RL1 - SULSO - GREMLIN Contacts

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RL1 - 50S ribosomal protein L1

UniProt:	P96038	Sequences: MQIVDRSNLEASLKLALSPENNPKRNFVQSVEIIVTFKEVDMKKGDLKLREIVVLPKPPEKTKKVLVVPTIQQLEYAKKAEPNTILTKEELQKLQGNKRAIKKIARQNDWFLIAPDSMALVGRILGPALGPRGKFPTPLPNTADISEYILRFKRSTLVKTKDQPQTQVFIGTESQQIADLAENALAVLNVIESKGYAQKVRNIYVKTTMGKVVKVELR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	218 (204)
Sequences:	3055 (1414)
Seq/√Len:	99.0

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
176_Q	179_D	3.847	1.00
170_I	184_A	3.492	1.00
75_E	79_K	3.396	1.00
73_Q	76_Y	3.353	1.00
57_K	182_E	3.282	1.00
57_K	179_D	3.153	1.00
28_V	174_S	3.107	1.00
112_L	152_F	2.974	1.00
40_V	160_T	2.960	1.00
144_D	147_E	2.837	1.00
17_L	21_N	2.813	1.00
75_E	78_K	2.738	1.00
17_L	177_I	2.615	1.00
35_V	191_I	2.405	1.00
92_Q	96_G	2.342	1.00
19_P	207_T	2.203	1.00
95_Q	123_R	2.170	1.00
13_L	181_A	2.156	1.00
204_Y	212_V	2.144	1.00
68_V	111_F	2.101	1.00
93_K	105_A	2.068	1.00
168_V	187_V	1.992	1.00
25_R	29_Q	1.967	1.00
30_S	169_F	1.953	1.00
20_E	176_Q	1.938	1.00
88_K	120_L	1.931	1.00
31_V	173_E	1.918	1.00
66_L	84_T	1.889	1.00
84_T	105_A	1.885	1.00
91_L	120_L	1.872	1.00
33_I	184_A	1.783	1.00
171_G	180_L	1.732	1.00
78_K	85_I	1.722	1.00
12_S	184_A	1.716	1.00
146_S	150_L	1.693	1.00
42_M	160_T	1.671	1.00
39_E	195_G	1.653	1.00
27_F	209_M	1.651	1.00
151_R	155_S	1.638	1.00
23_P	29_Q	1.598	1.00
147_E	151_R	1.595	1.00
178_A	182_E	1.574	1.00
35_V	188_L	1.525	1.00
68_V	90_E	1.446	1.00
87_T	117_S	1.441	1.00
69_P	74_L	1.440	1.00
66_L	111_F	1.436	1.00
72_Q	75_E	1.427	1.00
33_I	187_V	1.408	1.00
16_A	180_L	1.397	1.00
16_A	205_V	1.370	0.99
86_L	90_E	1.355	0.99
34_I	206_K	1.349	0.99
66_L	90_E	1.348	0.99
31_V	207_T	1.345	0.99
11_A	14_K	1.339	0.99
92_Q	95_Q	1.335	0.99
66_L	105_A	1.333	0.99
190_V	193_S	1.332	0.99
74_L	85_I	1.329	0.99
35_V	203_I	1.317	0.99
4_V	18_S	1.312	0.99
5_D	8_N	1.311	0.99
11_A	216_E	1.308	0.99
19_P	173_E	1.280	0.99
8_N	14_K	1.275	0.99
207_T	210_G	1.271	0.99
70_T	120_L	1.237	0.99
19_P	213_V	1.236	0.99
64_K	107_Q	1.232	0.99
16_A	177_I	1.227	0.99
70_T	116_D	1.223	0.99
22_N	210_G	1.207	0.99
83_N	153_K	1.201	0.98
181_A	185_L	1.163	0.98
192_E	200_V	1.160	0.98
76_Y	146_S	1.155	0.98
150_L	154_R	1.154	0.98
19_P	23_P	1.153	0.98
4_V	10_E	1.130	0.98
108_N	111_F	1.130	0.98
96_G	104_I	1.119	0.98
73_Q	143_A	1.110	0.97
67_V	112_L	1.109	0.97
74_L	87_T	1.108	0.97
203_I	215_V	1.106	0.97
34_I	167_Q	1.101	0.97
165_Q	202_N	1.076	0.97
179_D	182_E	1.073	0.97
23_P	173_E	1.072	0.97
30_S	172_T	1.064	0.97
13_L	17_L	1.064	0.97
79_K	146_S	1.063	0.97
16_A	181_A	1.063	0.97
