RS8 - BACSU - GREMLIN Contacts

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RS8 - 30S ribosomal protein S8

UniProt:	P12879	Sequences: MVMTDPIADMLTRIRNANMVRHEKLEIPASKLKREIAEILKREGFIRDVEFVEDSKQGIIRVFLKYGQNNERVITGLKRISKPGLRVYAKSNEVPRVLNGLGIAIISTSQGVLTDKEARAKQAGGEVLAYVW	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	132 (129)
Sequences:	2445 (1161)
Seq/√Len:	102.2

ECOLI - RS8
BACSU - RS8
HALSA - RS8
SULSO - RS8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
41_K	48_D	3.591	1.00
110_Q	121_K	3.420	1.00
12_T	15_R	3.351	1.00
91_S	122_Q	3.284	1.00
35_E	38_E	2.956	1.00
38_E	42_R	2.900	1.00
26_E	61_R	2.690	1.00
10_M	37_A	2.614	1.00
42_R	117_E	2.505	1.00
115_D	119_R	2.414	1.00
117_E	121_K	2.318	1.00
76_G	132_W	2.307	1.00
18_N	72_R	2.279	1.00
9_D	13_R	2.106	1.00
11_L	129_A	2.076	1.00
52_V	61_R	1.916	1.00
7_I	36_I	1.914	1.00
34_R	51_F	1.886	1.00
6_P	33_K	1.809	1.00
26_E	59_I	1.762	1.00
46_I	49_V	1.754	1.00
53_E	58_G	1.749	1.00
24_K	61_R	1.727	1.00
37_A	62_V	1.716	1.00
5_D	79_R	1.682	1.00
17_A	25_L	1.606	1.00
10_M	27_I	1.539	1.00
40_L	131_V	1.525	1.00
90_K	93_E	1.522	1.00
41_K	46_I	1.467	1.00
78_K	130_Y	1.431	1.00
117_E	120_A	1.405	1.00
36_I	112_V	1.404	1.00
94_V	115_D	1.398	1.00
39_I	112_V	1.387	1.00
32_L	128_L	1.381	1.00
30_S	33_K	1.355	0.99
38_E	49_V	1.339	0.99
104_A	130_Y	1.333	0.99
29_A	34_R	1.313	0.99
7_I	32_L	1.306	0.99
27_I	60_I	1.281	0.99
89_A	94_V	1.280	0.99
97_V	104_A	1.268	0.99
50_E	61_R	1.226	0.99
67_G	70_N	1.213	0.99
50_E	63_F	1.174	0.98
17_A	20_V	1.142	0.98
21_R	70_N	1.137	0.98
67_G	71_E	1.123	0.98
27_I	62_V	1.087	0.97
28_P	33_K	1.076	0.97
45_F	103_I	1.072	0.97
105_I	129_A	1.069	0.97
24_K	63_F	1.056	0.97
85_L	130_Y	1.043	0.97
80_I	87_V	1.038	0.97
44_G	65_K	1.033	0.96
29_A	58_G	1.020	0.96
38_E	41_K	1.012	0.96
56_K	59_I	1.010	0.96
6_P	30_S	1.007	0.96
94_V	106_I	1.007	0.96
34_R	58_G	1.003	0.96
34_R	38_E	0.993	0.96
89_A	106_I	0.987	0.95
41_K	49_V	0.984	0.95
94_V	127_V	0.971	0.95
127_V	130_Y	0.971	0.95
76_G	98_L	0.963	0.95
29_A	51_F	0.942	0.94
53_E	56_K	0.920	0.93
34_R	60_I	0.915	0.93
18_N	132_W	0.899	0.93
113_L	117_E	0.885	0.92
39_I	105_I	0.880	0.92
76_G	130_Y	0.876	0.92
95_P	104_A	0.868	0.91
51_F	58_G	0.867	0.91
43_E	117_E	0.852	0.90
89_A	127_V	0.848	0.90
79_R	86_R	0.841	0.90
54_D	59_I	0.834	0.89
52_V	59_I	0.833	0.89
113_L	121_K	0.827	0.89
45_F	101_L	0.815	0.88
96_R	115_D	0.801	0.87
10_M	36_I	0.800	0.87
65_K	74_I	0.798	0.87
86_R	126_E	0.797	0.87
7_I	132_W	0.796	0.87
54_D	58_G	0.794	0.87
10_M	33_K	0.780	0.86
8_A	33_K	0.779	0.86
110_Q	113_L	0.778	0.86
54_D	57_Q	0.767	0.85
104_A	115_D	0.766	0.85
32_L	112_V	0.760	0.85
