RL1 - BACSU - GREMLIN Contacts

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RL1 - 50S ribosomal protein L1

UniProt:	Q06797	Sequences: MAKKGKKYVEAAKLVDRSKAYDVSEAVALVKKTNTAKFDATVEVAFRLGVDPRKNDQQIRGAVVLPNGTGKTQRVLVFAKGEKAKEAEAAGADFVGDTDYINKIQQGWFDFDVIVATPDMMGEVGKIGRVLGPKGLMPNPKTGTVTFEVEKAIGEIKAGKVEYRVDKAGNIHVPIGKVSFEDEKLVENFTTMYDTILKAKPAAAKGVYVKNVAVTSTMGPGVKVDSSTFNVK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	232 (223)
Sequences:	3148 (1446)
Seq/√Len:	96.8

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
181_E	184_K	3.801	1.00
175_I	189_F	3.550	1.00
67_N	187_E	3.250	1.00
85_K	89_A	3.246	1.00
67_N	184_K	3.121	1.00
83_K	86_E	3.113	1.00
39_D	179_S	3.057	1.00
115_V	156_I	3.016	1.00
14_L	32_K	3.005	1.00
50_V	165_V	2.879	1.00
10_E	13_K	2.869	1.00
148_E	151_K	2.734	1.00
28_A	32_K	2.712	1.00
85_K	88_E	2.648	1.00
28_A	182_D	2.574	1.00
46_F	196_I	2.311	1.00
4_K	8_Y	2.264	1.00
30_V	216_S	2.184	1.00
195_T	199_A	2.148	1.00
24_S	186_V	2.123	1.00
103_K	108_W	2.105	1.00
213_A	221_G	2.087	1.00
78_F	114_I	2.047	1.00
173_V	192_M	1.960	1.00
5_G	8_Y	1.929	1.00
105_Q	126_K	1.896	1.00
31_K	181_E	1.889	1.00
41_T	174_P	1.877	1.00
42_V	178_V	1.863	1.00
36_A	40_A	1.858	1.00
7_K	35_T	1.838	1.00
76_L	94_F	1.837	1.00
9_V	13_K	1.809	1.00
102_N	106_Q	1.808	1.00
98_T	123_E	1.795	1.00
88_E	95_V	1.795	1.00
94_F	108_W	1.777	1.00
49_G	204_A	1.766	1.00
101_I	123_E	1.747	1.00
44_V	189_F	1.724	1.00
4_K	9_V	1.687	1.00
52_P	165_V	1.683	1.00
176_G	185_L	1.681	1.00
23_V	189_F	1.641	1.00
150_E	154_G	1.616	1.00
97_D	120_M	1.588	1.00
38_F	218_M	1.576	1.00
46_F	193_Y	1.571	1.00
151_K	155_E	1.550	1.00
155_E	160_K	1.536	1.00
183_E	187_E	1.527	1.00
79_A	84_A	1.526	1.00
34_N	40_A	1.524	1.00
76_L	114_I	1.480	1.00
44_V	192_M	1.414	1.00
19_K	25_E	1.368	0.99
27_V	214_V	1.365	0.99
27_V	185_L	1.362	0.99
45_A	215_T	1.357	0.99
82_E	85_K	1.345	0.99
163_Y	199_A	1.341	0.99
42_V	216_S	1.336	0.99
84_A	95_V	1.336	0.99
22_D	25_E	1.322	0.99
8_Y	12_A	1.322	0.99
14_L	33_T	1.293	0.99
30_V	222_V	1.270	0.99
30_V	178_V	1.263	0.99
103_K	106_Q	1.255	0.99
46_F	212_V	1.253	0.99
76_L	100_Y	1.230	0.99
186_V	190_T	1.224	0.99
27_V	182_D	1.224	0.99
76_L	108_W	1.200	0.98
86_E	150_E	1.193	0.98
216_S	219_G	1.192	0.98
30_V	34_N	1.191	0.98
197_L	209_V	1.185	0.98
74_R	110_D	1.182	0.98
80_K	123_E	1.182	0.98
16_D	19_K	1.180	0.98
80_K	119_D	1.178	0.98
77_V	115_V	1.173	0.98
15_V	29_L	1.162	0.98
22_D	225_D	1.158	0.98
93_D	157_K	1.154	0.98
170_N	211_N	1.135	0.98
96_G	99_D	1.133	0.98
45_A	172_H	1.125	0.97
5_G	9_V	1.122	0.97
10_E	14_L	1.118	0.97
102_N	105_Q	1.113	0.97
34_N	178_V	1.109	0.97
33_T	219_G	1.102	0.97
27_V	186_V	1.096	0.97
7_K	10_E	1.090	0.97
212_V	224_V	1.088	0.97
