RL6 - HALSA - GREMLIN Contacts

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RL6 - 50S ribosomal protein L6

UniProt:	Q9HPB8	Sequences: MARVEIEIPDDVTAEVDHLDLTVEGPEGSVTRRLWYPDVDVSVEDDAVVVASEVDDAKTDSTVGTFESHVANMFHGVSEGWEYKLEVHYSHFPMQVDVEGEEVVIQNFLGEKAARRTQIRGDTDVVVDDEEVTLSGPSIEDVGQTAADIEQLTRVTDKDTRVFQDGVYIVEKPAKGGA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	178 (169)
Sequences:	3825 (2216)
Seq/√Len:	170.4

ECOLI - RL6
BACSU - RL6
HALSA - RL6
SULSO - RL6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
75_H	79_E	3.079	1.00
71_A	75_H	2.940	1.00
119_I	125_V	2.567	1.00
24_E	29_S	2.549	1.00
42_S	51_A	2.437	1.00
126_V	135_S	2.386	1.00
82_E	135_S	2.354	1.00
102_E	118_Q	2.234	1.00
102_E	116_R	2.173	1.00
84_K	165_D	2.137	1.00
13_T	24_E	2.041	1.00
144_Q	148_D	2.036	1.00
50_V	70_V	2.029	1.00
109_L	152_L	2.019	1.00
54_V	59_T	1.952	1.00
163_F	169_I	1.933	1.00
134_L	142_V	1.885	1.00
35_W	38_D	1.872	1.00
22_T	29_S	1.864	1.00
32_R	140_E	1.843	1.00
88_H	163_F	1.828	1.00
117_T	145_T	1.774	1.00
20_D	31_T	1.741	1.00
38_D	59_T	1.732	1.00
98_V	127_V	1.729	1.00
136_G	142_V	1.728	1.00
117_T	152_L	1.685	1.00
124_D	135_S	1.673	1.00
84_K	133_T	1.656	1.00
84_K	131_E	1.622	1.00
52_S	63_V	1.599	1.00
32_R	73_M	1.572	1.00
138_S	141_D	1.565	1.00
20_D	33_R	1.558	1.00
86_E	166_G	1.522	1.00
105_I	109_L	1.519	1.00
16_V	21_L	1.492	1.00
40_D	51_A	1.481	1.00
98_V	119_I	1.475	1.00
104_V	116_R	1.475	1.00
43_V	48_V	1.468	1.00
7_E	47_A	1.465	1.00
22_T	31_T	1.457	1.00
99_E	104_V	1.426	1.00
99_E	102_E	1.409	1.00
101_E	121_G	1.396	1.00
109_L	162_V	1.391	1.00
25_G	28_G	1.383	1.00
8_I	14_A	1.382	1.00
131_E	165_D	1.359	1.00
173_P	176_G	1.356	1.00
122_D	141_D	1.348	1.00
40_D	53_E	1.343	1.00
128_D	133_T	1.340	1.00
8_I	43_V	1.319	1.00
32_R	69_H	1.300	1.00
115_R	152_L	1.297	1.00
117_T	148_D	1.296	1.00
16_V	43_V	1.290	1.00
65_T	69_H	1.263	1.00
21_L	70_V	1.258	1.00
79_E	82_E	1.245	1.00
123_T	145_T	1.205	1.00
27_E	137_P	1.181	1.00
101_E	118_Q	1.180	1.00
52_S	60_D	1.180	1.00
125_V	145_T	1.178	1.00
62_T	66_F	1.177	1.00
34_L	41_V	1.165	1.00
111_E	115_R	1.156	1.00
87_V	96_V	1.133	1.00
86_E	165_D	1.128	1.00
23_V	73_M	1.120	1.00
58_K	61_S	1.119	1.00
7_E	46_D	1.112	1.00
150_E	155_V	1.111	1.00
