RS3A - HALSA - GREMLIN Contacts

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RS3A - 30S ribosomal protein S3Ae

UniProt:	Q9HRA5	Sequences: MSERSVSKQDQEKRWYTVLAPEEFDRAELGETLAEEPDQVYDRTIQAALSDVRDGGDNNIKLTFQIDDVGSDSASTQFVQAELTRDYQRSLVRRGSSKVAVTVTVLTTDDYRVRIQPVAYTTKQADQSQQHAIRRTMIDLVEEAGEERTFEALLNSIIEGRLSSAIYDEANTIYPLRRVEVEKATLEAHPEEVHEEEETAVDFSGE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	206 (192)
Sequences:	455 (290)
Seq/√Len:	21.0

HALSA - RS3A
SULSO - RS3A

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
85_R	89_R	6.844	1.00
66_I	74_A	3.989	1.00
12_E	35_E	3.446	1.00
115_I	141_V	3.392	1.00
54_D	57_D	3.142	1.00
81_A	184_A	2.889	0.99
45_I	66_I	2.513	0.98
164_S	167_Y	2.501	0.98
35_E	39_Q	2.484	0.98
113_V	153_L	2.468	0.97
153_L	157_I	2.451	0.97
115_I	153_L	2.436	0.97
7_S	10_D	2.409	0.97
17_T	28_E	2.373	0.97
157_I	184_A	2.333	0.96
43_R	109_D	2.268	0.96
116_Q	185_T	2.247	0.96
121_T	125_A	2.159	0.94
165_A	169_E	2.041	0.93
89_R	92_V	2.036	0.93
17_T	31_E	1.960	0.91
137_M	166_I	1.923	0.90
43_R	114_R	1.854	0.88
125_A	129_Q	1.808	0.87
145_G	153_L	1.788	0.86
114_R	134_R	1.747	0.85
43_R	134_R	1.723	0.84
65_Q	79_V	1.688	0.83
135_R	138_I	1.673	0.83
4_R	33_L	1.650	0.82
149_T	152_A	1.643	0.81
88_Q	118_V	1.626	0.81
91_L	96_S	1.624	0.81
13_K	21_P	1.583	0.79
7_S	93_R	1.579	0.79
108_T	149_T	1.577	0.79
117_P	181_V	1.512	0.75
118_V	130_Q	1.500	0.75
135_R	139_D	1.480	0.74
127_Q	131_H	1.394	0.69
65_Q	130_Q	1.388	0.69
37_P	74_A	1.387	0.69
38_D	41_Y	1.383	0.69
106_L	112_R	1.378	0.68
117_P	137_M	1.370	0.68
111_Y	190_P	1.367	0.68
20_A	42_D	1.364	0.67
83_L	180_E	1.348	0.67
62_L	153_L	1.334	0.66
17_T	40_V	1.332	0.66
50_S	130_Q	1.320	0.65
162_L	181_V	1.310	0.64
144_A	156_S	1.309	0.64
109_D	134_R	1.307	0.64
36_E	94_R	1.307	0.64
65_Q	189_H	1.301	0.64
14_R	36_E	1.279	0.62
129_Q	166_I	1.243	0.60
137_M	141_V	1.235	0.60
32_T	111_Y	1.235	0.60
107_T	111_Y	1.229	0.59
153_L	160_G	1.228	0.59
39_Q	74_A	1.228	0.59
65_Q	89_R	1.224	0.59
125_A	130_Q	1.191	0.57
8_K	18_V	1.189	0.57
137_M	179_V	1.187	0.56
65_Q	97_S	1.184	0.56
45_I	174_Y	1.152	0.54
43_R	66_I	1.150	0.54
89_R	147_E	1.136	0.53
117_P	141_V	1.125	0.52
186_L	189_H	1.125	0.52
139_D	144_A	1.111	0.51
167_Y	178_R	1.107	0.51
83_L	148_R	1.104	0.51
101_V	138_I	1.102	0.51
136_T	139_D	1.081	0.49
189_H	192_E	1.076	0.49
116_Q	182_E	1.075	0.49
32_T	40_V	1.065	0.48
46_Q	61_K	1.038	0.47
33_L	172_T	1.033	0.46
18_V	29_L	1.009	0.45
69_V	73_S	0.999	0.44
129_Q	133_I	0.997	0.44
133_I	137_M	0.993	0.44
