RL31 - HALSA - GREMLIN Contacts

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RL31 - 50S ribosomal protein L31e

UniProt:	Q9HMN0	Sequences: MSASEFDDRFVTVPLRDVTKVPSHERAGEAMNIIRQHLAKQFAVDEDAVRLDPSINDAVWSEGNNNPPRKLRVHAGSFAEDGETVVEADYEG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	92 (78)
Sequences:	146 (100)
Seq/√Len:	11.3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
34_I	59_V	4.731	1.00
58_A	61_S	2.966	0.95
11_V	37_H	2.838	0.93
23_S	65_N	2.810	0.93
42_F	75_A	2.743	0.92
49_V	73_V	2.574	0.89
38_L	75_A	2.510	0.88
11_V	50_R	1.982	0.72
55_I	70_K	1.952	0.70
31_M	34_I	1.782	0.63
13_V	34_I	1.707	0.60
78_F	86_V	1.680	0.58
19_T	63_G	1.474	0.48
51_L	55_I	1.371	0.43
33_I	36_Q	1.365	0.43
32_N	36_Q	1.351	0.42
50_R	77_S	1.294	0.40
5_E	79_A	1.268	0.38
26_R	62_E	1.258	0.38
34_I	49_V	1.246	0.37
28_G	64_N	1.241	0.37
22_P	81_D	1.230	0.37
17_D	27_A	1.224	0.36
39_A	48_A	1.204	0.36
53_P	63_G	1.201	0.35
29_E	33_I	1.163	0.34
19_T	66_N	1.160	0.34
8_D	74_H	1.158	0.34
82_G	86_V	1.139	0.33
21_V	29_E	1.115	0.32
14_P	57_D	1.101	0.31
42_F	71_L	1.100	0.31
9_R	37_H	1.070	0.30
8_D	57_D	1.069	0.30
12_T	83_E	1.048	0.29
12_T	72_R	1.042	0.29
13_V	31_M	1.033	0.28
13_V	53_P	1.011	0.27
7_D	37_H	0.992	0.27
38_L	55_I	0.986	0.27
21_V	27_A	0.972	0.26
23_S	66_N	0.965	0.26
55_I	71_L	0.958	0.25
38_L	50_R	0.953	0.25
40_K	55_I	0.938	0.25
24_H	66_N	0.925	0.24
13_V	33_I	0.925	0.24
76_G	83_E	0.915	0.24
23_S	62_E	0.914	0.24
6_F	74_H	0.908	0.24
65_N	73_V	0.892	0.23
75_A	78_F	0.886	0.23
22_P	32_N	0.878	0.23
29_E	41_Q	0.869	0.22
10_F	54_S	0.856	0.22
16_R	49_V	0.836	0.21
67_P	74_H	0.834	0.21
38_L	72_R	0.828	0.21
11_V	41_Q	0.823	0.21
25_E	43_A	0.823	0.21
12_T	29_E	0.819	0.21
72_R	78_F	0.810	0.20
53_P	57_D	0.807	0.20
38_L	87_E	0.805	0.20
47_D	51_L	0.804	0.20
43_A	62_E	0.796	0.20
19_T	69_R	0.787	0.20
13_V	66_N	0.784	0.20
13_V	73_V	0.782	0.19
25_E	28_G	0.742	0.18
7_D	36_Q	0.739	0.18
21_V	33_I	0.733	0.18
25_E	39_A	0.718	0.18
14_P	78_F	0.708	0.17
27_A	87_E	0.694	0.17
24_H	65_N	0.693	0.17
43_A	68_P	0.674	0.16
34_I	83_E	0.654	0.16
15_L	86_V	0.651	0.16
31_M	59_V	0.648	0.16
8_D	19_T	0.646	0.16
12_T	76_G	0.646	0.16
50_R	82_G	0.642	0.16
20_K	29_E	0.638	0.15
34_I	50_R	0.633	0.15
6_F	42_F	0.632	0.15
7_D	51_L	0.632	0.15
22_P	35_R	0.623	0.15
74_H	87_E	0.623	0.15
12_T	18_V	0.622	0.15
56_N	66_N	0.613	0.15
14_P	75_A	0.605	0.15
30_A	73_V	0.598	0.14
75_A	86_V	0.597	0.14
47_D	70_K	0.593	0.14
27_A	64_N	0.579	0.14
63_G	69_R	0.560	0.14
55_I	87_E	0.548	0.13
62_E	66_N	0.546	0.13
24_H	72_R	0.544	0.13
7_D	55_I	0.540	0.13
20_K	48_A	0.538	0.13
8_D	14_P	0.538	0.13
7_D	17_D	0.537	0.13
18_V	21_V	0.534	0.13
49_V	56_N	0.534	0.13
8_D	17_D	0.533	0.13
46_E	81_D	0.532	0.13
9_R	79_A	0.527	0.13
22_P	71_L	0.527	0.13
58_A	77_S	0.525	0.13
21_V	42_F	0.522	0.13
7_D	65_N	0.518	0.13
38_L	54_S	0.517	0.13
57_D	61_S	0.515	0.13
83_E	87_E	0.508	0.12
8_D	75_A	0.500	0.12

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
1vq8X	1	0.8913	100	0.264	Contact Map
3j21a	1	0.913	99.9	0.341	Contact Map
4a17W	1	0.9674	99.9	0.402	Contact Map
4ujrQ	1	0.9565	99.9	0.427	Contact Map
1vx77	1	0.9022	99.9	0.429	Contact Map
3j61d	1	0.9783	99.9	0.43	Contact Map
3zf7h	1	0.9783	99.9	0.438	Contact Map
4w20d	1	0.9457	99.9	0.441	Contact Map
2hw2A	1	0.5543	8.9	0.935	Contact Map
4r80A	1	0.5	4.7	0.943	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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