RS9 - ECOLI - GREMLIN Contacts

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RS9 - 30S ribosomal protein S9

UniProt:	P0A7X3	Sequences: MAENQYYGTGRRKSSAARVFIKPGNGKIVINQRSLEQYFGRETARMVVRQPLELVDMVEKLDLYITVKGGGISGQAGAIRHGITRALMEYDESLRSELRKAGFVTRDARQVERKKVGLRKARRRPQFSKR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10908
Length:	130 (126)
Sequences:	2839 (1237)
Seq/√Len:	110.2

ECOLI - RS9
BACSU - RS9
HALSA - RS9
SULSO - RS9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
118_L	124_R	4.547	1.00
65_I	79_I	2.954	1.00
84_T	104_V	2.846	1.00
19_V	82_G	2.713	1.00
88_M	104_V	2.494	1.00
118_L	125_P	2.389	1.00
111_V	120_K	2.376	1.00
119_R	125_P	2.232	1.00
120_K	123_R	2.147	1.00
61_L	90_Y	2.095	1.00
36_E	45_R	2.033	1.00
50_Q	103_F	2.020	1.00
7_Y	20_F	1.941	1.00
96_S	100_K	1.931	1.00
42_E	45_R	1.886	1.00
26_G	62_D	1.817	1.00
5_Q	20_F	1.814	1.00
14_S	110_Q	1.812	1.00
50_Q	80_R	1.794	1.00
95_R	99_R	1.779	1.00
27_K	62_D	1.720	1.00
52_L	63_L	1.719	1.00
11_R	85_R	1.719	1.00
35_L	45_R	1.712	1.00
27_K	34_S	1.688	1.00
22_K	64_Y	1.687	1.00
88_M	95_R	1.639	1.00
119_R	123_R	1.623	1.00
53_E	58_V	1.606	1.00
40_G	45_R	1.554	1.00
5_Q	22_K	1.530	1.00
54_L	101_A	1.517	1.00
24_G	62_D	1.469	1.00
55_V	94_L	1.446	1.00
33_R	37_Q	1.442	1.00
39_F	79_I	1.432	1.00
57_M	94_L	1.426	1.00
67_V	79_I	1.393	1.00
35_L	48_V	1.367	1.00
47_V	50_Q	1.351	1.00
25_N	62_D	1.327	1.00
73_S	77_G	1.295	0.99
77_G	80_R	1.260	0.99
34_S	37_Q	1.202	0.99
111_V	114_K	1.184	0.99
8_G	86_A	1.173	0.99
57_M	60_K	1.170	0.99
119_R	124_R	1.116	0.98
23_P	60_K	1.086	0.98
29_V	64_Y	1.080	0.98
57_M	61_L	1.079	0.98
12_R	77_G	1.076	0.98
11_R	16_A	1.070	0.98
49_R	58_V	1.069	0.98
112_E	115_K	1.044	0.97
120_K	125_P	1.032	0.97
55_V	98_L	1.026	0.97
82_G	106_R	1.010	0.97
47_V	77_G	0.996	0.96
21_I	86_A	0.993	0.96
80_R	103_F	0.987	0.96
11_R	110_Q	0.968	0.96
70_G	74_G	0.965	0.96
22_K	62_D	0.961	0.96
48_V	51_P	0.948	0.95
11_R	81_H	0.931	0.95
21_I	63_L	0.925	0.95
40_G	72_I	0.922	0.95
46_M	50_Q	0.915	0.94
9_T	82_G	0.909	0.94
74_G	77_G	0.909	0.94
120_K	124_R	0.907	0.94
116_V	127_F	0.896	0.94
32_Q	66_T	0.887	0.93
84_T	88_M	0.884	0.93
49_R	52_L	0.879	0.93
57_M	91_D	0.873	0.93
18_R	66_T	0.870	0.93
41_R	44_A	0.868	0.93
90_Y	94_L	0.864	0.92
20_F	66_T	0.856	0.92
44_A	72_I	0.853	0.92
6_Y	90_Y	0.852	0.92
114_K	120_K	0.849	0.92
47_V	76_A	0.846	0.92
41_R	72_I	0.844	0.92
15_S	74_G	0.827	0.91
8_G	89_E	0.827	0.91
105_T	108_A	0.814	0.90
111_V	123_R	0.813	0.90
99_R	105_T	0.811	0.90
54_L	103_F	0.810	0.90
114_K	119_R	0.801	0.89
28_I	35_L	0.796	0.89
25_N	46_M	0.792	0.89
