RS8 - ECOLI - GREMLIN Contacts

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RS8 - 30S ribosomal protein S8

UniProt:	P0A7W7	Sequences: MSMQDPIADMLTRIRNGQAANKAAVTMPSSKLKVAIANVLKEEGFIEDFKVEGDTKPELELTLKYFQGKAVVESIQRVSRPGLRIYKRKDELPKVMAGLGIAVVSTSKGVMTDRAARQAGLGGEIICYVA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10907
Length:	130 (127)
Sequences:	2584 (1229)
Seq/√Len:	109.1

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	3.648	1.00
108_K	119_A	3.356	1.00
89_K	120_G	3.332	1.00
12_T	15_R	3.330	1.00
35_A	38_N	2.932	1.00
38_N	42_E	2.857	1.00
10_M	37_A	2.808	1.00
26_T	60_E	2.746	1.00
42_E	115_A	2.742	1.00
113_D	117_R	2.427	1.00
9_D	13_R	2.356	1.00
115_A	119_A	2.351	1.00
18_Q	70_A	2.278	1.00
7_I	36_I	2.043	1.00
11_L	127_C	1.996	1.00
34_V	51_V	1.923	1.00
37_A	61_L	1.917	1.00
6_P	33_K	1.806	1.00
24_A	60_E	1.720	1.00
26_T	58_E	1.715	1.00
46_I	49_F	1.704	1.00
17_G	25_V	1.689	1.00
52_E	60_E	1.681	1.00
53_G	57_P	1.647	1.00
5_D	77_R	1.611	1.00
40_L	129_V	1.536	1.00
39_V	110_V	1.517	1.00
88_R	91_E	1.516	1.00
115_A	118_Q	1.508	1.00
10_M	27_M	1.475	1.00
76_Q	128_Y	1.475	1.00
32_L	126_I	1.472	1.00
41_K	46_I	1.450	1.00
30_S	33_K	1.392	1.00
92_L	113_D	1.372	1.00
36_I	110_V	1.365	1.00
38_N	49_F	1.317	0.99
27_M	59_L	1.313	0.99
7_I	32_L	1.296	0.99
50_K	60_E	1.281	0.99
66_F	69_K	1.274	0.99
102_A	128_Y	1.248	0.99
29_S	34_V	1.221	0.99
44_G	64_K	1.197	0.99
50_K	62_T	1.185	0.99
87_K	92_L	1.183	0.99
66_F	70_A	1.164	0.99
95_V	102_A	1.149	0.99
45_F	101_I	1.128	0.98
6_P	30_S	1.126	0.98
24_A	62_T	1.082	0.98
87_K	104_V	1.062	0.98
29_S	57_P	1.049	0.97
83_L	128_Y	1.046	0.97
38_N	41_K	1.043	0.97
28_P	33_K	1.036	0.97
74_S	96_M	1.036	0.97
21_N	68_G	1.016	0.97
55_T	58_E	1.015	0.97
92_L	104_V	1.014	0.97
34_V	38_N	1.010	0.97
17_G	20_A	0.994	0.96
84_R	124_E	0.985	0.96
105_S	109_G	0.972	0.96
39_V	103_V	0.971	0.96
51_V	57_P	0.961	0.96
34_V	57_P	0.953	0.95
74_S	128_Y	0.944	0.95
103_V	127_C	0.942	0.95
106_T	111_M	0.942	0.95
78_V	85_I	0.941	0.95
125_I	128_Y	0.941	0.95
41_K	49_F	0.939	0.95
29_S	51_V	0.937	0.95
27_M	61_L	0.933	0.95
45_F	99_L	0.932	0.95
34_V	59_L	0.929	0.95
77_R	84_R	0.918	0.94
10_M	36_I	0.880	0.93
36_I	127_C	0.868	0.92
8_A	33_K	0.865	0.92
54_D	58_E	0.855	0.92
110_V	126_I	0.854	0.92
47_E	62_T	0.839	0.91
10_M	33_K	0.834	0.91
48_D	62_T	0.830	0.91
78_V	125_I	0.829	0.91
65_Y	70_A	0.823	0.90
87_K	125_I	0.808	0.90
43_E	115_A	0.807	0.89
32_L	110_V	0.807	0.89
54_D	57_P	0.797	0.89
87_K	91_E	0.793	0.89
111_M	115_A	0.791	0.89
102_A	113_D	0.768	0.87
93_P	102_A	0.754	0.86
94_K	113_D	0.754	0.86
