	0.61
153_D	167_H	1.285	0.61
168_F	222_V	1.283	0.60
79_I	96_V	1.282	0.60
187_I	223_I	1.279	0.60
53_T	128_S	1.273	0.60
196_Q	216_I	1.272	0.60
68_N	140_S	1.255	0.59
8_L	129_G	1.251	0.58
71_S	206_V	1.240	0.58
5_Q	23_F	1.228	0.57
5_Q	9_S	1.225	0.57
121_V	143_A	1.204	0.55
158_D	165_V	1.204	0.55
60_I	75_V	1.199	0.55
55_E	80_G	1.186	0.54
79_I	87_F	1.175	0.54
93_Y	114_A	1.175	0.54
5_Q	10_V	1.159	0.53
23_F	126_T	1.149	0.52
58_Y	126_T	1.148	0.52
56_A	60_I	1.147	0.52
20_T	57_Q	1.137	0.51
186_D	208_D	1.128	0.51
215_T	219_Y	1.123	0.50
112_D	128_S	1.119	0.50
54_S	125_T	1.111	0.49
52_D	182_Q	1.107	0.49
204_V	215_T	1.107	0.49
99_D	102_G	1.104	0.49
25_A	40_V	1.104	0.49
169_Q	173_G	1.103	0.49
194_N	205_R	1.092	0.48
159_T	203_T	1.091	0.48
15_P	46_V	1.088	0.48
131_R	211_G	1.084	0.48
66_L	71_S	1.084	0.48
57_Q	119_N	1.082	0.48
132_T	178_A	1.080	0.47
135_N	141_N	1.073	0.47
49_Y	145_D	1.072	0.47
81_M	154_S	1.067	0.47
125_T	135_N	1.062	0.46
174_A	184_A	1.061	0.46
176_V	184_A	1.060	0.46
23_F	120_K	1.059	0.46
91_D	195_V	1.053	0.46
41_V	56_A	1.048	0.45
174_A	190_I	1.044	0.45
94_Y	142_L	1.043	0.45
125_T	133_Q	1.039	0.45
82_F	117_K	1.030	0.44
159_T	165_V	1.026	0.44
133_Q	139_G	1.025	0.44
174_A	205_R	1.015	0.43
3_N	18_R	0.997	0.42
147_D	186_D	0.992	0.42
165_V	168_F	0.989	0.42
11_P	14_W	0.989	0.42
144_L	147_D	0.984	0.41
109_I	113_A	0.981	0.41
120_K	187_I	0.976	0.41
8_L	178_A	0.973	0.41
128_S	189_E	0.971	0.41
158_D	163_E	0.966	0.40
184_A	211_G	0.965	0.40
30_G	121_V	0.961	0.40
23_F	225_E	0.961	0.40
173_G	204_V	0.958	0.40
155_V	159_T	0.950	0.39
20_T	128_S	0.949	0.39
121_V	158_D	0.947	0.39
39_L	78_P	0.943	0.39
114_A	156_V	0.936	0.38
69_G	159_T	0.934	0.38
43_L	65_V	0.933	0.38
40_V	53_T	0.931	0.38
115_G	174_A	0.930	0.38
39_L	79_I	0.925	0.38
53_T	76_N	0.924	0.38
156_V	219_Y	0.922	0.38
20_T	36_G	0.912	0.37
210_N	220_V	0.912	0.37
58_Y	87_F	0.907	0.37
83_D	95_R	0.899	0.36
23_F	42_V	0.894	0.36
49_Y	90_R	0.893	0.36
24_T	78_P	0.887	0.35
22_T	29_A	0.886	0.35
171_E	206_V	0.882	0.35
6_K	198_G	0.882	0.35
26_K	178_A	0.880	0.35
206_V	220_V	0.873	0.35
204_V	220_V	0.870	0.34
196_Q	200_A	0.869	0.34
181_G	185_G	0.869	0.34
103_R	118_L	0.868	0.34
117_K	160_D	0.866	0.34
32_H	68_N	0.865	0.34
128_S	160_D	0.862	0.34
133_Q	149_Y	0.862	0.34
208_D	213_F	0.860	0.34
