RL31B - BACSU - GREMLIN Contacts

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RL31B - 50S ribosomal protein L31 type B

UniProt:	O34967	Sequences: MKEGIHPKNHKVIFQDVNSGYRFLSTSTKTSNETAEWEDGNTYPVIKVEVSSDTHPFYTGRQKFNEKGGRVEQFKKRYNMGK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	82 (79)
Sequences:	985 (364)
Seq/√Len:	41.0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
36_E	42_T	4.308	1.00
13_I	35_A	4.165	1.00
29_K	46_I	2.952	1.00
33_E	47_K	2.767	1.00
31_S	46_I	2.639	1.00
10_H	31_S	2.568	1.00
10_H	30_T	2.181	0.99
21_Y	53_D	2.029	0.99
15_Q	22_R	2.026	0.99
24_L	37_W	1.920	0.99
19_S	53_D	1.789	0.98
23_F	52_S	1.771	0.98
11_K	26_T	1.755	0.98
11_K	41_N	1.739	0.97
37_W	41_N	1.706	0.97
68_G	72_E	1.695	0.97
13_I	37_W	1.679	0.97
17_V	47_K	1.583	0.95
22_R	37_W	1.540	0.95
22_R	35_A	1.522	0.94
34_T	42_T	1.509	0.94
10_H	29_K	1.465	0.93
15_Q	45_V	1.427	0.92
15_Q	47_K	1.195	0.83
58_Y	63_K	1.181	0.83
48_V	51_S	1.177	0.82
76_K	79_N	1.169	0.82
63_K	68_G	1.082	0.77
19_S	47_K	1.066	0.76
15_Q	19_S	0.996	0.70
49_E	58_Y	0.989	0.70
19_S	51_S	0.982	0.69
61_R	72_E	0.981	0.69
15_Q	20_G	0.968	0.68
66_E	75_K	0.959	0.67
15_Q	35_A	0.939	0.66
13_I	22_R	0.930	0.65
66_E	73_Q	0.901	0.63
21_Y	38_E	0.894	0.62
50_V	62_Q	0.891	0.62
18_N	54_T	0.883	0.61
24_L	43_Y	0.861	0.59
19_S	54_T	0.860	0.59
37_W	43_Y	0.854	0.58
31_S	45_V	0.848	0.58
50_V	71_V	0.826	0.56
21_Y	25_S	0.825	0.56
30_T	46_I	0.821	0.55
35_A	45_V	0.814	0.55
71_V	75_K	0.814	0.55
21_Y	37_W	0.805	0.54
26_T	68_G	0.800	0.53
20_G	53_D	0.793	0.53
67_K	71_V	0.780	0.52
2_K	73_Q	0.766	0.50
24_L	35_A	0.762	0.50
66_E	71_V	0.757	0.49
14_F	52_S	0.755	0.49
62_Q	76_K	0.749	0.49
64_F	67_K	0.749	0.49
11_K	24_L	0.745	0.48
75_K	79_N	0.743	0.48
20_G	70_R	0.738	0.48
18_N	68_G	0.737	0.48
4_G	30_T	0.735	0.47
17_V	78_Y	0.722	0.46
20_G	48_V	0.717	0.46
8_K	34_T	0.713	0.45
4_G	8_K	0.710	0.45
48_V	75_K	0.708	0.45
70_R	73_Q	0.700	0.44
72_E	76_K	0.700	0.44
20_G	38_E	0.698	0.44
38_E	75_K	0.691	0.43
8_K	30_T	0.686	0.43
64_F	76_K	0.678	0.42
3_E	62_Q	0.671	0.42
32_N	73_Q	0.671	0.42
9_N	44_P	0.668	0.41
66_E	72_E	0.667	0.41
2_K	6_H	0.662	0.41
28_T	46_I	0.651	0.40
57_F	71_V	0.648	0.39
1_M	6_H	0.643	0.39
33_E	75_K	0.636	0.38
3_E	18_N	0.627	0.38
69_G	74_F	0.626	0.38
19_S	22_R	0.618	0.37
48_V	78_Y	0.617	0.37
33_E	45_V	0.612	0.36
67_K	70_R	0.603	0.36
4_G	61_R	0.599	0.35
67_K	73_Q	0.596	0.35
11_K	79_N	0.596	0.35
24_L	70_R	0.594	0.35
36_E	39_D	0.591	0.35
17_V	58_Y	0.581	0.34
57_F	66_E	0.580	0.34
66_E	78_Y	0.575	0.33
66_E	70_R	0.563	0.32
14_F	77_R	0.555	0.32
56_P	69_G	0.555	0.32
67_K	76_K	0.554	0.32
49_E	54_T	0.553	0.31
47_K	72_E	0.548	0.31
64_F	71_V	0.545	0.31
13_I	78_Y	0.540	0.30
38_E	77_R	0.536	0.30
21_Y	52_S	0.526	0.29
70_R	77_R	0.525	0.29
4_G	25_S	0.523	0.29
64_F	77_R	0.522	0.29
1_M	7_P	0.514	0.28
14_F	54_T	0.510	0.28
69_G	78_Y	0.508	0.28
2_K	5_I	0.506	0.28
18_N	73_Q	0.504	0.28
36_E	48_V	0.500	0.27

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
3f1f4	1	0.3659	100	0.354	Contact Map
1nkwY	1	0.8171	100	0.359	Contact Map
4rb64	1	0.8171	100	0.361	Contact Map
1vs6Z	1	0.8293	100	0.362	Contact Map
3bbo1	1	0.8171	99.9	0.37	Contact Map
1vw4V	1	0.5854	99.8	0.507	Contact Map
4dapA	1	0.5488	6.7	0.942	Contact Map
2k89A	1	0.622	6.7	0.942	Contact Map
2ketA	1	0.1707	6.2	0.943	Contact Map
5aj3U	1	0.3537	5.1	0.945	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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