195_T	198_K	1.087	0.97
98_T	102_N	1.083	0.97
80_K	97_D	1.082	0.97
15_V	21_Y	1.075	0.97
111_F	114_I	1.070	0.97
200_K	204_A	1.067	0.97
7_K	11_A	1.066	0.97
151_K	154_G	1.061	0.96
83_K	147_F	1.060	0.96
31_K	182_D	1.051	0.96
26_A	224_V	1.050	0.96
96_G	100_Y	1.037	0.96
78_F	100_Y	1.035	0.96
190_T	194_D	1.035	0.96
154_G	158_A	1.032	0.96
184_K	187_E	1.030	0.96
94_F	100_Y	1.018	0.95
149_V	153_I	1.006	0.95
41_T	177_K	0.999	0.95
30_V	33_T	0.996	0.95
43_E	174_P	0.996	0.95
52_P	169_G	0.991	0.95
104_I	111_F	0.990	0.95
94_F	103_K	0.988	0.95
89_A	150_E	0.987	0.95
171_I	196_I	0.979	0.94
146_T	152_A	0.975	0.94
24_S	28_A	0.950	0.93
84_A	97_D	0.937	0.93
78_F	124_V	0.929	0.93
94_F	109_F	0.921	0.92
163_Y	195_T	0.921	0.92
72_T	93_D	0.921	0.92
82_E	147_F	0.920	0.92
43_E	215_T	0.915	0.92
47_R	210_K	0.913	0.92
82_E	86_E	0.911	0.92
182_D	186_V	0.906	0.92
58_Q	165_V	0.903	0.92
15_V	18_S	0.891	0.91
20_A	226_S	0.883	0.91
83_K	119_D	0.876	0.90
113_V	156_I	0.872	0.90
61_G	163_Y	0.868	0.90
78_F	116_A	0.868	0.90
211_N	223_K	0.864	0.90
123_E	126_K	0.859	0.89
21_Y	29_L	0.852	0.89
5_G	11_A	0.850	0.89
64_V	155_E	0.845	0.89
25_E	28_A	0.840	0.88
196_I	209_V	0.839	0.88
31_K	34_N	0.827	0.88
193_Y	209_V	0.825	0.88
117_T	147_F	0.820	0.87
63_V	195_T	0.819	0.87
183_E	186_V	0.816	0.87
40_A	178_V	0.816	0.87
42_V	185_L	0.811	0.87
78_F	101_I	0.811	0.87
84_A	88_E	0.809	0.86
113_V	166_D	0.802	0.86
124_V	128_G	0.794	0.85
165_V	169_G	0.786	0.85
163_Y	192_M	0.781	0.85
81_G	84_A	0.780	0.84
175_I	214_V	0.778	0.84
52_P	58_Q	0.772	0.84
43_E	177_K	0.766	0.83
20_A	225_D	0.766	0.83
124_V	127_I	0.766	0.83
33_T	222_V	0.762	0.83
109_F	114_I	0.761	0.83
200_K	208_Y	0.758	0.83
44_V	173_V	0.757	0.83
59_I	204_A	0.756	0.83
114_I	124_V	0.755	0.82
16_D	21_Y	0.753	0.82
189_F	214_V	0.750	0.82
24_S	183_E	0.746	0.82
79_A	117_T	0.746	0.82
150_E	153_I	0.743	0.81
50_V	59_I	0.736	0.81
50_V	55_N	0.735	0.81
101_I	124_V	0.734	0.81
94_F	110_D	0.731	0.80
193_Y	212_V	0.730	0.80
97_D	123_E	0.729	0.80
127_I	130_V	0.728	0.80
212_V	226_S	0.727	0.80
186_V	189_F	0.726	0.80
78_F	104_I	0.725	0.80
29_L	33_T	0.723	0.80
87_A	91_G	0.722	0.80
7_K	12_A	0.716	0.79
161_V	173_V	0.708	0.78
46_F	209_V	0.706	0.78
101_I	127_I	0.704	0.78
23_V	186_V	0.694	0.77
76_L	109_F	0.693	0.77
7_K	37_K	0.692	0.77
166_D	170_N	0.691	0.77
35_T	178_V	0.691	0.77
8_Y	11_A	0.689	0.76
45_A	173_V	0.688	0.76
165_V	171_I	0.687	0.76
22_D	27_V	0.682	0.76
72_T	158_A	0.680	0.75
194_D	198_K	0.677	0.75
23_V	190_T	0.676	0.75
114_I	127_I	0.676	0.75
44_V	193_Y	0.675	0.75
11_A	35_T	0.675	0.75
104_I	108_W	0.675	0.75
87_A	90_A	0.674	0.75
33_T	40_A	0.674	0.75
29_L	222_V	0.668	0.74
55_N	122_G	0.666	0.74
79_A	116_A	0.662	0.73