97_S	130_Q	0.993	0.44
24_F	49_L	0.976	0.43
31_E	167_Y	0.974	0.42
60_I	81_A	0.973	0.42
66_I	115_I	0.970	0.42
160_G	178_R	0.965	0.42
138_I	142_E	0.957	0.41
82_E	103_V	0.955	0.41
91_L	160_G	0.952	0.41
49_L	120_Y	0.945	0.41
120_Y	182_E	0.944	0.41
81_A	157_I	0.942	0.40
15_W	21_P	0.938	0.40
33_L	65_Q	0.935	0.40
64_F	130_Q	0.930	0.40
49_L	91_L	0.928	0.39
16_Y	37_P	0.926	0.39
29_L	170_A	0.926	0.39
48_A	59_N	0.923	0.39
69_V	74_A	0.922	0.39
62_L	157_I	0.917	0.39
100_A	182_E	0.916	0.39
163_S	176_L	0.911	0.38
97_S	139_D	0.910	0.38
19_L	28_E	0.904	0.38
53_R	57_D	0.903	0.38
104_T	110_D	0.902	0.38
109_D	114_R	0.901	0.38
58_N	93_R	0.898	0.38
16_Y	125_A	0.894	0.37
78_F	86_D	0.892	0.37
85_R	90_S	0.889	0.37
101_V	176_L	0.888	0.37
66_I	177_R	0.884	0.37
115_I	145_G	0.884	0.37
114_R	186_L	0.884	0.37
17_T	72_D	0.881	0.37
87_Y	94_R	0.881	0.37
22_E	26_R	0.880	0.36
93_R	149_T	0.876	0.36
141_V	169_E	0.869	0.36
5_S	44_T	0.867	0.36
18_V	155_N	0.864	0.36
45_I	170_A	0.853	0.35
46_Q	90_S	0.849	0.35
95_G	116_Q	0.842	0.34
10_D	33_L	0.841	0.34
125_A	174_Y	0.839	0.34
45_I	52_V	0.838	0.34
50_S	53_R	0.832	0.34
55_G	91_L	0.822	0.33
48_A	77_Q	0.818	0.33
52_V	68_D	0.816	0.33
164_S	170_A	0.812	0.32
16_Y	175_P	0.810	0.32
140_L	166_I	0.810	0.32
27_A	146_E	0.808	0.32
24_F	32_T	0.804	0.32
64_F	190_P	0.801	0.32
64_F	102_T	0.797	0.32
45_I	152_A	0.794	0.31
52_V	115_I	0.789	0.31
100_A	120_Y	0.782	0.31
88_Q	173_I	0.779	0.31
119_A	176_L	0.776	0.30
54_D	191_E	0.773	0.30
69_V	92_V	0.768	0.30
43_R	121_T	0.767	0.30
29_L	83_L	0.766	0.30
44_T	65_Q	0.765	0.30
85_R	138_I	0.761	0.30
184_A	188_A	0.753	0.29
87_Y	180_E	0.753	0.29
39_Q	176_L	0.753	0.29
65_Q	93_R	0.752	0.29
11_Q	108_T	0.747	0.29
112_R	158_I	0.743	0.29
22_E	187_E	0.743	0.29
63_T	146_E	0.740	0.28
80_Q	134_R	0.740	0.28
64_F	76_T	0.738	0.28
62_L	113_V	0.735	0.28
114_R	124_Q	0.733	0.28
70_G	73_S	0.726	0.28
61_K	157_I	0.718	0.27
49_L	111_Y	0.718	0.27
27_A	34_A	0.716	0.27
7_S	11_Q	0.714	0.27
51_D	114_R	0.713	0.27
58_N	96_S	0.713	0.27
113_V	128_S	0.710	0.27
155_N	166_I	0.708	0.27
112_R	187_E	0.704	0.26
112_R	139_D	0.704	0.26
68_D	193_V	0.702	0.26
46_Q	174_Y	0.694	0.26
119_A	141_V	0.692	0.26
37_P	69_V	0.691	0.26
181_V	190_P	0.688	0.26
96_S	120_Y	0.683	0.25
166_I	182_E	0.681	0.25
54_D	128_S	0.678	0.25
112_R	186_L	0.678	0.25
5_S	45_I	0.672	0.25
17_T	56_G	0.671	0.25
165_A	168_D	0.669	0.25
66_I	88_Q	0.668	0.25
36_E	44_T	0.666	0.25
30_G	166_I	0.663	0.24
55_G	58_N	0.661	0.24
39_Q	138_I	0.661	0.24
40_V	63_T	0.659	0.24