65_T	68_S	1.107	1.00
42_S	49_V	1.099	1.00
151_Q	154_R	1.084	1.00
15_E	22_T	1.064	1.00
125_V	134_L	1.059	1.00
105_I	152_L	1.057	0.99
56_D	59_T	1.033	0.99
39_V	53_E	1.030	0.99
145_T	149_I	1.029	0.99
140_E	144_Q	1.021	0.99
97_D	104_V	1.021	0.99
128_D	131_E	1.019	0.99
27_E	135_S	1.017	0.99
126_V	133_T	1.015	0.99
104_V	114_A	1.015	0.99
103_V	125_V	1.012	0.99
96_V	105_I	1.008	0.99
67_E	71_A	1.007	0.99
163_F	171_E	1.003	0.99
150_E	167_V	1.002	0.99
53_E	59_T	0.997	0.99
82_E	133_T	0.996	0.99
48_V	70_V	0.984	0.99
18_H	33_R	0.981	0.99
19_L	33_R	0.971	0.99
86_E	131_E	0.971	0.99
119_I	145_T	0.968	0.99
155_V	160_T	0.966	0.99
52_S	55_D	0.964	0.99
17_D	20_D	0.964	0.99
88_H	169_I	0.954	0.99
13_T	29_S	0.949	0.99
35_W	62_T	0.938	0.99
98_V	125_V	0.935	0.99
14_A	48_V	0.932	0.99
111_E	152_L	0.930	0.99
97_D	106_Q	0.930	0.99
96_V	132_V	0.920	0.99
102_E	119_I	0.914	0.99
28_G	77_V	0.913	0.99
106_Q	114_A	0.911	0.98
103_V	149_I	0.906	0.98
141_D	145_T	0.903	0.98
38_D	54_V	0.898	0.98
119_I	134_L	0.898	0.98
99_E	116_R	0.895	0.98
39_V	59_T	0.892	0.98
117_T	125_V	0.882	0.98
156_T	169_I	0.880	0.98
134_L	149_I	0.876	0.98
86_E	163_F	0.874	0.98
25_G	77_V	0.869	0.98
32_R	66_F	0.869	0.98
123_T	136_G	0.858	0.98
61_S	68_S	0.856	0.98
157_D	171_E	0.853	0.98
121_G	141_D	0.851	0.98
30_V	73_M	0.851	0.98
144_Q	151_Q	0.833	0.97
27_E	80_G	0.832	0.97
39_V	50_V	0.818	0.97
101_E	124_D	0.817	0.97
10_D	46_D	0.808	0.97
58_K	62_T	0.806	0.97
111_E	153_T	0.799	0.97
27_E	124_D	0.793	0.96
39_V	62_T	0.792	0.96
92_F	153_T	0.790	0.96
83_Y	166_G	0.784	0.96
120_R	141_D	0.783	0.96
38_D	53_E	0.778	0.96
109_L	113_A	0.778	0.96
122_D	136_G	0.778	0.96
163_F	166_G	0.775	0.96
38_D	58_K	0.773	0.96
23_V	78_S	0.762	0.96
150_E	164_Q	0.746	0.95
60_D	63_V	0.745	0.95
28_G	137_P	0.742	0.95
35_W	58_K	0.741	0.95
34_L	70_V	0.735	0.95
44_E	49_V	0.732	0.94
61_S	65_T	0.728	0.94
30_V	137_P	0.719	0.94
146_A	164_Q	0.718	0.94
88_H	166_G	0.716	0.94
63_V	176_G	0.716	0.94
44_E	47_A	0.715	0.94
15_E	24_E	0.715	0.94
85_L	132_V	0.714	0.94
8_I	48_V	0.713	0.94
145_T	148_D	0.696	0.93
4_V	67_E	0.695	0.93
50_V	66_F	0.692	0.93
12_V	78_S	0.689	0.92
95_Q	129_D	0.682	0.92
6_I	74_F	0.681	0.92
35_W	39_V	0.675	0.92
35_W	66_F	0.675	0.92
17_D	22_T	0.671	0.91
