RS4 - SULSO - GREMLIN Contacts

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RS4 - 30S ribosomal protein S4

UniProt:	P95987	Sequences: MGDPKKSRKKWETPGHPWIKERIGYEQELLGKYGLRNKREIWIAQSIIRKFRHQARSLLALPPAERAVREKQLVGKLLKMGLLKKETATVDDILSLTEQDLLERRLQTIVYKKGLSNTIYQARQLITHGHIAVNGKRVTSPGYIVNVDEENLIDYYVTSSFKSRPPVMSQQEGGEIGVKQA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	181 (167)
Sequences:	613 (357)
Seq/√Len:	27.6

HALSA - RS4
SULSO - RS4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
110_V	131_I	4.527	1.00
143_Y	149_E	3.290	1.00
130_H	159_S	3.107	1.00
82_L	101_L	3.079	1.00
166_P	169_S	2.676	1.00
14_P	17_P	2.516	0.99
32_K	99_Q	2.439	0.99
36_R	40_E	2.416	0.99
56_R	94_L	2.374	0.99
31_G	120_Y	2.292	0.98
63_P	66_R	2.271	0.98
109_I	153_I	2.185	0.98
107_Q	126_I	2.184	0.98
78_L	147_V	2.157	0.98
52_R	56_R	2.075	0.97
97_T	100_D	2.009	0.96
30_L	41_I	1.977	0.96
113_K	116_S	1.950	0.96
52_R	55_A	1.918	0.95
83_L	93_I	1.881	0.95
107_Q	123_R	1.829	0.94
133_V	143_Y	1.801	0.93
103_E	112_K	1.788	0.93
89_T	124_Q	1.764	0.93
118_T	121_Q	1.680	0.91
121_Q	124_Q	1.673	0.90
34_G	123_R	1.670	0.90
109_I	112_K	1.656	0.90
90_V	106_L	1.614	0.89
20_K	24_G	1.611	0.89
133_V	142_G	1.611	0.89
14_P	34_G	1.589	0.88
77_L	82_L	1.576	0.87
133_V	153_I	1.495	0.84
6_K	9_K	1.444	0.82
23_I	27_Q	1.428	0.82
89_T	92_D	1.419	0.81
33_Y	96_L	1.413	0.81
16_H	19_I	1.409	0.81
119_I	126_I	1.382	0.79
35_L	98_E	1.377	0.79
107_Q	110_V	1.365	0.79
61_L	65_E	1.364	0.78
58_L	69_R	1.355	0.78
33_Y	103_E	1.339	0.77
34_G	40_E	1.325	0.76
33_Y	83_L	1.322	0.76
6_K	10_K	1.279	0.74
19_I	56_R	1.237	0.71
35_L	42_W	1.237	0.71
41_I	97_T	1.233	0.71
121_Q	125_L	1.226	0.71
20_K	131_I	1.219	0.70
53_H	82_L	1.215	0.70
32_K	97_T	1.213	0.70
64_A	72_Q	1.199	0.69
88_A	92_D	1.197	0.69
36_R	39_R	1.187	0.68
27_Q	120_Y	1.161	0.66
66_R	70_E	1.160	0.66
70_E	89_T	1.160	0.66
41_I	45_Q	1.138	0.65
58_L	90_V	1.132	0.64
23_I	36_R	1.116	0.63
98_E	150_E	1.115	0.63
36_R	123_R	1.107	0.62
35_L	40_E	1.097	0.62
17_P	59_L	1.088	0.61
136_K	142_G	1.085	0.61
108_T	119_I	1.081	0.61
155_Y	159_S	1.074	0.60
109_I	151_N	1.072	0.60
8_R	11_W	1.068	0.60
35_L	94_L	1.061	0.59
7_S	127_T	1.055	0.59
148_D	161_F	1.053	0.59
132_A	156_Y	1.049	0.58
72_Q	114_G	1.049	0.58
163_S	167_V	1.042	0.58
12_E	15_G	1.036	0.57
26_E	122_A	1.025	0.56
17_P	26_E	1.020	0.56
125_L	149_E	1.020	0.56
47_I	101_L	1.012	0.55
16_H	22_R	1.002	0.55
142_G	147_V	1.000	0.55
61_L	66_R	0.991	0.54
101_L	150_E	0.990	0.54
87_T	92_D	0.986	0.53
90_V	93_I	0.973	0.53
93_I	96_L	0.972	0.52
42_W	58_L	0.970	0.52
40_E	123_R	0.966	0.52
119_I	125_L	0.966	0.52
132_A	140_S	0.958	0.51
91_D	94_L	0.956	0.51
4_P	171_Q	0.954	0.51
28_E	143_Y	0.953	0.51
146_N	149_E	0.941	0.50
8_R	18_W	0.927	0.49
55_A	71_K	0.909	0.48
138_V	153_I	0.904	0.47
15_G	19_I	0.903	0.47
5_K	10_K	0.893	0.46
100_D	151_N	0.876	0.45
55_A	92_D	0.875	0.45
134_N	154_D	0.873	0.45
76_K	80_M	0.870	0.45
7_S	64_A	0.866	0.44
14_P	55_A	0.860	0.44
80_M	144_I	0.859	0.44
47_I	144_I	0.859	0.44
66_R	134_N	0.858	0.44
35_L	108_T	0.853	0.43
118_T	128_H	0.850	0.43
147_V	151_N	0.847	0.43
44_A	101_L	0.845	0.43
127_T	132_A	0.842	0.43
51_F	83_L	0.837	0.42
167_V	171_Q	0.835	0.42
132_A	152_L	0.831	0.42
92_D	124_Q	0.831	0.42
22_R	35_L	0.827	0.41
60_A	88_A	0.820	0.41
117_N	131_I	0.819	0.41
