RL3 - BACSU - GREMLIN Contacts

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RL3 - 50S ribosomal protein L3

UniProt:	P42920	Sequences: MTKGILGRKIGMTQVFAENGDLIPVTVIEAAPNVVLQKKTAENDGYEAIQLGFDDKREKLSNKPEKGHVAKAETAPKRFVKELRGVEMDAYEVGQEVKVEIFSAGEIVDVTGVSKGKGFQGAIKRHGQSRGPMSHGSRYHRRPGSMGPVDPNRVFKGKLLPGRMGGEQITVQNLEIVKVDAERNLLLIKGNVPGAKKSLITVKSAVKSK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	209 (204)
Sequences:	3139 (1627)
Seq/√Len:	113.9

ECOLI - RL3
BACSU - RL3
HALSA - RL3
SULSO - RL3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
163_R	166_G	4.954	1.00
28_I	188_I	3.589	1.00
7_G	28_I	3.589	1.00
111_T	168_Q	3.533	1.00
92_E	95_Q	3.478	1.00
120_Q	164_M	3.394	1.00
114_S	169_I	3.123	1.00
123_I	130_R	2.898	1.00
57_R	60_L	2.719	1.00
130_R	133_M	2.529	1.00
50_Q	68_H	2.314	1.00
41_A	47_E	2.280	1.00
117_K	164_M	2.244	1.00
149_V	152_N	2.242	1.00
66_K	70_A	2.224	1.00
28_I	192_V	2.193	1.00
36_L	80_V	2.190	1.00
180_D	183_R	2.189	1.00
113_V	168_Q	2.128	1.00
17_A	21_D	2.108	1.00
104_A	178_K	2.084	1.00
139_Y	142_R	2.064	1.00
87_E	90_A	2.009	1.00
37_Q	68_H	1.955	1.00
8_R	29_E	1.911	1.00
146_M	154_V	1.878	1.00
27_V	187_L	1.875	1.00
186_L	202_V	1.812	1.00
175_E	189_K	1.799	1.00
119_F	161_P	1.795	1.00
153_R	156_K	1.780	1.00
131_G	139_Y	1.774	1.00
128_Q	159_L	1.769	1.00
14_Q	22_L	1.767	1.00
108_V	202_V	1.717	1.00
111_T	203_K	1.709	1.00
110_V	202_V	1.690	1.00
192_V	200_I	1.682	1.00
122_A	143_P	1.677	1.00
107_I	175_E	1.640	1.00
5_I	30_A	1.631	1.00
168_Q	201_T	1.587	1.00
65_E	69_V	1.519	1.00
55_D	75_A	1.483	1.00
79_F	199_L	1.447	1.00
131_G	142_R	1.444	1.00
103_S	106_E	1.388	1.00
195_A	198_S	1.386	1.00
38_K	93_V	1.378	1.00
91_Y	95_Q	1.374	1.00
126_H	159_L	1.363	1.00
36_L	52_G	1.332	1.00
81_K	201_T	1.310	1.00
131_G	137_S	1.282	0.99
125_R	162_G	1.279	0.99
146_M	158_K	1.269	0.99
100_E	181_A	1.259	0.99
138_R	142_R	1.256	0.99
55_D	77_K	1.255	0.99
62_N	65_E	1.243	0.99
65_E	68_H	1.240	0.99
117_K	120_Q	1.239	0.99
112_G	198_S	1.236	0.99
25_V	177_V	1.232	0.99
146_M	160_L	1.232	0.99
173_N	205_A	1.225	0.99
5_I	97_V	1.221	0.99
39_K	44_D	1.219	0.99
120_Q	124_K	1.218	0.99
56_K	61_S	1.195	0.99
61_S	65_E	1.192	0.99
13_T	27_V	1.188	0.99
31_A	53_F	1.184	0.99
106_E	204_S	1.154	0.99
36_L	69_V	1.146	0.99
122_A	161_P	1.145	0.99
58_E	66_K	1.145	0.99
129_S	132_P	1.141	0.99
56_K	78_R	1.139	0.99
127_G	164_M	1.123	0.99
115_K	195_A	1.122	0.99
51_L	83_L	1.119	0.98
174_L	188_I	1.118	0.98
126_H	161_P	1.100	0.98
6_L	79_F	1.090	0.98
137_S	140_H	1.088	0.98
111_T	201_T	1.083	0.98
4_G	83_L	1.078	0.98
36_L	74_T	1.074	0.98
29_E	184_N	1.064	0.98
143_P	160_L	1.063	0.98
51_L	97_V	1.055	0.98
172_Q	206_V	1.044	0.98