95_R	143_A	0.859	0.34
30_G	188_G	0.853	0.33
139_G	176_V	0.853	0.33
102_G	213_F	0.846	0.33
176_V	189_E	0.841	0.33
92_E	107_T	0.837	0.33
85_L	92_E	0.835	0.32
7_R	95_R	0.832	0.32
89_D	115_G	0.828	0.32
139_G	157_V	0.820	0.32
99_D	213_F	0.820	0.32
85_L	115_G	0.819	0.32
20_T	41_V	0.819	0.32
45_D	68_N	0.815	0.31
90_R	128_S	0.808	0.31
66_L	220_V	0.804	0.31
60_I	133_Q	0.802	0.31
93_Y	168_F	0.801	0.31
5_Q	16_V	0.800	0.30
102_G	198_G	0.795	0.30
23_F	202_N	0.794	0.30
10_V	155_V	0.788	0.30
37_V	103_R	0.786	0.30
165_V	193_I	0.775	0.29
118_L	154_S	0.773	0.29
114_A	178_A	0.768	0.29
23_F	190_I	0.765	0.29
43_L	60_I	0.765	0.29
74_D	160_D	0.762	0.28
125_T	128_S	0.761	0.28
7_R	14_W	0.761	0.28
186_D	198_G	0.760	0.28
195_V	202_N	0.760	0.28
4_H	8_L	0.759	0.28
3_N	14_W	0.759	0.28
124_K	133_Q	0.759	0.28
29_A	77_R	0.757	0.28
16_V	50_V	0.757	0.28
99_D	118_L	0.756	0.28
85_L	97_F	0.753	0.28
134_L	155_V	0.752	0.28
119_N	155_V	0.752	0.28
49_Y	94_Y	0.743	0.27
18_R	137_H	0.740	0.27
6_K	153_D	0.737	0.27
114_A	128_S	0.736	0.27
86_A	159_T	0.731	0.27
191_A	212_G	0.724	0.26
156_V	184_A	0.720	0.26
61_N	160_D	0.719	0.26
12_K	152_G	0.718	0.26
183_H	195_V	0.716	0.26
15_P	34_E	0.716	0.26
90_R	147_D	0.716	0.26
7_R	30_G	0.716	0.26
4_H	9_S	0.715	0.26
134_L	174_A	0.714	0.26
63_D	95_R	0.710	0.26
15_P	26_K	0.710	0.26
183_H	202_N	0.710	0.26
177_T	196_Q	0.708	0.26
43_L	76_N	0.708	0.26
3_N	25_A	0.702	0.25
28_G	150_A	0.701	0.25
157_V	189_E	0.701	0.25
61_N	76_N	0.699	0.25
27_A	36_G	0.697	0.25
85_L	123_D	0.694	0.25
48_E	65_V	0.692	0.25
23_F	184_A	0.689	0.25
147_D	208_D	0.689	0.25
39_L	149_Y	0.686	0.25
178_A	213_F	0.683	0.24
24_T	81_M	0.683	0.24
136_F	144_L	0.680	0.24
82_F	137_H	0.676	0.24
68_N	72_V	0.672	0.24
189_E	218_E	0.671	0.24
95_R	140_S	0.670	0.24
58_Y	211_G	0.669	0.24
72_V	85_L	0.663	0.24
91_D	111_A	0.663	0.24
11_P	31_P	0.663	0.24
9_S	130_G	0.662	0.23
41_V	204_V	0.662	0.23
26_K	202_N	0.656	0.23
30_G	153_D	0.656	0.23
23_F	156_V	0.656	0.23
96_V	175_L	0.655	0.23
77_R	87_F	0.654	0.23
67_V	121_V	0.653	0.23
157_V	162_N	0.653	0.23
29_A	184_A	0.652	0.23
120_K	182_Q	0.649	0.23
82_F	120_K	0.647	0.23
37_V	51_D	0.637	0.22
30_G	138_D	0.636	0.22
191_A	207_D	0.636	0.22
117_K	137_H	0.635	0.22
106_L	146_E	0.633	0.22
156_V	165_V	0.631	0.22
176_V	199_S	0.627	0.22