77_V	137_P	0.670	0.91
87_V	109_L	0.666	0.91
57_A	61_S	0.665	0.91
14_A	23_V	0.662	0.91
98_V	126_V	0.647	0.90
5_E	47_A	0.646	0.90
95_Q	106_Q	0.645	0.90
41_V	50_V	0.642	0.90
123_T	134_L	0.642	0.90
141_D	148_D	0.638	0.89
96_V	127_V	0.634	0.89
11_D	26_P	0.633	0.89
13_T	43_V	0.630	0.89
5_E	67_E	0.626	0.88
67_E	74_F	0.626	0.88
156_T	171_E	0.626	0.88
103_V	132_V	0.624	0.88
84_K	128_D	0.616	0.88
68_S	72_N	0.612	0.87
55_D	63_V	0.610	0.87
115_R	162_V	0.608	0.87
111_E	154_R	0.603	0.86
8_I	11_D	0.601	0.86
164_Q	167_V	0.593	0.86
12_V	77_V	0.589	0.85
85_L	134_L	0.585	0.85
159_D	171_E	0.584	0.85
5_E	49_V	0.583	0.85
62_T	65_T	0.575	0.84
89_Y	161_R	0.574	0.84
6_I	71_A	0.573	0.84
16_V	48_V	0.571	0.83
148_D	152_L	0.570	0.83
145_T	152_L	0.568	0.83
9_P	12_V	0.566	0.83
88_H	130_E	0.565	0.83
23_V	32_R	0.565	0.83
83_Y	164_Q	0.563	0.82
155_V	169_I	0.561	0.82
142_V	146_A	0.560	0.82
65_T	176_G	0.559	0.82
3_R	60_D	0.557	0.82
153_T	162_V	0.557	0.82
19_L	40_D	0.556	0.82
119_I	123_T	0.555	0.82
71_A	79_E	0.551	0.81
19_L	53_E	0.545	0.80
55_D	58_K	0.543	0.80
156_T	173_P	0.541	0.80
97_D	132_V	0.541	0.80
82_E	165_D	0.540	0.80
85_L	146_A	0.540	0.80
123_T	141_D	0.537	0.79
16_V	41_V	0.537	0.79
30_V	77_V	0.536	0.79
68_S	71_A	0.533	0.79
144_Q	147_A	0.530	0.79
8_I	74_F	0.529	0.78
148_D	151_Q	0.529	0.78
17_D	33_R	0.524	0.78
103_V	127_V	0.522	0.78
83_Y	168_Y	0.521	0.77
30_V	138_S	0.521	0.77
6_I	67_E	0.520	0.77
81_W	142_V	0.516	0.77
33_R	73_M	0.516	0.77
171_E	174_A	0.516	0.77
63_V	174_A	0.514	0.76
21_L	43_V	0.509	0.76
39_V	52_S	0.509	0.76
156_T	159_D	0.509	0.76
26_P	78_S	0.508	0.76
23_V	30_V	0.505	0.75
119_I	142_V	0.504	0.75
91_H	161_R	0.503	0.75
55_D	60_D	0.503	0.75
97_D	100_G	0.500	0.74
163_F	168_Y	0.500	0.74

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
1vq8E	1	0.9663	100	0.078	Contact Map
3j21F	1	1	100	0.092	Contact Map
3bboI	1	0.9719	100	0.105	Contact Map
1nkwE	1	0.9663	100	0.108	Contact Map
2zjrE	1	0.9494	100	0.112	Contact Map
4rb6H	1	0.9551	100	0.112	Contact Map
1rl6A	1	0.9101	100	0.117	Contact Map
4tp9G	1	0.9663	100	0.118	Contact Map
1vw4F	1	0.927	100	0.139	Contact Map
4ujqK	1	1	100	0.145	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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