15_V	187_L	1.042	0.98
122_A	139_Y	1.039	0.98
171_V	174_L	1.034	0.97
172_Q	203_K	1.033	0.97
37_Q	44_D	1.033	0.97
143_P	146_M	1.027	0.97
38_K	92_E	1.026	0.97
163_R	167_E	1.025	0.97
115_K	196_K	1.016	0.97
112_G	193_P	1.012	0.97
56_K	60_L	1.011	0.97
133_M	140_H	0.997	0.97
61_S	69_V	0.995	0.97
56_K	65_E	0.988	0.97
8_R	54_D	0.987	0.97
124_K	164_M	0.983	0.97
109_D	172_Q	0.975	0.96
69_V	80_V	0.974	0.96
174_L	191_N	0.973	0.96
117_K	124_K	0.968	0.96
122_A	130_R	0.964	0.96
37_Q	50_Q	0.963	0.96
171_V	191_N	0.962	0.96
143_P	161_P	0.959	0.96
74_T	77_K	0.959	0.96
32_P	184_N	0.959	0.96
32_P	96_E	0.949	0.96
17_A	23_I	0.946	0.96
34_V	77_K	0.943	0.96
52_G	77_K	0.936	0.95
6_L	201_T	0.919	0.95
131_G	138_R	0.916	0.95
128_Q	143_P	0.909	0.95
3_K	204_S	0.909	0.95
113_V	166_G	0.906	0.95
17_A	175_E	0.884	0.94
49_I	91_Y	0.878	0.94
87_E	91_Y	0.875	0.94
6_L	199_L	0.870	0.93
36_L	93_V	0.869	0.93
88_M	91_Y	0.865	0.93
66_K	76_P	0.861	0.93
85_G	90_A	0.856	0.93
97_V	101_I	0.850	0.93
142_R	161_P	0.842	0.92
104_A	179_V	0.839	0.92
132_P	139_Y	0.829	0.92
30_A	99_V	0.825	0.91
63_K	66_K	0.813	0.91
62_N	66_K	0.810	0.91
127_G	169_I	0.803	0.90
122_A	142_R	0.802	0.90
69_V	74_T	0.799	0.90
177_V	187_L	0.794	0.90
13_T	25_V	0.788	0.89
111_T	170_T	0.786	0.89
134_S	150_D	0.783	0.89
123_I	128_Q	0.781	0.89
120_Q	163_R	0.780	0.89
42_E	47_E	0.774	0.89
23_I	177_V	0.772	0.88
108_V	176_I	0.771	0.88
6_L	81_K	0.770	0.88
138_R	143_P	0.767	0.88
70_A	73_E	0.766	0.88
8_R	199_L	0.765	0.88
128_Q	146_M	0.761	0.88
122_A	128_Q	0.748	0.87
154_V	160_L	0.746	0.87
28_I	200_I	0.746	0.87
110_V	188_I	0.741	0.86
179_V	186_L	0.737	0.86
29_E	32_P	0.736	0.86
122_A	126_H	0.731	0.86
110_V	174_L	0.730	0.85
61_S	66_K	0.728	0.85
148_P	152_N	0.721	0.85
30_A	33_N	0.719	0.85
178_K	183_R	0.715	0.84
101_I	204_S	0.710	0.84
58_E	70_A	0.706	0.84
170_T	203_K	0.702	0.83
68_H	72_A	0.701	0.83
114_S	171_V	0.697	0.83
178_K	187_L	0.695	0.83
85_G	88_M	0.695	0.83
114_S	167_E	0.694	0.82
86_V	90_A	0.690	0.82
138_R	149_V	0.686	0.82
108_V	188_I	0.685	0.82
158_K	161_P	0.684	0.82
69_V	76_P	0.682	0.81
65_E	80_V	0.681	0.81
15_V	177_V	0.680	0.81
126_H	167_E	0.674	0.81
30_A	53_F	0.670	0.80
112_G	200_I	0.669	0.80
147_G	151_P	0.668	0.80
151_P	155_F	0.666	0.80
180_D	185_L	0.665	0.80
46_Y	82_E	0.662	0.79
99_V	181_A	0.658	0.79
36_L	50_Q	0.657	0.79
104_A	175_E	0.657	0.79
38_K	49_I	0.653	0.78
30_A	186_L	0.650	0.78
120_Q	127_G	0.648	0.78
167_E	171_V	0.648	0.78
129_S	133_M	0.647	0.78
34_V	52_G	0.646	0.78
109_D	205_A	0.646	0.78
43_N	71_K	0.640	0.77
132_P	137_S	0.640	0.77
152_N	158_K	0.640	0.77
142_R	150_D	0.637	0.77
15_V	25_V	0.637	0.77
122_A	146_M	0.634	0.76
69_V	77_K	0.634	0.76