95_R	104_V	0.788	0.89
15_S	70_G	0.786	0.88
33_R	40_G	0.779	0.88
7_Y	66_T	0.777	0.88
42_E	46_M	0.776	0.88
48_V	76_A	0.776	0.88
81_H	106_R	0.774	0.88
88_M	94_L	0.774	0.88
91_D	94_L	0.774	0.88
17_A	67_V	0.773	0.88
97_E	101_A	0.772	0.88
29_V	34_S	0.769	0.87
36_E	49_R	0.766	0.87
8_G	19_V	0.764	0.87
54_L	97_E	0.760	0.87
44_A	73_S	0.753	0.86
29_V	32_Q	0.740	0.85
88_M	99_R	0.737	0.85
6_Y	21_I	0.734	0.85
7_Y	18_R	0.728	0.84
49_R	53_E	0.727	0.84
6_Y	88_M	0.724	0.84
116_V	125_P	0.722	0.84
52_L	59_E	0.721	0.84
123_R	127_F	0.713	0.83
47_V	103_F	0.712	0.83
18_R	67_V	0.710	0.83
21_I	61_L	0.708	0.83
43_T	46_M	0.690	0.81
35_L	40_G	0.686	0.81
30_I	39_F	0.678	0.80
55_V	58_V	0.673	0.79
10_G	16_A	0.669	0.79
22_K	90_Y	0.666	0.79
111_V	119_R	0.658	0.78
29_V	66_T	0.648	0.77
19_V	123_R	0.645	0.76
52_L	57_M	0.644	0.76
46_M	49_R	0.637	0.76
40_G	44_A	0.634	0.75
30_I	34_S	0.632	0.75
39_F	48_V	0.632	0.75
85_R	106_R	0.630	0.75
97_E	100_K	0.619	0.73
46_M	53_E	0.618	0.73
17_A	30_I	0.617	0.73
45_R	48_V	0.609	0.72
114_K	118_L	0.607	0.72
47_V	80_R	0.605	0.72
39_F	73_S	0.604	0.72
119_R	127_F	0.602	0.71
28_I	48_V	0.602	0.71
92_E	97_E	0.598	0.71
10_G	17_A	0.597	0.71
42_E	72_I	0.595	0.71
114_K	117_G	0.591	0.70
92_E	99_R	0.589	0.70
122_R	130_R	0.584	0.69
81_H	85_R	0.577	0.68
10_G	81_H	0.576	0.68
52_L	61_L	0.572	0.68
15_S	78_A	0.569	0.67
52_L	83_I	0.567	0.67
119_R	126_Q	0.567	0.67
17_A	79_I	0.560	0.66
8_G	21_I	0.560	0.66
9_T	98_L	0.559	0.66
20_F	64_Y	0.559	0.66
118_L	123_R	0.558	0.66
39_F	113_R	0.556	0.65
111_V	116_V	0.555	0.65
90_Y	96_S	0.555	0.65
50_Q	127_F	0.551	0.65
20_F	111_V	0.549	0.64
98_L	106_R	0.548	0.64
5_Q	64_Y	0.545	0.64
67_V	72_I	0.544	0.64
33_R	110_Q	0.543	0.64
20_F	74_G	0.541	0.63
38_Y	113_R	0.541	0.63
16_A	116_V	0.537	0.63
60_K	68_K	0.535	0.62
119_R	128_S	0.532	0.62
99_R	104_V	0.530	0.62
28_I	49_R	0.529	0.62
41_R	73_S	0.520	0.60
83_I	98_L	0.516	0.60
16_A	68_K	0.513	0.59
33_R	74_G	0.511	0.59
21_I	83_I	0.507	0.58
42_E	76_A	0.506	0.58
8_G	87_L	0.505	0.58
120_K	128_S	0.501	0.57
14_S	81_H	0.500	0.57

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
4rb5I	1	0.9769	100	0.034	Contact Map
4tp8I	1	0.9769	100	0.04	Contact Map
3bbnI	1	0.9692	100	0.042	Contact Map
5aj3I	1	0.9923	100	0.052	Contact Map
4bpeI	1	0.9923	100	0.071	Contact Map
3j60Q	1	0.8692	100	0.072	Contact Map
3j7aM	1	0.9615	100	0.074	Contact Map
4ujpR	1	0.9846	100	0.076	Contact Map
4w23Q	1	0.9846	100	0.076	Contact Map
3j20K	1	0.9769	100	0.083	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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