108_T	113_L	0.756	0.84
47_R	63_F	0.755	0.84
95_P	130_Y	0.755	0.84
80_I	127_V	0.754	0.84
31_K	34_R	0.753	0.84
48_D	63_F	0.753	0.84
36_I	105_I	0.751	0.84
53_E	57_Q	0.750	0.84
107_S	112_V	0.746	0.83
34_R	41_K	0.743	0.83
14_I	74_I	0.741	0.83
21_R	72_R	0.739	0.83
110_Q	123_A	0.739	0.83
66_Y	72_R	0.731	0.82
98_L	132_W	0.730	0.82
36_I	129_A	0.720	0.81
100_G	115_D	0.718	0.81
55_S	58_G	0.717	0.81
14_I	77_L	0.708	0.80
112_V	128_L	0.706	0.80
52_V	56_K	0.695	0.79
40_L	103_I	0.689	0.78
18_N	77_L	0.689	0.78
26_E	52_V	0.682	0.78
89_A	93_E	0.672	0.77
94_V	104_A	0.655	0.75
4_T	109_S	0.648	0.74
66_Y	74_I	0.628	0.72
42_R	113_L	0.624	0.71
51_F	60_I	0.624	0.71
113_L	123_A	0.621	0.71
68_Q	71_E	0.621	0.71
18_N	67_G	0.620	0.71
32_L	35_E	0.620	0.71
97_V	103_I	0.614	0.70
34_R	49_V	0.614	0.70
11_L	15_R	0.613	0.70
39_I	129_A	0.605	0.69
10_M	87_V	0.602	0.68
13_R	28_P	0.600	0.68
18_N	73_V	0.593	0.67
97_V	130_Y	0.593	0.67
55_S	112_V	0.588	0.67
108_T	111_G	0.586	0.66
92_N	109_S	0.585	0.66
97_V	100_G	0.584	0.66
113_L	118_A	0.581	0.66
71_E	75_T	0.580	0.66
3_M	26_E	0.579	0.65
10_M	43_E	0.579	0.65
106_I	127_V	0.573	0.65
37_A	60_I	0.570	0.64
96_R	119_R	0.570	0.64
73_V	101_L	0.569	0.64
89_A	132_W	0.568	0.64
23_E	47_R	0.563	0.63
42_R	120_A	0.561	0.63
32_L	37_A	0.560	0.63
64_L	72_R	0.555	0.62
18_N	74_I	0.554	0.62
23_E	72_R	0.552	0.62
28_P	101_L	0.551	0.62
22_H	25_L	0.547	0.61
15_R	129_A	0.546	0.61
85_L	89_A	0.543	0.61
49_V	62_V	0.543	0.61
46_I	105_I	0.541	0.60
6_P	10_M	0.540	0.60
98_L	116_K	0.540	0.60
35_E	50_E	0.538	0.60
35_E	42_R	0.537	0.60
27_I	33_K	0.535	0.59
24_K	50_E	0.533	0.59
84_G	126_E	0.533	0.59
13_R	22_H	0.532	0.59
109_S	123_A	0.532	0.59
14_I	62_V	0.531	0.59
24_K	47_R	0.530	0.59
103_I	131_V	0.530	0.59
80_I	130_Y	0.529	0.59
112_V	121_K	0.527	0.58
82_K	112_V	0.526	0.58
4_T	33_K	0.524	0.58
75_T	98_L	0.523	0.58
30_S	45_F	0.522	0.58
4_T	8_A	0.520	0.57
36_I	39_I	0.519	0.57
18_N	82_K	0.518	0.57
76_G	129_A	0.518	0.57
3_M	20_V	0.513	0.56
43_E	114_T	0.511	0.56
15_R	77_L	0.510	0.56
95_P	119_R	0.509	0.56
12_T	77_L	0.504	0.55
23_E	31_K	0.502	0.55
39_I	103_I	0.500	0.54

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
4pdbA	1	0.9773	100	0.104	Contact Map
4rb5H	1	0.9848	100	0.115	Contact Map
1seiA	2	0.9848	100	0.128	Contact Map
1s03H	1	0.9621	100	0.138	Contact Map
3bbnH	1	0.9924	100	0.146	Contact Map
3rf2A	1	0.9773	100	0.165	Contact Map
1i6uA	1	0.9318	100	0.242	Contact Map
4bpeH	1	0.9242	100	0.258	Contact Map
4ujpX	1	0.9242	100	0.285	Contact Map
3qd7X	1	0.5	38.1	0.935	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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