55_G	178_R	0.659	0.24
136_T	141_V	0.659	0.24
18_V	76_T	0.659	0.24
156_S	161_R	0.649	0.24
33_L	58_N	0.649	0.24
9_Q	116_Q	0.641	0.23
4_R	50_S	0.640	0.23
64_F	88_Q	0.639	0.23
11_Q	36_E	0.634	0.23
33_L	146_E	0.630	0.23
106_L	156_S	0.629	0.23
49_L	180_E	0.625	0.23
4_R	12_E	0.625	0.23
50_S	100_A	0.622	0.22
95_G	98_K	0.621	0.22
55_G	62_L	0.620	0.22
103_V	138_I	0.617	0.22
39_Q	151_E	0.616	0.22
141_V	189_H	0.615	0.22
79_V	157_I	0.613	0.22
5_S	14_R	0.611	0.22
44_T	143_E	0.611	0.22
25_D	102_T	0.610	0.22
61_K	84_T	0.608	0.22
54_D	179_V	0.606	0.22
20_A	64_F	0.603	0.22
102_T	115_I	0.602	0.22
14_R	17_T	0.601	0.21
80_Q	86_D	0.600	0.21
51_D	73_S	0.599	0.21
91_L	98_K	0.597	0.21
16_Y	71_S	0.594	0.21
88_Q	166_I	0.589	0.21
104_T	187_E	0.587	0.21
105_V	145_G	0.585	0.21
144_A	148_R	0.583	0.21
140_L	181_V	0.580	0.21
7_S	194_H	0.578	0.20
51_D	70_G	0.575	0.20
48_A	74_A	0.575	0.20
159_E	165_A	0.572	0.20
90_S	120_Y	0.568	0.20
110_D	149_T	0.566	0.20
80_Q	186_L	0.566	0.20
46_Q	179_V	0.562	0.20
54_D	108_T	0.561	0.20
133_I	174_Y	0.561	0.20
113_V	143_E	0.560	0.20
140_L	191_E	0.558	0.20
38_D	67_D	0.556	0.20
41_Y	69_V	0.554	0.19
6_V	112_R	0.552	0.19
30_G	133_I	0.551	0.19
83_L	118_V	0.551	0.19
32_T	52_V	0.549	0.19
124_Q	133_I	0.549	0.19
167_Y	185_T	0.544	0.19
93_R	99_V	0.544	0.19
148_R	156_S	0.543	0.19
75_S	158_I	0.538	0.19
15_W	134_R	0.537	0.19
152_A	173_I	0.537	0.19
52_V	79_V	0.535	0.19
57_D	91_L	0.533	0.19
37_P	41_Y	0.533	0.19
92_V	125_A	0.530	0.18
22_E	72_D	0.528	0.18
46_Q	190_P	0.527	0.18
34_A	37_P	0.525	0.18
56_G	62_L	0.525	0.18
11_Q	94_R	0.523	0.18
82_E	140_L	0.522	0.18
154_L	194_H	0.520	0.18
70_G	79_V	0.516	0.18
135_R	181_V	0.515	0.18
58_N	83_L	0.514	0.18
14_R	82_E	0.514	0.18
20_A	186_L	0.513	0.18
192_E	195_E	0.511	0.18
110_D	130_Q	0.510	0.18
61_K	123_K	0.509	0.18
48_A	180_E	0.509	0.18
66_I	146_E	0.508	0.18
29_L	65_Q	0.507	0.18
57_D	93_R	0.507	0.18
98_K	118_V	0.506	0.18
113_V	133_I	0.504	0.17
72_D	115_I	0.501	0.17
139_D	143_E	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
3j38B	1	0.9757	100	0.033	Contact Map
4w23B	1	0.9563	100	0.034	Contact Map
3j7aB	1	0.9369	100	0.035	Contact Map
3j60B	1	0.9417	100	0.038	Contact Map
3zey0	1	0.966	100	0.039	Contact Map
4ujpC	1	0.9563	100	0.041	Contact Map
4bpe4	1	0.9126	100	0.044	Contact Map
3j20A	1	0.9175	100	0.063	Contact Map
3bk6A	3	0.5728	14.1	0.964	Contact Map
1gd8A	1	0.2573	11.2	0.965	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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