185_L	189_N	1.058	0.97
202_N	214_K	1.052	0.96
20_E	177_I	1.049	0.96
87_T	90_E	1.044	0.96
84_T	93_K	1.035	0.96
94_L	108_N	1.031	0.96
166_T	191_I	1.029	0.96
158_V	190_V	1.028	0.96
147_E	150_L	1.025	0.96
70_T	87_T	1.005	0.95
32_E	169_F	1.003	0.95
36_T	201_R	0.988	0.95
84_T	106_R	0.983	0.95
15_L	215_V	0.980	0.95
19_P	22_N	0.958	0.94
31_V	180_L	0.951	0.94
145_I	149_I	0.949	0.94
42_M	164_P	0.938	0.93
48_K	160_T	0.933	0.93
106_R	111_F	0.925	0.93
62_T	83_N	0.924	0.93
4_V	7_S	0.916	0.93
96_G	105_A	0.909	0.92
74_L	78_K	0.903	0.92
68_V	113_I	0.901	0.92
84_T	90_E	0.900	0.92
177_I	181_A	0.899	0.92
10_E	18_S	0.891	0.92
121_V	126_G	0.891	0.92
88_K	92_Q	0.887	0.91
110_W	152_F	0.882	0.91
29_Q	173_E	0.879	0.91
84_T	107_Q	0.877	0.91
22_N	213_V	0.871	0.91
110_W	161_K	0.869	0.91
91_L	121_V	0.856	0.90
53_V	190_V	0.854	0.90
120_L	123_R	0.852	0.90
93_K	96_G	0.842	0.89
68_V	121_V	0.842	0.89
72_Q	76_Y	0.837	0.89
178_A	181_A	0.837	0.89
32_E	206_K	0.829	0.88
146_S	149_I	0.824	0.88
188_L	200_V	0.823	0.88
14_K	17_L	0.822	0.88
51_E	158_V	0.822	0.88
72_Q	143_A	0.818	0.88
121_V	125_L	0.818	0.88
91_L	125_L	0.817	0.88
68_V	91_L	0.806	0.87
158_V	187_V	0.801	0.87
71_I	74_L	0.800	0.87
35_V	200_V	0.797	0.86
24_K	173_E	0.796	0.86
188_L	203_I	0.795	0.86
54_V	151_R	0.793	0.86
13_L	178_A	0.788	0.86
184_A	205_V	0.786	0.86
40_V	45_G	0.777	0.85
160_T	164_P	0.776	0.85
40_V	49_L	0.773	0.85
33_I	168_V	0.773	0.85
9_L	216_E	0.770	0.84
94_L	105_A	0.768	0.84
181_A	184_A	0.765	0.84
73_Q	116_D	0.763	0.84
114_A	143_A	0.760	0.84
77_A	81_E	0.758	0.83
170_I	205_V	0.755	0.83
33_I	188_L	0.752	0.83
62_T	154_R	0.749	0.83
49_L	195_G	0.748	0.83
42_M	48_K	0.741	0.82
18_S	21_N	0.736	0.82
125_L	128_A	0.731	0.81
22_N	29_Q	0.730	0.81
25_R	209_M	0.729	0.81
111_F	121_V	0.729	0.81
156_T	168_V	0.727	0.81
189_N	193_S	0.725	0.81
160_T	166_T	0.716	0.80
186_A	190_V	0.711	0.79
161_K	165_Q	0.710	0.79
18_S	213_V	0.707	0.79
32_E	172_T	0.701	0.78
11_A	16_A	0.699	0.78
206_K	212_V	0.699	0.78
20_E	23_P	0.696	0.78
69_P	113_I	0.690	0.77
9_L	12_S	0.690	0.77
68_V	94_L	0.688	0.77
22_N	207_T	0.684	0.77
191_I	200_V	0.679	0.76
45_G	119_A	0.677	0.76
18_S	22_N	0.675	0.76
12_S	181_A	0.674	0.76
139_L	145_I	0.672	0.75
25_R	173_E	0.667	0.75
94_L	111_F	0.665	0.75
111_F	125_L	0.654	0.73
66_L	106_R	0.653	0.73
194_K	199_K	0.651	0.73
12_S	205_V	0.651	0.73
119_A	122_G	0.646	0.73
6_R	214_K	0.645	0.72
29_Q	210_G	0.639	0.72
69_P	114_A	0.635	0.71
184_A	188_L	0.634	0.71
94_L	104_I	0.633	0.71
34_I	168_V	0.631	0.71
45_G	48_K	0.629	0.71
19_P	210_G	0.626	0.70
44_K	48_K	0.623	0.70
52_I	190_V	0.622	0.70
118_M	138_P	0.622	0.70
87_T	120_L	0.621	0.70
