RS8 - HALSA - GREMLIN Contacts

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RS8 - 30S ribosomal protein S8

UniProt:	Q9HPB9	Sequences: MTANDPLSDALSGIDNAESVGHLTHTVAPASNMVGSVLEVFYDRGYIDGFEFVDNGKAGRFEVELKGAINECGPVNPRYSVGADGFEQWEKRYLPARDYGSLVVTTSHGIMSHYEAREAGIGGQVIAYVY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	130 (127)
Sequences:	2873 (1326)
Seq/√Len:	117.7

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
108_H	119_A	3.791	1.00
42_Y	49_G	3.518	1.00
12_S	15_D	3.185	1.00
39_E	43_D	2.739	1.00
36_S	39_E	2.736	1.00
26_T	62_E	2.664	1.00
115_E	119_A	2.638	1.00
43_D	115_E	2.593	1.00
10_A	38_L	2.518	1.00
77_P	130_Y	2.393	1.00
113_H	117_R	2.230	1.00
18_E	73_G	2.217	1.00
7_L	37_V	2.185	1.00
11_L	127_A	2.045	1.00
53_V	62_E	1.999	1.00
9_D	13_G	1.974	1.00
38_L	63_V	1.894	1.00
35_G	52_F	1.866	1.00
47_I	50_F	1.813	1.00
6_P	34_V	1.798	1.00
24_T	62_E	1.798	1.00
26_T	60_R	1.771	1.00
17_A	25_H	1.653	1.00
10_A	27_V	1.612	1.00
54_D	59_G	1.593	1.00
94_L	113_H	1.528	1.00
42_Y	47_I	1.520	1.00
33_M	126_I	1.499	1.00
115_E	118_E	1.441	1.00
102_L	128_Y	1.435	1.00
30_A	35_G	1.426	1.00
40_V	110_I	1.424	1.00
41_F	129_V	1.424	1.00
5_D	80_S	1.396	1.00
39_E	50_F	1.340	1.00
31_S	34_V	1.325	1.00
79_Y	128_Y	1.318	1.00
51_E	62_E	1.315	1.00
37_V	110_I	1.307	1.00
7_L	33_M	1.291	1.00
27_V	61_F	1.291	1.00
90_E	94_L	1.273	0.99
68_A	72_C	1.238	0.99
68_A	73_G	1.206	0.99
24_T	64_E	1.178	0.99
30_A	52_F	1.143	0.99
35_G	61_F	1.134	0.99
21_G	71_E	1.131	0.99
57_K	60_R	1.083	0.98
30_A	59_G	1.081	0.98
86_F	128_Y	1.078	0.98
108_H	121_I	1.078	0.98
51_E	64_E	1.069	0.98
35_G	39_E	1.068	0.98
55_N	59_G	1.068	0.98
77_P	128_Y	1.067	0.98
54_D	57_K	1.065	0.98
10_A	34_V	1.062	0.98
90_E	104_V	1.055	0.98
95_P	128_Y	1.042	0.98
42_Y	50_F	1.036	0.98
39_E	42_Y	1.023	0.98
95_P	102_L	1.007	0.97
18_E	130_Y	1.006	0.97
94_L	125_V	0.993	0.97
52_F	59_G	0.993	0.97
27_V	63_V	0.992	0.97
29_P	34_V	0.986	0.97
46_Y	101_S	0.984	0.97
33_M	110_I	0.980	0.97
94_L	104_V	0.969	0.97
103_V	127_A	0.932	0.96
6_P	31_S	0.925	0.96
96_A	113_H	0.916	0.95
80_S	87_E	0.893	0.95
48_D	64_E	0.892	0.95
35_G	59_G	0.873	0.94
17_A	20_V	0.870	0.94
87_E	124_Q	0.858	0.93
18_E	68_A	0.856	0.93
26_T	53_V	0.855	0.93
105_T	124_Q	0.853	0.93
81_V	88_Q	0.844	0.93
111_M	119_A	0.844	0.93
7_L	130_Y	0.838	0.93
53_V	60_R	0.838	0.93
10_A	37_V	0.821	0.92
55_N	58_A	0.799	0.91
102_L	113_H	0.793	0.90
21_G	73_G	0.792	0.90
98_D	113_H	0.789	0.90
55_N	60_R	0.786	0.90
111_M	115_E	0.786	0.90
125_V	128_Y	0.784	0.90
54_D	58_A	0.779	0.90
45_G	66_K	0.778	0.90
90_E	93_Y	0.770	0.89
