RL1 - HALSA - GREMLIN Contacts

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RL1 - 50S ribosomal protein L1

UniProt:	P13575	Sequences: MADNDIEEAVARALEDAPQRNFRETVDLAVNLRDLDLNDPSQRVDEGVVLPSGTGQETQIVVFADGETAVRADDVADDVLDEDDLSDLADDTDAAKDLADETDFFVAEAPMMQDIAGALGQVLGPRGKMPTPLQPDDDVVDTVNRMKNTVQIRSRDRRTFHTRVGAEDMSAEDIASNIDVIMRRLHANLEKGPLNVDSVYVKTTMGPAVEVA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	212 (200)
Sequences:	2995 (1392)
Seq/√Len:	98.4

ECOLI - RL1
BACSU - RL1
HALSA - RL1
SULSO - RL1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
170_S	173_D	4.019	1.00
164_V	178_I	3.641	1.00
70_V	74_D	3.352	1.00
68_T	71_R	3.267	1.00
52_S	176_S	3.255	1.00
52_S	173_D	3.153	1.00
23_R	168_D	3.113	1.00
106_V	146_M	3.016	1.00
35_L	154_S	2.980	1.00
138_D	141_D	2.798	1.00
70_V	73_D	2.747	1.00
11_A	171_A	2.722	1.00
11_A	16_D	2.578	1.00
30_V	185_L	2.403	1.00
14_L	203_T	2.303	1.00
184_R	188_N	2.225	1.00
200_Y	208_A	2.221	1.00
63_F	105_F	2.220	1.00
7_E	175_A	2.128	1.00
25_T	163_R	1.997	1.00
162_T	181_I	1.966	1.00
20_R	24_E	1.953	1.00
26_V	167_E	1.946	1.00
73_D	80_L	1.945	1.00
165_G	174_I	1.923	1.00
96_K	117_G	1.910	1.00
79_V	99_A	1.898	1.00
61_V	79_V	1.883	1.00
83_D	114_D	1.856	1.00
94_A	99_A	1.850	1.00
15_E	170_S	1.814	1.00
86_S	114_D	1.812	1.00
28_L	178_I	1.788	1.00
140_V	144_N	1.740	1.00
82_E	111_M	1.709	1.00
34_D	193_P	1.702	1.00
37_L	154_S	1.664	1.00
172_E	176_S	1.633	1.00
145_R	149_T	1.632	1.00
141_D	145_R	1.618	1.00
22_F	205_M	1.601	1.00
6_I	178_I	1.590	1.00
64_A	69_A	1.565	1.00
30_V	182_M	1.550	1.00
87_D	97_D	1.506	1.00
18_P	24_E	1.505	1.00
94_A	97_D	1.453	1.00
61_V	105_F	1.448	1.00
28_L	181_I	1.415	1.00
81_D	84_D	1.408	1.00
29_A	202_K	1.385	0.99
69_A	80_L	1.368	0.99
67_E	70_V	1.363	0.99
10_V	174_I	1.356	0.99
26_V	203_T	1.344	0.99
10_V	175_A	1.320	0.99
65_D	110_P	1.316	0.99
203_T	206_G	1.314	0.99
17_A	206_G	1.290	0.99
10_V	201_V	1.282	0.99
152_I	188_N	1.282	0.99
65_D	114_D	1.275	0.99
65_D	82_E	1.262	0.99
61_V	99_A	1.258	0.99
10_V	171_A	1.257	0.99
30_V	199_V	1.249	0.99
87_D	96_K	1.243	0.99
186_H	196_V	1.241	0.99
78_D	147_K	1.235	0.99
14_L	167_E	1.233	0.99
5_D	8_E	1.217	0.99
61_V	85_L	1.216	0.99
175_A	179_D	1.213	0.99
71_R	140_V	1.199	0.98
29_A	161_H	1.192	0.98
199_V	211_V	1.172	0.98
62_V	106_V	1.171	0.98
59_Q	101_E	1.166	0.98
189_L	193_P	1.153	0.98
18_P	167_E	1.141	0.98
83_D	87_D	1.138	0.98
68_T	137_D	1.137	0.98
14_L	18_P	1.136	0.98
14_L	209_V	1.132	0.98
102_T	105_F	1.131	0.98
95_A	98_L	1.125	0.98
9_A	211_V	1.124	0.98
25_T	166_A	1.121	0.98
184_R	187_A	1.115	0.97
179_D	183_R	1.078	0.97
159_T	198_S	1.071	0.97
