RL13 - SULSO - GREMLIN Contacts

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RL13 - 50S ribosomal protein L13

UniProt:	P95991	Sequences: MSTQVQEQVVIINAEGQILGRMASNVVRLLKEGKKVIIVNGEKAVISGEKNRVIESYKLLLTVKTLFNPYRNGIRRPRSPINIVKRTIRGMLPKSSKGRRMLKNVKIYVGVPKEFEGRQFIKFPDSDVSRLKGKYVTVEVVSKELGWSG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	149 (120)
Sequences:	2998 (1639)
Seq/√Len:	149.6

ECOLI - RL13
BACSU - RL13
HALSA - RL13
SULSO - RL13

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
8_Q	121_I	2.811	1.00
52_R	73_G	2.718	1.00
79_S	82_N	2.485	1.00
19_L	46_I	2.476	1.00
57_Y	69_P	2.400	1.00
26_V	38_I	2.285	1.00
46_I	72_N	2.284	1.00
15_E	43_K	2.088	1.00
55_E	69_P	2.064	1.00
35_K	106_K	1.998	1.00
57_Y	67_F	1.974	1.00
82_N	85_K	1.750	1.00
12_I	26_V	1.733	1.00
51_N	72_N	1.672	1.00
16_G	45_V	1.660	1.00
51_N	76_R	1.643	1.00
24_S	28_R	1.632	1.00
84_V	88_I	1.624	1.00
29_L	36_V	1.617	1.00
49_E	53_V	1.577	1.00
30_L	105_V	1.575	1.00
41_G	107_I	1.573	1.00
25_N	28_R	1.569	1.00
29_L	123_F	1.566	1.00
23_A	87_T	1.559	1.00
108_Y	115_F	1.551	1.00
42_E	109_V	1.487	1.00
74_I	78_R	1.475	1.00
108_Y	114_E	1.448	1.00
100_R	103_K	1.444	1.00
89_R	102_L	1.436	1.00
70_Y	75_R	1.435	1.00
42_E	110_G	1.426	1.00
72_N	76_R	1.389	1.00
76_R	83_I	1.384	1.00
14_A	22_M	1.373	1.00
85_K	102_L	1.369	1.00
72_N	83_I	1.366	1.00
11_I	39_V	1.364	1.00
39_V	111_V	1.356	1.00
31_K	104_N	1.355	1.00
63_V	66_L	1.351	1.00
55_E	71_R	1.329	1.00
7_E	104_N	1.321	1.00
71_R	74_I	1.321	1.00
17_Q	124_P	1.319	1.00
70_Y	78_R	1.313	1.00
56_S	72_N	1.300	1.00
70_Y	74_I	1.294	1.00
49_E	52_R	1.291	1.00
86_R	90_G	1.262	1.00
17_Q	25_N	1.246	1.00
92_L	98_G	1.237	1.00
15_E	18_I	1.214	1.00
26_V	88_I	1.206	1.00
14_A	38_I	1.195	1.00
92_L	101_M	1.165	1.00
92_L	102_L	1.116	0.99
51_N	83_I	1.115	0.99
86_R	89_R	1.107	0.99
58_K	70_Y	1.092	0.99
82_N	86_R	1.087	0.99
41_G	80_P	1.084	0.99
19_L	44_A	1.078	0.99
26_V	84_V	1.058	0.99
51_N	73_G	1.053	0.99
88_I	105_V	1.048	0.99
22_M	84_V	1.034	0.99
81_I	109_V	1.023	0.99
10_V	123_F	1.014	0.99
18_I	45_V	1.005	0.99
98_G	101_M	1.005	0.99
80_P	109_V	0.995	0.99
25_N	123_F	0.993	0.99
15_E	111_V	0.975	0.99
22_M	26_V	0.965	0.98
32_E	104_N	0.962	0.98
21_R	24_S	0.952	0.98
101_M	104_N	0.932	0.98
74_I	77_P	0.930	0.98
60_L	68_N	0.925	0.98
35_K	104_N	0.901	0.98
11_I	37_I	0.900	0.97
55_E	67_F	0.900	0.97
106_K	114_E	0.896	0.97
81_I	85_K	0.859	0.97
22_M	44_A	0.851	0.96
14_A	44_A	0.851	0.96
58_K	68_N	0.844	0.96
94_K	98_G	0.839	0.96
