RL18E - HALSA - GREMLIN Contacts

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RL18E - 50S ribosomal protein L18e

UniProt:	Q9V2W0	Sequences: MSKTSPRLSSLIAELKSVARDSGADVWHDVADRLEKPRSTHAEVNLSRIERYASEDETVIVPGKVLGSGALRKSVTVAAVDFSSSAATKIEHADGEAVHLEQAVEQNPDGTDVRVIR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	117 (113)
Sequences:	179 (137)
Seq/√Len:	12.8

HALSA - RL18E
SULSO - RL18E

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_A	73_K	5.934	1.00
29_D	33_R	3.835	0.99
49_I	75_V	3.456	0.99
49_I	65_V	3.356	0.98
50_E	72_R	3.174	0.97
33_R	42_A	2.642	0.93
90_I	95_G	2.521	0.91
57_E	114_R	2.378	0.88
96_E	106_Q	2.357	0.88
100_L	103_A	2.196	0.84
50_E	73_K	2.080	0.80
65_V	82_F	1.813	0.70
82_F	97_A	1.794	0.69
60_I	97_A	1.717	0.65
67_G	85_S	1.668	0.63
103_A	113_V	1.630	0.61
16_K	35_E	1.606	0.60
65_V	90_I	1.584	0.59
56_D	60_I	1.575	0.58
47_S	52_Y	1.532	0.56
29_D	42_A	1.442	0.52
55_E	73_K	1.426	0.51
26_V	115_V	1.360	0.47
52_Y	82_F	1.318	0.45
20_R	35_E	1.316	0.45
18_V	22_S	1.312	0.45
47_S	51_R	1.309	0.45
107_N	110_G	1.305	0.44
87_A	91_E	1.278	0.43
35_E	80_V	1.276	0.43
77_V	95_G	1.264	0.42
78_A	100_L	1.247	0.42
43_E	61_V	1.246	0.41
8_L	32_D	1.242	0.41
12_I	34_L	1.235	0.41
24_A	108_P	1.218	0.40
49_I	52_Y	1.213	0.40
43_E	57_E	1.210	0.40
18_V	104_V	1.199	0.39
5_S	30_V	1.195	0.39
26_V	50_E	1.194	0.39
47_S	70_A	1.187	0.39
13_A	46_L	1.170	0.38
75_V	82_F	1.166	0.38
8_L	25_D	1.140	0.36
44_V	116_I	1.123	0.35
84_S	88_T	1.114	0.35
30_V	75_V	1.109	0.35
38_R	89_K	1.076	0.33
44_V	111_T	1.075	0.33
9_S	13_A	1.060	0.33
6_P	57_E	1.011	0.30
41_H	80_V	0.996	0.30
29_D	74_S	0.994	0.30
102_Q	109_D	0.958	0.28
37_P	48_R	0.949	0.28
13_A	16_K	0.948	0.28
19_A	24_A	0.942	0.27
18_V	24_A	0.940	0.27
5_S	64_K	0.935	0.27
61_V	116_I	0.929	0.27
51_R	71_L	0.925	0.27
56_D	104_V	0.924	0.27
103_A	107_N	0.905	0.26
43_E	101_E	0.902	0.26
7_R	101_E	0.888	0.25
79_A	82_F	0.884	0.25
74_S	102_Q	0.876	0.25
10_S	116_I	0.876	0.25
21_D	58_T	0.875	0.25
75_V	87_A	0.868	0.24
103_A	108_P	0.844	0.24
32_D	92_H	0.842	0.23
50_E	71_L	0.822	0.23
32_D	88_T	0.819	0.23
53_A	72_R	0.805	0.22
32_D	40_T	0.805	0.22
58_T	105_E	0.804	0.22
54_S	73_K	0.802	0.22
7_R	11_L	0.802	0.22
111_T	115_V	0.801	0.22
48_R	80_V	0.799	0.22
58_T	88_T	0.798	0.22
41_H	48_R	0.797	0.22
78_A	111_T	0.796	0.22
11_L	99_H	0.796	0.22
