RS18 - BACSU - GREMLIN Contacts

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RS18 - 30S ribosomal protein S18

UniProt:	P21475	Sequences: MAGGRRGGRAKRRKVCYFTSNGITHIDYKDVDLLKKFVSERGKILPRRVTGTNAKYQRKLTAAIKRARQMALLPYVSGE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	79 (69)
Sequences:	1466 (634)
Seq/√Len:	76.3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
53_N	56_Y	4.092	1.00
19_T	53_N	3.837	1.00
19_T	56_Y	3.239	1.00
69_Q	75_Y	2.942	1.00
52_T	60_L	2.777	1.00
38_V	73_L	2.700	1.00
16_C	19_T	2.606	1.00
34_L	73_L	2.140	1.00
16_C	53_N	2.140	1.00
16_C	56_Y	1.865	1.00
54_A	58_R	1.832	1.00
26_I	63_A	1.827	1.00
30_D	33_L	1.806	1.00
17_Y	21_N	1.790	1.00
44_I	64_I	1.629	1.00
17_Y	36_K	1.619	1.00
31_V	72_L	1.602	1.00
17_Y	52_T	1.516	0.99
26_I	60_L	1.333	0.98
26_I	70_M	1.176	0.96
18_F	60_L	1.143	0.95
22_G	26_I	1.132	0.95
23_I	33_L	1.121	0.95
42_G	49_V	1.096	0.94
23_I	59_K	1.083	0.94
32_D	35_K	1.034	0.92
14_K	51_G	1.027	0.92
61_T	69_Q	0.995	0.91
18_F	56_Y	0.970	0.89
47_R	69_Q	0.958	0.89
24_T	33_L	0.945	0.88
35_K	73_L	0.896	0.85
8_G	13_R	0.895	0.85
27_D	66_R	0.888	0.85
40_E	48_R	0.872	0.84
45_L	49_V	0.858	0.83
62_A	66_R	0.814	0.79
18_F	26_I	0.810	0.79
27_D	63_A	0.790	0.77
38_V	42_G	0.784	0.77
41_R	47_R	0.783	0.77
35_K	47_R	0.764	0.75
45_L	50_T	0.764	0.75
63_A	66_R	0.761	0.75
45_L	69_Q	0.758	0.74
8_G	11_K	0.758	0.74
69_Q	76_V	0.756	0.74
34_L	64_I	0.750	0.73
56_Y	59_K	0.747	0.73
17_Y	37_F	0.738	0.72
15_V	18_F	0.726	0.71
17_Y	32_D	0.720	0.70
25_H	59_K	0.715	0.70
47_R	76_V	0.711	0.69
40_E	76_V	0.706	0.69
33_L	72_L	0.705	0.69
35_K	69_Q	0.700	0.68
28_Y	76_V	0.699	0.68
37_F	45_L	0.692	0.67
41_R	70_M	0.691	0.67
35_K	40_E	0.687	0.67
15_V	25_H	0.682	0.66
60_L	64_I	0.672	0.65
43_K	48_R	0.667	0.65
30_D	63_A	0.665	0.64
57_Q	61_T	0.662	0.64
47_R	54_A	0.656	0.63
18_F	52_T	0.654	0.63
10_A	13_R	0.647	0.62
55_K	66_R	0.636	0.61
31_V	39_S	0.631	0.60
52_T	61_T	0.631	0.60
67_A	71_A	0.629	0.60
37_F	60_L	0.625	0.60
11_K	49_V	0.617	0.59
23_I	26_I	0.616	0.58
8_G	17_Y	0.612	0.58
42_G	58_R	0.610	0.58
15_V	20_S	0.605	0.57
33_L	60_L	0.602	0.57
12_R	47_R	0.601	0.57
39_S	45_L	0.599	0.56
27_D	72_L	0.599	0.56
40_E	49_V	0.596	0.56
31_V	35_K	0.583	0.54
33_L	63_A	0.576	0.53
37_F	55_K	0.564	0.52
24_T	31_V	0.550	0.50
17_Y	39_S	0.544	0.49
38_V	64_I	0.544	0.49
36_K	45_L	0.540	0.49
14_K	19_T	0.534	0.48
8_G	75_Y	0.532	0.48
40_E	43_K	0.526	0.47
38_V	52_T	0.522	0.47
19_T	51_G	0.516	0.46
39_S	60_L	0.511	0.45
36_K	61_T	0.511	0.45
13_R	49_V	0.506	0.45
34_L	37_F	0.506	0.45
46_P	51_G	0.505	0.44
32_D	50_T	0.505	0.44
11_K	46_P	0.500	0.44
22_G	53_N	0.500	0.44

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
4kiyR	1	0.6962	100	0.208	Contact Map
4rb5R	1	0.8354	100	0.216	Contact Map
5aj3p	1	1	100	0.222	Contact Map
3j7yr	1	0.9873	99.9	0.238	Contact Map
3bbnR	1	0.7215	99.9	0.245	Contact Map
5aj3R	1	0.962	99.9	0.265	Contact Map
4tp8R	1	0.6962	99.9	0.339	Contact Map
1ltrD	5	0.443	11.1	0.922	Contact Map
4ftfA	1	0.3671	10.7	0.922	Contact Map
1b44D	3	0.443	10.5	0.923	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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