120_K	223_I	0.624	0.22
126_T	204_V	0.622	0.22
174_A	225_E	0.617	0.21
6_K	102_G	0.617	0.21
69_G	142_L	0.616	0.21
28_G	217_A	0.615	0.21
96_V	115_G	0.613	0.21
183_H	186_D	0.613	0.21
39_L	215_T	0.602	0.21
103_R	143_A	0.602	0.21
85_L	112_D	0.601	0.21
35_S	161_T	0.596	0.21
123_D	141_N	0.595	0.20
46_V	87_F	0.592	0.20
60_I	129_G	0.592	0.20
166_A	220_V	0.590	0.20
132_T	144_L	0.586	0.20
48_E	142_L	0.585	0.20
8_L	57_Q	0.585	0.20
36_G	96_V	0.581	0.20
21_E	24_T	0.579	0.20
13_S	82_F	0.579	0.20
82_F	221_V	0.579	0.20
176_V	197_P	0.576	0.20
18_R	46_V	0.575	0.20
6_K	14_W	0.575	0.20
23_F	68_N	0.573	0.20
136_F	149_Y	0.573	0.20
144_L	149_Y	0.573	0.20
57_Q	151_G	0.571	0.20
85_L	176_V	0.570	0.19
132_T	147_D	0.567	0.19
13_S	170_Y	0.565	0.19
23_F	197_P	0.564	0.19
122_T	205_R	0.563	0.19
80_G	83_D	0.562	0.19
21_E	72_V	0.561	0.19
124_K	160_D	0.561	0.19
34_E	74_D	0.557	0.19
74_D	215_T	0.556	0.19
29_A	41_V	0.556	0.19
118_L	221_V	0.553	0.19
30_G	80_G	0.553	0.19
118_L	158_D	0.551	0.19
155_V	225_E	0.549	0.19
53_T	93_Y	0.547	0.19
135_N	151_G	0.546	0.19
112_D	165_V	0.544	0.18
78_P	188_G	0.542	0.18
188_G	206_V	0.541	0.18
6_K	13_S	0.533	0.18
13_S	219_Y	0.529	0.18
70_D	140_S	0.528	0.18
156_V	223_I	0.528	0.18
67_V	168_F	0.527	0.18
29_A	137_H	0.525	0.18
67_V	79_I	0.524	0.18
119_N	176_V	0.523	0.18
25_A	76_N	0.523	0.18
42_V	61_N	0.523	0.18
171_E	225_E	0.521	0.18
91_D	130_G	0.520	0.18
7_R	153_D	0.518	0.17
129_G	134_L	0.517	0.17
117_K	173_G	0.517	0.17
44_R	82_F	0.513	0.17
9_S	74_D	0.513	0.17
218_E	225_E	0.512	0.17
102_G	202_N	0.512	0.17
56_A	140_S	0.512	0.17
54_S	68_N	0.509	0.17
49_Y	70_D	0.508	0.17
106_L	211_G	0.507	0.17
82_F	168_F	0.505	0.17
50_V	68_N	0.503	0.17
67_V	140_S	0.503	0.17
57_Q	149_Y	0.502	0.17
169_Q	179_V	0.501	0.17
184_A	191_A	0.500	0.17

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
3zey1	1	0.9657	100	0.051	Contact Map
4ujpF	1	0.9957	100	0.059	Contact Map
3j60E	1	0.8155	100	0.06	Contact Map
3j7aF	1	0.9957	100	0.061	Contact Map
4bpeW	1	0.9957	100	0.064	Contact Map
3j20E	1	1	100	0.205	Contact Map
3kbgA	2	0.8197	100	0.395	Contact Map
2cqjA	1	0.2961	96.5	0.928	Contact Map
1p9kA	1	0.3305	95.7	0.932	Contact Map
1jilA	2	0.0987	90.4	0.945	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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