136_D	142_T	1.056	0.96
173_D	176_S	1.050	0.96
14_L	17_A	1.043	0.96
160_F	185_L	1.034	0.96
7_E	11_A	1.031	0.96
95_A	102_T	1.025	0.96
27_D	163_R	1.013	0.96
141_D	144_N	1.010	0.95
15_E	171_A	1.006	0.95
198_S	210_E	1.006	0.95
69_A	73_D	0.978	0.95
63_F	107_A	0.967	0.94
43_R	154_S	0.955	0.94
31_N	197_D	0.948	0.94
152_I	184_R	0.931	0.93
139_V	143_V	0.928	0.93
67_E	137_D	0.927	0.93
46_E	152_I	0.920	0.93
37_L	158_R	0.916	0.92
74_D	140_V	0.913	0.92
26_V	174_I	0.904	0.92
57_E	78_D	0.899	0.92
63_F	85_L	0.897	0.92
63_F	115_I	0.894	0.92
79_V	85_L	0.892	0.91
17_A	209_V	0.890	0.91
172_E	175_A	0.887	0.91
7_E	172_E	0.872	0.91
114_D	117_G	0.857	0.90
68_T	110_P	0.850	0.89
24_E	167_E	0.849	0.89
49_V	145_R	0.849	0.89
115_I	119_L	0.847	0.89
79_V	100_D	0.842	0.89
104_F	146_M	0.842	0.89
100_D	105_F	0.839	0.89
115_I	120_G	0.837	0.89
69_A	82_E	0.835	0.89
86_S	115_I	0.833	0.88
48_V	184_R	0.833	0.88
61_V	100_D	0.830	0.88
35_L	40_P	0.830	0.88
171_A	175_A	0.830	0.88
154_S	158_R	0.828	0.88
164_V	201_V	0.827	0.88
189_L	195_N	0.826	0.88
119_L	122_V	0.823	0.88
27_D	202_K	0.822	0.88
67_E	71_R	0.819	0.88
28_L	162_T	0.816	0.87
79_V	94_A	0.811	0.87
63_F	86_S	0.811	0.87
66_G	69_A	0.806	0.87
104_F	155_R	0.806	0.87
37_L	43_R	0.801	0.86
140_V	143_V	0.795	0.86
6_I	175_A	0.795	0.86
30_V	196_V	0.790	0.86
182_M	199_V	0.789	0.86
35_L	44_V	0.786	0.85
8_E	11_A	0.785	0.85
178_I	201_V	0.778	0.85
155_R	159_T	0.766	0.84
13_A	209_V	0.762	0.84
182_M	196_V	0.761	0.83
72_A	75_V	0.759	0.83
105_F	115_I	0.757	0.83
175_A	178_I	0.757	0.83
28_L	182_M	0.756	0.83
4_N	13_A	0.755	0.83
72_A	76_A	0.745	0.82
150_V	162_T	0.736	0.81
82_E	114_D	0.735	0.81
15_E	18_P	0.735	0.81
17_A	24_E	0.732	0.81
3_D	6_I	0.727	0.81
19_Q	167_E	0.727	0.81
202_K	208_A	0.722	0.80
108_E	137_D	0.720	0.80
86_S	119_L	0.714	0.79
20_R	167_E	0.712	0.79
133_L	139_V	0.712	0.79
64_A	107_A	0.712	0.79
152_I	181_I	0.704	0.78
154_S	160_F	0.699	0.78
19_Q	24_E	0.696	0.78
5_D	10_V	0.694	0.77
6_I	179_D	0.693	0.77
21_N	179_D	0.674	0.75
180_V	184_R	0.673	0.75
13_A	17_A	0.672	0.75
44_V	193_P	0.670	0.75
185_L	196_V	0.656	0.73
27_D	166_A	0.655	0.73
79_V	101_E	0.655	0.73
40_P	113_Q	0.654	0.73
183_R	187_A	0.653	0.73
94_A	98_L	0.652	0.73
17_A	203_T	0.648	0.72
71_R	74_D	0.642	0.72
105_F	119_L	0.640	0.72
32_L	37_L	0.634	0.71
6_I	164_V	0.632	0.71
30_V	181_I	0.628	0.70
75_V	80_L	0.627	0.70
29_A	162_T	0.625	0.70
40_P	43_R	0.621	0.69
24_E	206_G	0.620	0.69
112_M	132_P	0.617	0.69
21_N	156_D	0.615	0.69
10_V	178_I	0.611	0.68
20_R	205_M	0.608	0.68
48_V	180_V	0.607	0.68
28_L	164_V	0.603	0.67
30_V	44_V	0.603	0.67
134_Q	151_Q	0.602	0.67