113_K	151_N	0.815	0.41
93_I	110_V	0.814	0.41
51_F	73_L	0.810	0.40
110_V	115_L	0.809	0.40
94_L	123_R	0.799	0.39
25_Y	45_Q	0.798	0.39
93_I	156_Y	0.798	0.39
27_Q	31_G	0.795	0.39
53_H	57_S	0.793	0.39
19_I	53_H	0.790	0.39
4_P	127_T	0.789	0.39
13_T	138_V	0.783	0.38
84_K	161_F	0.778	0.38
113_K	167_V	0.773	0.38
16_H	37_N	0.771	0.37
27_Q	91_D	0.768	0.37
75_G	79_K	0.767	0.37
164_R	167_V	0.766	0.37
22_R	94_L	0.765	0.37
34_G	124_Q	0.763	0.37
115_L	131_I	0.761	0.37
20_K	73_L	0.759	0.37
91_D	124_Q	0.752	0.36
64_A	90_V	0.743	0.35
21_E	30_L	0.741	0.35
62_P	66_R	0.740	0.35
155_Y	162_K	0.739	0.35
41_I	136_K	0.736	0.35
49_R	53_H	0.732	0.35
51_F	101_L	0.717	0.34
97_T	133_V	0.715	0.33
102_L	111_Y	0.714	0.33
94_L	121_Q	0.708	0.33
29_L	36_R	0.707	0.33
8_R	129_G	0.707	0.33
34_G	38_K	0.706	0.33
73_L	77_L	0.700	0.32
82_L	118_T	0.696	0.32
14_P	24_G	0.696	0.32
89_T	119_I	0.695	0.32
59_L	70_E	0.693	0.32
14_P	123_R	0.693	0.32
9_K	14_P	0.689	0.32
161_F	169_S	0.687	0.32
19_I	25_Y	0.681	0.31
26_E	93_I	0.676	0.31
6_K	18_W	0.673	0.31
22_R	120_Y	0.672	0.31
119_I	124_Q	0.672	0.31
13_T	48_I	0.671	0.31
48_I	98_E	0.670	0.31
7_S	10_K	0.667	0.30
49_R	52_R	0.661	0.30
108_T	145_V	0.661	0.30
32_K	109_I	0.658	0.30
151_N	154_D	0.657	0.30
51_F	93_I	0.654	0.29
137_R	156_Y	0.650	0.29
134_N	155_Y	0.649	0.29
41_I	102_L	0.647	0.29
42_W	49_R	0.646	0.29
16_H	42_W	0.641	0.29
44_A	147_V	0.640	0.29
52_R	96_L	0.639	0.29
94_L	102_L	0.634	0.28
72_Q	76_K	0.633	0.28
27_Q	66_R	0.633	0.28
106_L	153_I	0.630	0.28
132_A	135_G	0.630	0.28
138_V	163_S	0.629	0.28
165_P	169_S	0.628	0.28
31_G	73_L	0.628	0.28
39_R	42_W	0.627	0.28
37_N	96_L	0.625	0.28
84_K	117_N	0.624	0.28
120_Y	124_Q	0.623	0.28
56_R	60_A	0.621	0.27
56_R	79_K	0.620	0.27
75_G	92_D	0.617	0.27
76_K	103_E	0.604	0.26
30_L	86_E	0.603	0.26
13_T	32_K	0.601	0.26
20_K	125_L	0.601	0.26
62_P	65_E	0.598	0.26
26_E	35_L	0.596	0.26
61_L	81_G	0.591	0.26
61_L	112_K	0.591	0.26
37_N	42_W	0.591	0.26
116_S	160_S	0.588	0.25
129_G	137_R	0.579	0.25
30_L	136_K	0.578	0.25
58_L	88_A	0.576	0.25
37_N	56_R	0.572	0.25
115_L	133_V	0.571	0.24
24_G	28_E	0.570	0.24
39_R	96_L	0.566	0.24
134_N	151_N	0.565	0.24
29_L	79_K	0.564	0.24
103_E	154_D	0.562	0.24
164_R	169_S	0.558	0.24
132_A	155_Y	0.555	0.24
134_N	165_P	0.555	0.24
95_S	162_K	0.554	0.24
56_R	59_L	0.554	0.24
19_I	28_E	0.553	0.23
53_H	96_L	0.548	0.23
67_A	70_E	0.541	0.23
50_K	126_I	0.540	0.23
34_G	119_I	0.540	0.23
55_A	121_Q	0.529	0.22
38_K	107_Q	0.524	0.22
83_L	126_I	0.520	0.22
27_Q	64_A	0.519	0.22
50_K	98_E	0.517	0.22
133_V	157_V	0.516	0.22
79_K	84_K	0.515	0.21
17_P	23_I	0.513	0.21
59_L	89_T	0.509	0.21
42_W	48_I	0.509	0.21
35_L	38_K	0.505	0.21
31_G	76_K	0.505	0.21
134_N	152_L	0.503	0.21
25_Y	30_L	0.502	0.21
19_I	49_R	0.500	0.21
155_Y	160_S	0.500	0.21

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
3zey6	1	0.989	100	0.339	Contact Map
4bpeD	2	0.9779	100	0.365	Contact Map
3j80J	1	0.989	100	0.378	Contact Map
4ujpK	1	0.9945	100	0.388	Contact Map
3j38J	1	0.9779	100	0.415	Contact Map
3j20D	1	0.9503	100	0.418	Contact Map
3j7aE	1	0.989	100	0.428	Contact Map
3bbnD	1	0.768	98.9	0.822	Contact Map
2cqjA	1	0.3923	98.8	0.826	Contact Map
1c05A	1	0.6851	98.6	0.841	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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