108_K	111_M	0.752	0.86
14_I	72_V	0.752	0.86
21_N	70_A	0.751	0.86
31_K	34_V	0.741	0.85
86_Y	124_E	0.723	0.84
69_K	73_E	0.718	0.83
92_L	125_I	0.718	0.83
34_V	41_K	0.715	0.83
98_G	113_D	0.715	0.83
14_I	75_I	0.710	0.82
93_P	128_Y	0.702	0.82
18_Q	66_F	0.696	0.81
27_M	33_K	0.693	0.81
52_E	58_E	0.689	0.81
64_K	72_V	0.688	0.80
78_V	128_Y	0.678	0.80
95_V	98_G	0.673	0.79
11_L	15_R	0.671	0.79
36_I	103_V	0.659	0.78
65_Y	72_V	0.654	0.77
15_R	127_C	0.652	0.77
111_M	119_A	0.646	0.76
30_S	45_F	0.645	0.76
39_V	127_C	0.644	0.76
108_K	121_L	0.636	0.75
106_T	109_G	0.634	0.75
18_Q	71_V	0.630	0.74
40_L	101_I	0.629	0.74
26_T	52_E	0.627	0.74
51_V	59_L	0.622	0.73
53_G	56_K	0.619	0.73
23_A	47_E	0.618	0.73
111_M	121_L	0.616	0.73
35_A	42_E	0.608	0.72
6_P	10_M	0.608	0.72
105_S	110_V	0.606	0.72
18_Q	75_I	0.604	0.71
95_V	128_Y	0.598	0.71
37_A	40_L	0.597	0.70
101_I	129_V	0.596	0.70
13_R	28_P	0.596	0.70
12_T	75_I	0.591	0.70
49_F	61_L	0.591	0.70
32_L	35_A	0.590	0.69
4_Q	107_S	0.590	0.69
37_A	59_L	0.588	0.69
18_Q	72_V	0.586	0.69
46_I	61_L	0.585	0.69
44_G	98_G	0.582	0.68
34_V	49_F	0.577	0.68
10_M	85_I	0.570	0.67
4_Q	33_K	0.570	0.67
82_G	124_E	0.568	0.67
52_E	55_T	0.567	0.66
7_I	23_A	0.563	0.66
110_V	119_A	0.559	0.65
104_V	125_I	0.558	0.65
90_D	107_S	0.557	0.65
14_I	61_L	0.551	0.64
46_I	103_V	0.550	0.64
79_S	84_R	0.547	0.64
96_M	114_R	0.547	0.64
18_Q	80_R	0.546	0.64
109_G	122_G	0.545	0.63
37_A	51_V	0.538	0.62
36_I	39_V	0.534	0.62
107_S	121_L	0.531	0.61
47_E	60_E	0.529	0.61
35_A	50_K	0.527	0.61
68_G	83_L	0.523	0.60
43_E	112_T	0.523	0.60
24_A	47_E	0.523	0.60
20_A	37_A	0.521	0.60
31_K	57_P	0.520	0.60
4_Q	80_R	0.517	0.59
91_E	116_A	0.517	0.59
66_F	71_V	0.516	0.59
88_R	107_S	0.514	0.59
4_Q	8_A	0.514	0.59
23_A	66_F	0.513	0.59
71_V	99_L	0.512	0.59
33_K	112_T	0.510	0.58
10_M	43_E	0.510	0.58
4_Q	96_M	0.509	0.58
106_T	122_G	0.505	0.58
5_D	8_A	0.505	0.58
23_A	118_Q	0.504	0.57
116_A	121_L	0.503	0.57
13_R	22_K	0.503	0.57
10_M	25_V	0.501	0.57
74_S	127_C	0.501	0.57
3_M	26_T	0.500	0.57
39_V	101_I	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
4pdbA	1	0.9769	100	0.1	Contact Map
1s03H	1	0.9769	100	0.112	Contact Map
4rb5H	1	0.9846	100	0.115	Contact Map
1seiA	2	0.9923	100	0.117	Contact Map
3rf2A	1	0.9769	100	0.137	Contact Map
3bbnH	1	0.9923	100	0.144	Contact Map
1i6uA	1	0.9385	100	0.228	Contact Map
4bpeH	1	0.9308	100	0.25	Contact Map
4ujpX	1	0.9308	100	0.278	Contact Map
3qd7X	1	0.5	24.3	0.937	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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