100_L	115_V	0.780	0.21
40_T	46_L	0.778	0.21
95_G	113_V	0.774	0.21
34_L	79_A	0.771	0.21
11_L	37_P	0.771	0.21
105_E	109_D	0.771	0.21
32_D	39_S	0.759	0.20
78_A	103_A	0.753	0.20
18_V	48_R	0.750	0.20
10_S	20_R	0.749	0.20
11_L	101_E	0.748	0.20
30_V	61_V	0.743	0.20
14_E	44_V	0.739	0.20
5_S	95_G	0.727	0.19
109_D	112_D	0.717	0.19
25_D	30_V	0.716	0.19
55_E	74_S	0.707	0.19
4_T	39_S	0.699	0.19
55_E	99_H	0.697	0.18
87_A	112_D	0.694	0.18
54_S	113_V	0.694	0.18
91_E	96_E	0.683	0.18
5_S	98_V	0.675	0.18
30_V	40_T	0.668	0.18
43_E	78_A	0.662	0.17
51_R	68_S	0.656	0.17
6_P	9_S	0.652	0.17
20_R	28_H	0.650	0.17
78_A	107_N	0.650	0.17
21_D	81_D	0.644	0.17
10_S	32_D	0.641	0.17
36_K	59_V	0.637	0.17
61_V	65_V	0.633	0.17
72_R	80_V	0.632	0.17
45_N	89_K	0.631	0.16
82_F	90_I	0.631	0.16
58_T	72_R	0.629	0.16
74_S	88_T	0.628	0.16
84_S	103_A	0.624	0.16
91_E	112_D	0.622	0.16
32_D	41_H	0.614	0.16
26_V	101_E	0.613	0.16
60_I	103_A	0.600	0.16
58_T	76_T	0.598	0.16
12_I	71_L	0.595	0.15
21_D	116_I	0.594	0.15
48_R	51_R	0.593	0.15
25_D	115_V	0.593	0.15
46_L	81_D	0.591	0.15
23_G	30_V	0.588	0.15
51_R	93_A	0.588	0.15
73_K	76_T	0.588	0.15
44_V	82_F	0.586	0.15
11_L	80_V	0.585	0.15
10_S	18_V	0.585	0.15
17_S	41_H	0.582	0.15
23_G	59_V	0.581	0.15
48_R	56_D	0.574	0.15
19_A	116_I	0.574	0.15
54_S	105_E	0.573	0.15
28_H	98_V	0.570	0.15
92_H	112_D	0.569	0.15
13_A	35_E	0.568	0.15
46_L	58_T	0.562	0.15
54_S	68_S	0.562	0.15
42_A	57_E	0.559	0.15
53_A	59_V	0.559	0.15
57_E	73_K	0.550	0.14
87_A	98_V	0.549	0.14
16_K	36_K	0.547	0.14
46_L	102_Q	0.544	0.14
8_L	60_I	0.540	0.14
19_A	55_E	0.538	0.14
45_N	95_G	0.531	0.14
62_P	114_R	0.527	0.14
53_A	114_R	0.526	0.14
106_Q	111_T	0.519	0.14
14_E	36_K	0.518	0.14
72_R	101_E	0.516	0.13
88_T	105_E	0.515	0.13
39_S	61_V	0.508	0.13
22_S	26_V	0.507	0.13
15_L	108_P	0.507	0.13
38_R	96_E	0.500	0.13

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
1vq8O	1	0.9829	100	0.418	Contact Map
3j21P	1	1	100	0.419	Contact Map
1vx7S	1	1	100	0.438	Contact Map
3j61Q	1	1	100	0.438	Contact Map
4w20Q	1	1	100	0.44	Contact Map
4ujrD	1	1	100	0.441	Contact Map
4a17N	1	1	100	0.441	Contact Map
3j39Q	1	1	100	0.442	Contact Map
3zf7I	1	1	100	0.452	Contact Map
1vq8L	1	0.812	99.4	0.723	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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