114_S	164_M	0.633	0.76
58_E	75_A	0.631	0.76
26_T	192_V	0.630	0.76
105_G	175_E	0.629	0.76
117_K	137_S	0.628	0.76
3_K	101_I	0.627	0.76
78_R	199_L	0.625	0.75
62_N	67_G	0.624	0.75
176_I	179_V	0.622	0.75
4_G	205_A	0.622	0.75
172_Q	205_A	0.622	0.75
123_I	133_M	0.620	0.75
34_V	96_E	0.620	0.75
8_R	197_K	0.619	0.75
44_D	50_Q	0.618	0.75
119_F	122_A	0.614	0.74
25_V	187_L	0.611	0.74
13_T	24_P	0.611	0.74
12_M	24_P	0.605	0.73
164_M	167_E	0.605	0.73
44_D	48_A	0.604	0.73
4_G	11_G	0.597	0.72
139_Y	143_P	0.594	0.72
56_K	79_F	0.594	0.72
10_I	29_E	0.591	0.71
154_V	157_G	0.590	0.71
129_S	150_D	0.589	0.71
35_V	38_K	0.586	0.71
54_D	199_L	0.586	0.71
114_S	117_K	0.584	0.70
88_M	92_E	0.582	0.70
126_H	164_M	0.582	0.70
61_S	64_P	0.581	0.70
107_I	173_N	0.580	0.70
149_V	158_K	0.579	0.70
137_S	142_R	0.579	0.70
132_P	138_R	0.577	0.70
16_F	22_L	0.575	0.69
13_T	187_L	0.575	0.69
150_D	153_R	0.574	0.69
146_M	204_S	0.570	0.69
148_P	155_F	0.567	0.68
5_I	32_P	0.567	0.68
123_I	140_H	0.566	0.68
177_V	189_K	0.563	0.68
61_S	74_T	0.562	0.68
6_L	51_L	0.561	0.67
72_A	93_V	0.560	0.67
186_L	200_I	0.558	0.67
123_I	129_S	0.556	0.67
39_K	82_E	0.556	0.67
138_R	161_P	0.551	0.66
48_A	82_E	0.549	0.66
146_M	149_V	0.548	0.66
114_S	142_R	0.547	0.65
180_D	186_L	0.544	0.65
144_G	160_L	0.541	0.65
102_F	106_E	0.541	0.65
137_S	152_N	0.539	0.64
19_N	187_L	0.538	0.64
14_Q	24_P	0.535	0.64
52_G	81_K	0.531	0.63
102_F	105_G	0.531	0.63
98_K	101_I	0.528	0.63
148_P	151_P	0.526	0.62
3_K	14_Q	0.526	0.62
10_I	173_N	0.525	0.62
33_N	51_L	0.524	0.62
138_R	150_D	0.522	0.62
130_R	134_S	0.518	0.61
10_I	185_L	0.517	0.61
123_I	138_R	0.517	0.61
47_E	88_M	0.517	0.61
67_G	70_A	0.516	0.61
40_T	48_A	0.515	0.61
3_K	34_V	0.515	0.61
190_G	194_G	0.514	0.61
34_V	75_A	0.512	0.60
173_N	196_K	0.512	0.60
120_Q	123_I	0.512	0.60
187_L	197_K	0.511	0.60
81_K	168_Q	0.510	0.60
149_V	155_F	0.510	0.60
99_V	179_V	0.510	0.60
33_N	99_V	0.509	0.60
43_N	47_E	0.508	0.60
98_K	181_A	0.507	0.60
99_V	186_L	0.506	0.60
111_T	206_V	0.505	0.59
20_G	52_G	0.505	0.59
130_R	138_R	0.503	0.59
135_H	140_H	0.503	0.59
166_G	195_A	0.501	0.59
56_K	69_V	0.500	0.59
188_I	192_V	0.500	0.59

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
3j3wD	1	0.9856	100	0.018	Contact Map
1vw3C	1	1	100	0.028	Contact Map
3bboF	1	0.7273	100	0.028	Contact Map
4ce4E	1	0.9809	100	0.03	Contact Map
4tp9D	1	0.9904	100	0.031	Contact Map
3j7yE	1	0.9904	100	0.033	Contact Map
4rb6E	1	0.9665	100	0.054	Contact Map
2zjrB	1	0.9713	100	0.055	Contact Map
1vq8B	1	1	100	0.107	Contact Map
1vx7E	1	0.9904	100	0.129	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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