19_L	87_T	0.836	0.96
84_V	107_I	0.836	0.96
90_G	94_K	0.831	0.96
102_L	107_I	0.808	0.95
58_K	86_R	0.801	0.95
73_G	77_P	0.798	0.95
85_K	107_I	0.790	0.95
59_L	65_T	0.790	0.95
10_V	36_V	0.789	0.95
25_N	29_L	0.787	0.95
85_K	103_K	0.782	0.94
7_E	31_K	0.774	0.94
12_I	22_M	0.772	0.94
75_R	86_R	0.771	0.94
100_R	104_N	0.771	0.94
94_K	101_M	0.770	0.94
13_N	40_N	0.767	0.94
42_E	80_P	0.764	0.94
75_R	79_S	0.760	0.94
5_V	32_E	0.749	0.93
7_E	35_K	0.748	0.93
96_S	99_R	0.741	0.93
46_I	51_N	0.729	0.92
60_L	66_L	0.723	0.92
44_A	84_V	0.711	0.91
54_I	83_I	0.705	0.91
39_V	42_E	0.703	0.91
59_L	63_V	0.699	0.90
10_V	17_Q	0.690	0.90
26_V	36_V	0.676	0.89
98_G	102_L	0.671	0.88
10_V	29_L	0.670	0.88
37_I	115_F	0.667	0.88
19_L	72_N	0.648	0.87
115_F	118_R	0.640	0.86
62_T	66_L	0.628	0.85
79_S	86_R	0.627	0.85
60_L	86_R	0.613	0.84
17_Q	22_M	0.603	0.83
46_I	83_I	0.597	0.82
19_L	84_V	0.597	0.82
92_L	95_S	0.594	0.82
18_I	47_S	0.593	0.81
10_V	121_I	0.587	0.81
37_I	114_E	0.583	0.80
59_L	66_L	0.582	0.80
41_G	109_V	0.578	0.80
89_R	94_K	0.576	0.80
42_E	111_V	0.574	0.79
43_K	110_G	0.564	0.78
72_N	75_R	0.564	0.78
79_S	85_K	0.561	0.78
117_G	120_F	0.561	0.78
63_V	96_S	0.557	0.77
81_I	106_K	0.555	0.77
41_G	81_I	0.555	0.77
112_P	116_E	0.555	0.77
9_V	65_T	0.553	0.77
41_G	84_V	0.553	0.77
119_Q	122_K	0.551	0.77
29_L	32_E	0.548	0.76
95_S	101_M	0.547	0.76
54_I	87_T	0.543	0.76
23_A	84_V	0.537	0.75
78_R	94_K	0.535	0.74
40_N	43_K	0.534	0.74
26_V	29_L	0.533	0.74
37_I	120_F	0.528	0.74
38_I	84_V	0.527	0.73
12_I	24_S	0.526	0.73
56_S	92_L	0.525	0.73
102_L	106_K	0.523	0.73
59_L	67_F	0.523	0.73
76_R	81_I	0.522	0.73
15_E	22_M	0.521	0.73
94_K	102_L	0.521	0.73
70_Y	77_P	0.521	0.73
36_V	123_F	0.520	0.72
53_V	72_N	0.519	0.72
95_S	99_R	0.517	0.72
9_V	50_K	0.516	0.72
11_I	118_R	0.514	0.72
93_P	98_G	0.510	0.71
58_K	67_F	0.507	0.71
53_V	71_R	0.507	0.71
28_R	92_L	0.503	0.70
30_L	102_L	0.502	0.70
4_Q	8_Q	0.502	0.70
25_N	90_G	0.501	0.70
121_I	124_P	0.500	0.69

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
3zf7O	1	0.953	100	0.122	Contact Map
1vq8J	1	0.9262	100	0.13	Contact Map
3j61O	1	0.9933	100	0.148	Contact Map
4cuwO	1	0	100	0.15	Contact Map
1j3aA	1	0.8523	100	0.151	Contact Map
4a17I	1	0.9664	100	0.151	Contact Map
3j39O	1	0.9866	100	0.153	Contact Map
4ujrB	1	0.9597	100	0.155	Contact Map
4w20O	1	0.9597	100	0.157	Contact Map
1vx7K	1	0.9664	100	0.159	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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