RS16 - BACSU - GREMLIN Contacts

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RS16 - 30S ribosomal protein S16

UniProt:	P21474	Sequences: MAVKIRLKRMGAKKSPFYRIVVADSRSPRDGRFIETVGTYNPVAKPAEVKIDEELALKWLQTGAKPSDTVRNLFSSQGIMEKFHNAKQGK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	90 (79)
Sequences:	2547 (1181)
Seq/√Len:	132.9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
58_K	62_T	3.289	1.00
55_L	58_K	3.064	1.00
37_V	56_A	2.464	1.00
41_N	44_A	2.184	1.00
5_I	22_V	2.137	1.00
35_E	55_L	1.943	1.00
8_K	36_T	1.872	1.00
44_A	48_E	1.781	1.00
66_P	74_F	1.776	1.00
22_V	37_V	1.744	1.00
23_A	27_S	1.617	1.00
39_T	50_K	1.605	1.00
53_E	57_L	1.572	1.00
23_A	33_F	1.504	1.00
4_K	67_S	1.496	1.00
12_A	15_S	1.491	1.00
4_K	25_S	1.360	1.00
60_L	66_P	1.328	1.00
3_V	34_I	1.326	1.00
19_R	36_T	1.311	1.00
68_D	71_R	1.290	1.00
10_M	19_R	1.268	1.00
57_L	78_G	1.252	1.00
57_L	61_Q	1.246	1.00
74_F	79_I	1.235	1.00
72_N	76_S	1.232	1.00
22_V	34_I	1.226	1.00
20_I	51_I	1.225	1.00
3_V	22_V	1.224	1.00
15_S	43_V	1.207	1.00
69_T	72_N	1.207	1.00
51_I	56_A	1.205	1.00
33_F	36_T	1.203	1.00
52_D	55_L	1.199	0.99
17_F	39_T	1.195	0.99
27_S	32_R	1.188	0.99
56_A	74_F	1.179	0.99
58_K	61_Q	1.159	0.99
16_P	43_V	1.143	0.99
8_K	33_F	1.130	0.99
41_N	48_E	1.119	0.99
47_A	50_K	1.097	0.99
75_S	80_M	1.096	0.99
28_P	33_F	1.069	0.99
5_I	64_A	1.069	0.99
55_L	62_T	1.058	0.99
36_T	39_T	1.015	0.98
72_N	75_S	1.010	0.98
57_L	79_I	1.005	0.98
71_R	80_M	0.993	0.98
10_M	36_T	0.977	0.98
9_R	16_P	0.949	0.97
5_I	70_V	0.924	0.97
57_L	80_M	0.914	0.97
20_I	70_V	0.908	0.97
7_L	67_S	0.904	0.96
53_E	77_Q	0.886	0.96
71_R	75_S	0.885	0.96
17_F	43_V	0.883	0.96
25_S	67_S	0.857	0.95
24_D	34_I	0.842	0.95
40_Y	69_T	0.807	0.93
53_E	79_I	0.796	0.93
7_L	73_L	0.795	0.93
2_A	65_K	0.794	0.93
69_T	76_S	0.788	0.93
51_I	73_L	0.779	0.92
17_F	41_N	0.772	0.92
3_V	24_D	0.772	0.92
44_A	47_A	0.761	0.91
7_L	20_I	0.757	0.91
57_L	60_L	0.754	0.91
59_W	62_T	0.740	0.90
28_P	32_R	0.733	0.90
35_E	59_W	0.729	0.89
28_P	31_G	0.722	0.89
56_A	66_P	0.714	0.88
51_I	74_F	0.704	0.88
8_K	30_D	0.701	0.88
10_M	17_F	0.688	0.87
43_V	47_A	0.684	0.86
74_F	78_G	0.684	0.86
66_P	70_V	0.677	0.86
60_L	74_F	0.658	0.84
19_R	40_Y	0.654	0.84
43_V	48_E	0.653	0.84
4_K	65_K	0.647	0.83
20_I	73_L	0.642	0.83
52_D	56_A	0.637	0.82
18_Y	76_S	0.630	0.81
48_E	76_S	0.630	0.81
70_V	73_L	0.627	0.81
44_A	73_L	0.614	0.80
39_T	48_E	0.610	0.79
23_A	32_R	0.604	0.79
23_A	28_P	0.601	0.78
27_S	33_F	0.600	0.78
53_E	78_G	0.578	0.76
60_L	65_K	0.577	0.75
53_E	80_M	0.573	0.75
49_V	73_L	0.569	0.74
53_E	74_F	0.559	0.73
35_E	58_K	0.554	0.73
20_I	60_L	0.551	0.72
3_V	26_R	0.550	0.72
60_L	79_I	0.546	0.71
75_S	79_I	0.539	0.70
54_E	57_L	0.538	0.70
22_V	64_A	0.536	0.70
35_E	64_A	0.532	0.69
61_Q	65_K	0.526	0.69
21_V	33_F	0.525	0.68
19_R	72_N	0.522	0.68
70_V	74_F	0.512	0.67
54_E	78_G	0.509	0.66
51_I	79_I	0.506	0.66
22_V	59_W	0.504	0.65
8_K	19_R	0.500	0.65

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
3bn0A	1	0.9111	100	0.073	Contact Map
5aj3P	1	1	100	0.088	Contact Map
4juwP	1	0.9111	100	0.097	Contact Map
3bbnP	1	0.8889	100	0.104	Contact Map
4tp8P	1	0.8889	100	0.119	Contact Map
3c0kA	2	0.9444	30.1	0.915	Contact Map
3ks9A	2	0.5444	18.9	0.922	Contact Map
4ms4B	1	0.6333	15.3	0.926	Contact Map
4ms4A	1	0.6889	13.7	0.927	Contact Map
3sm9A	2	0.5444	9.7	0.932	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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