RL27 - BACSU - GREMLIN Contacts

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RL27 - 50S ribosomal protein L27

UniProt:	P05657	Sequences: MLRLDLQFFASKKGVGSTKNGRDSEAKRLGAKRADGQFVTGGSILYRQRGTKIYPGENVGRGGDDTLFAKIDGTVKFERFGRDRKKVSVYPVAQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	94 (83)
Sequences:	2025 (715)
Seq/√Len:	78.4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
29_L	49_R	3.477	1.00
61_R	65_D	3.339	1.00
33_R	39_V	3.212	1.00
33_R	43_S	2.859	1.00
60_G	70_K	2.805	1.00
40_T	43_S	2.732	1.00
59_V	67_L	2.208	1.00
31_A	46_Y	2.064	1.00
54_Y	84_R	2.033	1.00
33_R	37_Q	1.957	1.00
78_E	88_S	1.941	1.00
76_K	90_Y	1.916	1.00
78_E	90_Y	1.782	1.00
60_G	68_F	1.726	1.00
38_F	74_T	1.684	1.00
62_G	66_T	1.660	1.00
79_R	85_K	1.608	1.00
25_E	28_R	1.595	1.00
46_Y	53_I	1.589	1.00
53_I	87_V	1.543	0.99
41_G	72_D	1.497	0.99
53_I	85_K	1.495	0.99
31_A	77_F	1.309	0.98
35_D	76_K	1.298	0.98
40_T	72_D	1.246	0.97
80_F	86_K	1.242	0.97
33_R	75_V	1.234	0.97
31_A	34_A	1.233	0.97
47_R	64_D	1.209	0.97
49_R	65_D	1.179	0.96
78_E	86_K	1.168	0.96
55_P	67_L	1.112	0.95
61_R	67_L	1.110	0.95
51_T	61_R	1.102	0.95
71_I	91_P	1.090	0.94
38_F	72_D	1.077	0.94
47_R	66_T	1.074	0.94
33_R	40_T	1.044	0.93
58_N	71_I	1.034	0.93
15_V	18_T	1.031	0.93
41_G	70_K	1.016	0.92
39_V	43_S	0.997	0.91
33_R	45_L	0.983	0.91
51_T	65_D	0.978	0.90
45_L	67_L	0.945	0.89
12_K	20_N	0.902	0.86
69_A	89_V	0.901	0.86
43_S	72_D	0.889	0.86
27_K	65_D	0.873	0.85
54_Y	61_R	0.846	0.83
59_V	89_V	0.845	0.83
39_V	45_L	0.838	0.82
67_L	87_V	0.834	0.82
9_F	35_D	0.834	0.82
57_E	90_Y	0.820	0.81
52_K	85_K	0.802	0.79
9_F	13_K	0.794	0.79
27_K	49_R	0.779	0.77
55_P	61_R	0.775	0.77
81_G	84_R	0.768	0.76
79_R	86_K	0.738	0.73
79_R	83_D	0.737	0.73
80_F	88_S	0.737	0.73
79_R	84_R	0.734	0.73
33_R	38_F	0.731	0.73
82_R	86_K	0.728	0.72
57_E	70_K	0.725	0.72
74_T	91_P	0.719	0.71
18_T	21_G	0.718	0.71
9_F	34_A	0.714	0.71
13_K	16_G	0.714	0.71
76_K	88_S	0.712	0.71
20_N	24_S	0.707	0.70
62_G	68_F	0.707	0.70
35_D	85_K	0.694	0.69
34_A	37_Q	0.693	0.69
9_F	19_K	0.690	0.68
12_K	46_Y	0.683	0.67
51_T	54_Y	0.681	0.67
53_I	77_F	0.677	0.67
80_F	83_D	0.677	0.67
86_K	90_Y	0.669	0.66
29_L	65_D	0.648	0.63
31_A	35_D	0.634	0.62
15_V	19_K	0.632	0.61
31_A	53_I	0.625	0.61
54_Y	79_R	0.617	0.60
52_K	65_D	0.615	0.59
55_P	62_G	0.615	0.59
13_K	17_S	0.613	0.59
37_Q	43_S	0.610	0.59
83_D	86_K	0.602	0.58
46_Y	87_V	0.602	0.58
75_V	87_V	0.586	0.56
51_T	55_P	0.581	0.55
57_E	88_S	0.579	0.55
50_G	64_D	0.576	0.55
71_I	90_Y	0.571	0.54
19_K	23_D	0.571	0.54
60_G	66_T	0.561	0.53
45_L	75_V	0.560	0.52
14_G	86_K	0.558	0.52
55_P	65_D	0.554	0.52
17_S	20_N	0.553	0.52
81_G	85_K	0.552	0.51
47_R	62_G	0.551	0.51
38_F	91_P	0.550	0.51
19_K	26_A	0.542	0.50
46_Y	77_F	0.533	0.49
12_K	54_Y	0.531	0.49
11_S	14_G	0.526	0.48
14_G	19_K	0.525	0.48
10_A	13_K	0.520	0.47
23_D	53_I	0.518	0.47
17_S	21_G	0.516	0.47
78_E	85_K	0.516	0.47
23_D	26_A	0.513	0.46
45_L	59_V	0.508	0.46
45_L	77_F	0.508	0.46
11_S	15_V	0.506	0.46
14_G	20_N	0.506	0.46
55_P	59_V	0.501	0.45
34_A	46_Y	0.501	0.45
55_P	58_N	0.500	0.45

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
3bboX	1	0.9043	100	0.064	Contact Map
4rb60	1	0.883	100	0.095	Contact Map
3j7yW	1	0.7872	100	0.109	Contact Map
4kixW	1	0.8298	100	0.113	Contact Map
1vw4R	1	0.8298	100	0.114	Contact Map
1pnuU	1	0.9043	100	0.118	Contact Map
4tp9W	1	0.7979	100	0.227	Contact Map
2ba0A	1	0.5319	87.9	0.882	Contact Map
4ifdG	1	0.6277	85.3	0.886	Contact Map
2nn6I	1	0.5851	81.5	0.892	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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