71_R	137_D	0.600	0.67
121_Q	152_I	0.599	0.67
36_D	55_G	0.599	0.67
66_G	80_L	0.597	0.66
39_D	43_R	0.597	0.66
6_I	201_V	0.594	0.66
14_L	211_V	0.593	0.66
14_L	206_G	0.591	0.65
8_E	13_A	0.590	0.65
9_A	179_D	0.586	0.65
54_T	169_M	0.584	0.65
11_A	170_S	0.583	0.64
46_E	188_N	0.581	0.64
127_G	148_N	0.580	0.64
113_Q	116_A	0.580	0.64
198_S	206_G	0.578	0.64
85_L	115_I	0.577	0.64
47_G	134_Q	0.577	0.64
35_L	43_R	0.576	0.64
66_G	72_A	0.576	0.64
95_A	99_A	0.576	0.64
64_A	108_E	0.573	0.63
75_V	140_V	0.573	0.63
44_V	184_R	0.572	0.63
10_V	15_E	0.572	0.63
59_Q	126_R	0.570	0.63
200_Y	210_E	0.567	0.62
171_A	201_V	0.566	0.62
15_E	173_D	0.564	0.62
100_D	126_R	0.562	0.62
13_A	16_D	0.560	0.61
29_A	157_R	0.558	0.61
203_T	208_A	0.557	0.61
82_E	108_E	0.557	0.61
120_G	158_R	0.557	0.61
112_M	116_A	0.556	0.61
14_L	26_V	0.556	0.61
144_N	173_D	0.556	0.61
172_E	179_D	0.556	0.61
47_G	184_R	0.555	0.61
62_V	69_A	0.552	0.60
28_L	199_V	0.552	0.60
107_A	110_P	0.551	0.60
10_V	164_V	0.551	0.60
178_I	182_M	0.550	0.60
24_E	205_M	0.550	0.60
48_V	162_T	0.549	0.60
128_K	155_R	0.549	0.60
76_A	80_L	0.549	0.60
37_L	41_S	0.548	0.60
115_I	137_D	0.548	0.60
30_V	159_T	0.546	0.59
105_F	114_D	0.545	0.59
52_S	170_S	0.545	0.59
77_D	80_L	0.543	0.59
65_D	111_M	0.543	0.59
107_A	111_M	0.541	0.59
7_E	171_A	0.540	0.59
121_Q	125_P	0.540	0.59
32_L	35_L	0.539	0.58
124_G	127_G	0.538	0.58
96_K	122_V	0.537	0.58
24_E	203_T	0.536	0.58
41_S	192_G	0.535	0.58
22_F	25_T	0.533	0.58
37_L	160_F	0.532	0.57
95_A	105_F	0.532	0.57
136_D	139_V	0.529	0.57
199_V	202_K	0.528	0.57
72_A	77_D	0.527	0.57
75_V	78_D	0.527	0.57
113_Q	117_G	0.527	0.57
186_H	210_E	0.526	0.57
52_S	172_E	0.526	0.57
142_T	146_M	0.521	0.56
40_P	154_S	0.517	0.55
26_V	164_V	0.516	0.55
131_T	134_Q	0.515	0.55
3_D	210_E	0.514	0.55
34_D	189_L	0.512	0.55
182_M	211_V	0.512	0.55
64_A	68_T	0.512	0.55
81_D	133_L	0.512	0.55
68_T	139_V	0.511	0.55
58_T	85_L	0.511	0.55
29_A	134_Q	0.510	0.54
82_E	117_G	0.509	0.54
32_L	36_D	0.508	0.54
47_G	151_Q	0.506	0.54
39_D	192_G	0.506	0.54
146_M	149_T	0.505	0.54
120_G	127_G	0.503	0.53
40_P	153_R	0.500	0.53

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
3bboD	1	0.9575	100	0.152	Contact Map
4lq4A	1	0.9906	100	0.154	Contact Map
4reoA	1	0.9623	100	0.163	Contact Map
3j21A	1	0.9953	100	0.168	Contact Map
3qoyA	1	0.9575	100	0.169	Contact Map
4cxdu	1	0.9811	100	0.178	Contact Map
3j8g5	1	0.9575	100	0.181	Contact Map
1mzpA	1	0.9906	100	0.185	Contact Map
3j3w5	1	0.467	100	0.185	Contact Map
4cuwt	1	0.9906	100	0.195	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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