12_S	185_L	0.621	0.70
52_I	140_P	0.621	0.70
4_V	8_N	0.620	0.69
127_P	158_V	0.616	0.69
95_Q	128_A	0.615	0.69
4_V	9_L	0.614	0.69
16_A	184_A	0.611	0.68
113_I	117_S	0.610	0.68
40_V	48_K	0.608	0.68
57_K	178_A	0.607	0.68
53_V	186_A	0.607	0.68
24_K	29_Q	0.602	0.67
203_I	206_K	0.596	0.66
76_Y	143_A	0.595	0.66
204_Y	216_E	0.590	0.66
26_N	162_D	0.590	0.66
49_L	190_V	0.587	0.65
45_G	160_T	0.586	0.65
37_F	42_M	0.585	0.65
12_S	170_I	0.585	0.65
204_Y	214_K	0.584	0.65
37_F	40_V	0.583	0.65
15_L	211_K	0.580	0.64
26_N	185_L	0.577	0.64
16_A	20_E	0.574	0.64
35_V	187_V	0.572	0.63
81_E	85_I	0.571	0.63
178_A	185_L	0.571	0.63
33_I	170_I	0.571	0.63
104_I	108_N	0.564	0.62
166_T	187_V	0.562	0.62
152_F	155_S	0.560	0.62
77_A	80_A	0.559	0.61
21_N	177_I	0.559	0.61
41_D	60_E	0.558	0.61
86_L	94_L	0.558	0.61
106_R	132_R	0.558	0.61
69_P	85_I	0.557	0.61
14_K	18_S	0.556	0.61
76_Y	79_K	0.554	0.61
16_A	19_P	0.554	0.61
22_N	211_K	0.553	0.61
42_M	166_T	0.552	0.61
71_I	85_I	0.551	0.60
42_M	46_D	0.551	0.60
177_I	205_V	0.549	0.60
29_Q	209_M	0.548	0.60
8_N	12_S	0.547	0.60
189_N	200_V	0.547	0.60
95_Q	125_L	0.546	0.60
126_G	164_P	0.544	0.59
84_T	94_L	0.543	0.59
70_T	117_S	0.539	0.59
5_D	214_K	0.537	0.58
75_E	151_R	0.537	0.58
29_Q	207_T	0.536	0.58
67_V	74_L	0.535	0.58
41_D	46_D	0.532	0.58
57_K	176_Q	0.531	0.58
37_F	41_D	0.529	0.57
53_V	168_V	0.529	0.57
207_T	212_V	0.529	0.57
94_L	106_R	0.527	0.57
34_I	163_Q	0.526	0.57
65_V	82_P	0.525	0.57
35_V	49_L	0.524	0.57
54_V	154_R	0.523	0.56
73_Q	145_I	0.523	0.56
113_I	116_D	0.522	0.56
68_V	191_I	0.520	0.56
64_K	132_R	0.520	0.56
121_V	143_A	0.518	0.56
9_L	215_V	0.517	0.56
119_A	143_A	0.517	0.56
36_T	165_Q	0.516	0.55
39_E	42_M	0.513	0.55
58_P	175_Q	0.513	0.55
27_F	30_S	0.513	0.55
5_D	10_E	0.513	0.55
66_L	93_K	0.512	0.55
140_P	157_L	0.512	0.55
132_R	208_T	0.510	0.55
35_V	165_Q	0.509	0.54
34_I	140_P	0.509	0.54
186_A	189_N	0.508	0.54
71_I	77_A	0.508	0.54
202_N	210_G	0.508	0.54
59_P	175_Q	0.505	0.54
134_K	161_K	0.505	0.54
150_L	179_D	0.504	0.54
118_M	122_G	0.504	0.54
15_L	19_P	0.504	0.54
32_E	35_V	0.501	0.53
111_F	120_L	0.500	0.53
80_A	146_S	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
4reoA	1	0.9633	100	0.161	Contact Map
3qoyA	1	0.9587	100	0.166	Contact Map
3bboD	1	0.9587	100	0.168	Contact Map
3j3w5	1	0.4817	100	0.187	Contact Map
3j8g5	1	0.9587	100	0.189	Contact Map
4lq4A	1	0.9541	100	0.197	Contact Map
4cxdu	1	0.9495	100	0.197	Contact Map
1mzpA	1	0.9771	100	0.202	Contact Map
3j21A	1	0.9725	100	0.202	Contact Map
4w27z	1	0.9679	100	0.218	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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