RL16 - BACSU - GREMLIN Contacts

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RL16 - 50S ribosomal protein L16

UniProt:	P14577	Sequences: MLLPKRVKYRREHRGKMRGRAKGGTEVHFGEFGIQALEASWITNRQIEAARIAMTRYMKRGGKVWIKIFPSKPYTAKPLEVRMGSGKGAPEGWVAVVKPGKVLFEISGVSEEVAREALRLASHKLPIKTKFVKREEIGGESNES	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	144 (135)
Sequences:	1925 (759)
Seq/√Len:	65.4

ECOLI - RL16
BACSU - RL16

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
111_E	115_R	3.680	1.00
27_V	33_G	3.512	1.00
118_L	131_F	3.243	1.00
36_A	127_I	2.840	1.00
116_E	119_R	2.833	1.00
31_E	107_S	2.721	1.00
42_I	68_I	2.547	1.00
74_Y	92_G	2.514	1.00
35_Q	130_K	2.442	1.00
41_W	96_V	2.376	1.00
111_E	133_K	2.300	1.00
72_K	96_V	2.225	1.00
110_S	113_V	2.125	1.00
58_M	106_I	2.050	1.00
22_K	25_T	2.011	1.00
115_R	131_F	1.982	1.00
38_E	128_K	1.923	1.00
122_S	129_T	1.901	1.00
54_M	64_V	1.867	1.00
54_M	106_I	1.816	1.00
50_A	104_F	1.775	1.00
17_M	39_A	1.742	1.00
48_E	51_R	1.728	1.00
15_G	72_K	1.694	0.99
77_K	81_V	1.687	0.99
64_V	106_I	1.623	0.99
34_I	122_S	1.620	0.99
55_T	64_V	1.616	0.99
29_F	67_K	1.601	0.99
35_Q	132_V	1.573	0.99
42_I	127_I	1.568	0.99
43_T	46_Q	1.567	0.99
50_A	125_L	1.560	0.99
32_F	131_F	1.557	0.99
76_A	91_E	1.536	0.99
42_I	103_L	1.532	0.99
14_R	41_W	1.527	0.99
12_E	73_P	1.481	0.98
58_M	113_V	1.461	0.98
78_P	81_V	1.404	0.98
71_S	101_K	1.391	0.98
46_Q	126_P	1.375	0.97
21_A	101_K	1.346	0.97
82_R	93_W	1.321	0.97
102_V	132_V	1.280	0.96
75_T	88_G	1.249	0.96
119_R	123_H	1.247	0.95
57_Y	113_V	1.240	0.95
58_M	61_G	1.160	0.93
24_G	28_H	1.143	0.93
109_V	114_A	1.137	0.93
17_M	96_V	1.136	0.93
35_Q	102_V	1.125	0.92
27_V	132_V	1.113	0.92
17_M	72_K	1.099	0.91
3_L	7_V	1.084	0.91
14_R	74_Y	1.071	0.90
33_G	132_V	1.046	0.89
7_V	93_W	1.032	0.89
24_G	101_K	1.031	0.89
14_R	77_K	1.014	0.88
40_S	104_F	1.014	0.88
34_I	129_T	1.010	0.87
50_A	53_A	1.010	0.87
85_S	93_W	0.982	0.86
27_V	102_V	0.980	0.86
76_A	92_G	0.977	0.86
78_P	82_R	0.973	0.85
19_G	98_K	0.972	0.85
7_V	12_E	0.964	0.85
40_S	127_I	0.945	0.84
41_W	72_K	0.938	0.83
16_K	39_A	0.934	0.83
54_M	121_A	0.929	0.83
52_I	85_S	0.929	0.83
114_A	131_F	0.922	0.82
31_E	134_R	0.918	0.82
74_Y	96_V	0.899	0.81
37_L	127_I	0.882	0.79
117_A	121_A	0.880	0.79
28_H	67_K	0.873	0.79
3_L	14_R	0.873	0.79
18_R	39_A	0.865	0.78
53_A	121_A	0.857	0.77
29_F	65_W	0.841	0.76
75_T	90_P	0.829	0.75
21_A	24_G	0.829	0.75
25_T	35_Q	0.825	0.75
71_S	93_W	0.819	0.74
42_I	126_P	0.807	0.73
11_R	15_G	0.804	0.73
39_A	99_P	0.803	0.73
68_I	127_I	0.791	0.71
12_E	72_K	0.783	0.71
107_S	134_R	0.783	0.71
57_Y	120_L	0.779	0.70
36_A	101_K	0.774	0.70
60_R	120_L	0.762	0.69
53_A	120_L	0.759	0.68
52_I	64_V	0.750	0.67
68_I	103_L	0.748	0.67