49_G	64_E	0.768	0.89
11_L	15_D	0.763	0.89
86_F	90_E	0.762	0.89
32_N	35_G	0.762	0.89
108_H	111_M	0.762	0.89
53_V	57_K	0.755	0.88
90_E	125_V	0.737	0.87
82_G	89_W	0.734	0.87
111_M	121_I	0.730	0.86
8_S	34_V	0.723	0.86
18_E	78_R	0.721	0.86
13_G	17_A	0.712	0.85
85_G	89_W	0.712	0.85
44_R	115_E	0.706	0.85
67_G	73_G	0.697	0.84
4_N	8_S	0.697	0.84
82_G	124_Q	0.686	0.83
110_I	126_I	0.681	0.82
43_D	111_M	0.680	0.82
35_G	42_Y	0.670	0.81
24_T	48_D	0.663	0.81
68_A	71_E	0.661	0.80
41_F	103_V	0.657	0.80
92_R	107_S	0.649	0.79
90_E	130_Y	0.648	0.79
24_T	51_E	0.644	0.79
106_T	111_M	0.644	0.79
32_N	59_G	0.643	0.79
14_I	78_R	0.639	0.78
14_I	63_V	0.635	0.78
72_C	76_N	0.633	0.78
82_G	87_E	0.632	0.77
23_L	48_D	0.631	0.77
44_R	112_S	0.629	0.77
40_V	101_S	0.628	0.77
56_G	59_G	0.624	0.77
40_V	127_A	0.623	0.76
37_V	127_A	0.621	0.76
35_G	50_F	0.617	0.76
68_A	76_N	0.616	0.76
111_M	116_A	0.614	0.75
38_L	61_F	0.613	0.75
46_Y	99_Y	0.612	0.75
66_K	75_V	0.612	0.75
81_V	128_Y	0.612	0.75
101_S	129_V	0.607	0.75
85_G	124_Q	0.606	0.74
8_S	12_S	0.605	0.74
96_A	117_R	0.597	0.73
86_F	114_Y	0.592	0.73
43_D	118_E	0.590	0.72
77_P	86_F	0.584	0.72
27_V	34_V	0.583	0.72
82_G	85_G	0.581	0.71
91_K	107_S	0.577	0.71
37_V	103_V	0.577	0.71
40_V	103_V	0.575	0.71
13_G	22_H	0.575	0.71
23_L	68_A	0.571	0.70
90_E	102_L	0.567	0.69
36_S	51_E	0.566	0.69
48_D	62_E	0.563	0.69
14_I	75_V	0.562	0.69
41_F	101_S	0.561	0.69
23_L	118_E	0.561	0.69
38_L	52_F	0.558	0.68
106_T	109_G	0.558	0.68
33_M	38_L	0.554	0.68
22_H	68_A	0.550	0.67
105_T	110_I	0.548	0.67
104_V	125_V	0.544	0.66
10_A	63_V	0.542	0.66
91_K	121_I	0.539	0.66
83_A	124_Q	0.537	0.65
50_F	63_V	0.535	0.65
52_F	61_F	0.534	0.65
107_S	121_I	0.531	0.64
101_S	126_I	0.529	0.64
2_T	127_A	0.527	0.64
4_N	34_V	0.523	0.63
40_V	112_S	0.522	0.63
41_F	87_E	0.522	0.63
18_E	74_P	0.521	0.63
22_H	25_H	0.520	0.63
77_P	127_A	0.519	0.63
43_D	56_G	0.517	0.62
4_N	13_G	0.515	0.62
2_T	120_G	0.511	0.62
102_L	125_V	0.511	0.62
95_P	100_G	0.507	0.61
84_D	124_Q	0.507	0.61
45_G	49_G	0.502	0.60
20_V	38_L	0.500	0.60

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	0.9692	100	0.078	Contact Map
4rb5H	1	0.9769	100	0.097	Contact Map
3rf2A	1	0.9692	100	0.11	Contact Map
3bbnH	1	0.9846	100	0.113	Contact Map
1seiA	2	0.9769	100	0.12	Contact Map
1s03H	1	0.9538	100	0.143	Contact Map
1i6uA	1	0.9923	100	0.165	Contact Map
4bpeH	1	0.9923	100	0.174	Contact Map
4ujpX	1	0.9923	100	0.199	Contact Map
3qd7X	1	0.5077	45.9	0.925	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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