58_M	64_V	0.748	0.67
47_I	68_I	0.747	0.67
103_L	129_T	0.745	0.67
14_R	17_M	0.744	0.67
54_M	61_G	0.742	0.67
3_L	44_N	0.737	0.66
27_V	134_R	0.730	0.65
35_Q	135_E	0.727	0.65
9_Y	12_E	0.723	0.64
61_G	85_S	0.721	0.64
15_G	96_V	0.719	0.64
57_Y	85_S	0.715	0.64
106_I	118_L	0.710	0.63
53_A	123_H	0.708	0.63
47_I	69_F	0.707	0.63
51_R	56_R	0.706	0.63
44_N	52_I	0.703	0.62
109_V	113_V	0.703	0.62
54_M	58_M	0.698	0.62
33_G	102_V	0.697	0.62
68_I	101_K	0.696	0.62
15_G	74_Y	0.694	0.61
29_F	45_R	0.682	0.60
27_V	31_E	0.681	0.60
12_E	71_S	0.681	0.60
41_W	74_Y	0.674	0.59
50_A	103_L	0.666	0.58
3_L	79_L	0.666	0.58
20_R	25_T	0.665	0.58
121_A	125_L	0.662	0.58
64_V	118_L	0.659	0.57
7_V	90_P	0.659	0.57
67_K	108_G	0.656	0.57
57_Y	83_M	0.654	0.57
115_R	119_R	0.651	0.56
5_K	93_W	0.650	0.56
98_K	101_K	0.648	0.56
73_P	93_W	0.647	0.56
1_M	5_K	0.647	0.56
2_L	70_P	0.641	0.55
90_P	93_W	0.639	0.55
15_G	41_W	0.636	0.55
21_A	25_T	0.635	0.55
106_I	114_A	0.634	0.54
12_E	93_W	0.632	0.54
73_P	90_P	0.629	0.54
73_P	101_K	0.619	0.53
20_R	99_P	0.618	0.53
58_M	104_F	0.615	0.52
33_G	105_E	0.605	0.51
111_E	131_F	0.603	0.51
45_R	80_E	0.602	0.51
26_E	128_K	0.601	0.51
56_R	117_A	0.598	0.50
23_G	26_E	0.592	0.50
121_A	129_T	0.592	0.50
18_R	72_K	0.586	0.49
9_Y	13_H	0.585	0.49
72_K	94_V	0.581	0.48
44_N	92_G	0.580	0.48
6_R	9_Y	0.579	0.48
68_I	97_V	0.577	0.48
15_G	19_G	0.576	0.48
41_W	94_V	0.566	0.47
61_G	121_A	0.559	0.46
17_M	41_W	0.558	0.46
55_T	120_L	0.558	0.46
57_Y	116_E	0.555	0.45
47_I	66_I	0.553	0.45
14_R	81_V	0.549	0.45
14_R	85_S	0.545	0.44
12_E	90_P	0.541	0.44
19_G	122_S	0.539	0.43
48_E	124_K	0.535	0.43
1_M	33_G	0.529	0.42
113_V	119_R	0.529	0.42
19_G	94_V	0.529	0.42
37_L	40_S	0.528	0.42
57_Y	119_R	0.526	0.42
38_E	42_I	0.526	0.42
30_G	65_W	0.524	0.42
63_K	107_S	0.523	0.42
55_T	106_I	0.521	0.41
41_W	90_P	0.519	0.41
95_A	103_L	0.516	0.41
31_E	133_K	0.516	0.41
15_G	39_A	0.515	0.41
98_K	130_K	0.514	0.41
72_K	99_P	0.513	0.40
22_K	42_I	0.512	0.40
29_F	35_Q	0.511	0.40
116_E	123_H	0.509	0.40
40_S	68_I	0.509	0.40
52_I	78_P	0.508	0.40
13_H	52_I	0.508	0.40
15_G	99_P	0.507	0.40
78_P	89_A	0.505	0.40
18_R	31_E	0.505	0.40
24_G	134_R	0.500	0.39
58_M	107_S	0.500	0.39
30_G	67_K	0.500	0.39

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
4rb6Q	1	0.9792	100	0.12	Contact Map
3bboO	1	0.9375	100	0.131	Contact Map
4tp9M	1	0.9444	100	0.141	Contact Map
1vw4K	1	1	100	0.167	Contact Map
3j7yN	1	0.9931	100	0.191	Contact Map
1ffkF	1	0.9514	100	0.357	Contact Map
1vq8H	1	0.9514	100	0.372	Contact Map
3j21N	1	0.9514	100	0.379	Contact Map
1vx7Q	1	0.9514	100	0.381	Contact Map
3zf7K	1	1	100	0.381	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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