36_A	218_M	0.662	0.73
86_E	147_F	0.661	0.73
86_E	89_A	0.658	0.73
54_K	203_A	0.655	0.73
27_V	189_F	0.650	0.72
215_T	221_G	0.644	0.71
20_A	23_V	0.632	0.70
156_I	160_K	0.630	0.70
36_A	178_V	0.626	0.69
33_T	216_S	0.626	0.69
189_F	193_Y	0.623	0.69
25_E	29_L	0.621	0.69
104_I	109_F	0.618	0.68
49_G	200_K	0.616	0.68
51_D	57_Q	0.615	0.68
4_K	12_A	0.614	0.68
51_D	70_G	0.614	0.68
63_V	191_T	0.612	0.68
23_V	214_V	0.610	0.67
15_V	19_K	0.609	0.67
46_F	192_M	0.607	0.67
40_A	216_S	0.604	0.67
50_V	58_Q	0.603	0.66
67_N	183_E	0.598	0.66
54_K	58_Q	0.597	0.66
30_V	214_V	0.593	0.65
37_K	167_K	0.592	0.65
35_T	40_A	0.591	0.65
62_A	195_T	0.591	0.65
45_A	142_T	0.590	0.65
191_T	195_T	0.590	0.65
67_N	181_E	0.589	0.65
55_N	165_V	0.589	0.65
103_K	109_F	0.587	0.64
182_D	214_V	0.586	0.64
94_F	104_I	0.585	0.64
81_G	95_V	0.583	0.64
80_K	120_M	0.582	0.64
121_M	140_P	0.582	0.64
62_A	142_T	0.581	0.64
69_T	180_F	0.580	0.63
129_R	163_Y	0.580	0.63
171_I	192_M	0.577	0.63
116_A	119_D	0.574	0.63
79_A	83_K	0.573	0.62
20_A	224_V	0.572	0.62
30_V	219_G	0.572	0.62
122_G	125_G	0.571	0.62
28_A	181_E	0.565	0.61
87_A	149_V	0.564	0.61
9_V	12_A	0.563	0.61
33_T	220_P	0.563	0.61
37_K	190_T	0.563	0.61
46_F	59_I	0.560	0.61
55_N	58_Q	0.559	0.61
26_A	220_P	0.556	0.60
116_A	120_M	0.556	0.60
27_V	31_K	0.554	0.60
213_A	223_K	0.553	0.60
59_I	195_T	0.551	0.59
44_V	175_I	0.549	0.59
56_D	203_A	0.548	0.59
97_D	117_T	0.547	0.59
142_T	162_E	0.545	0.59
134_K	217_T	0.544	0.59
79_A	95_V	0.544	0.59
91_G	95_V	0.544	0.59
154_G	184_K	0.544	0.59
32_K	182_D	0.543	0.58
51_D	68_G	0.543	0.58
7_K	13_K	0.540	0.58
40_A	218_M	0.538	0.58
23_V	175_I	0.536	0.57
194_D	209_V	0.535	0.57
44_V	212_V	0.533	0.57
14_L	216_S	0.531	0.57
14_L	28_A	0.531	0.57
16_D	223_K	0.531	0.57
213_A	225_D	0.527	0.56
212_V	215_T	0.527	0.56
141_K	149_V	0.526	0.56
128_G	169_G	0.525	0.56
134_K	156_I	0.524	0.56
5_G	10_E	0.524	0.56
107_G	130_V	0.522	0.55
94_F	111_F	0.522	0.55
47_R	170_N	0.521	0.55
77_V	84_A	0.519	0.55
126_K	196_I	0.518	0.55
63_V	173_V	0.518	0.55
34_N	219_G	0.517	0.55
64_V	156_I	0.517	0.55
104_I	114_I	0.515	0.54
78_F	211_N	0.515	0.54
45_A	169_G	0.514	0.54
52_P	171_I	0.514	0.54
45_A	170_N	0.514	0.54
122_G	126_K	0.513	0.54
184_K	209_V	0.512	0.54
23_V	27_V	0.512	0.54
113_V	140_P	0.512	0.54
12_A	15_V	0.512	0.54
73_Q	156_I	0.511	0.54
100_Y	124_V	0.510	0.54
61_G	199_A	0.509	0.54
102_N	126_K	0.508	0.53
23_V	32_K	0.507	0.53
15_V	222_V	0.504	0.53
95_V	99_D	0.504	0.53
81_G	87_A	0.504	0.53
31_K	184_K	0.504	0.53
10_E	33_T	0.504	0.53
105_Q	127_I	0.503	0.53
104_I	107_G	0.503	0.53
45_A	168_A	0.501	0.52
7_K	40_A	0.501	0.52
49_G	206_G	0.500	0.52
5_G	13_K	0.500	0.52

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	0.9483	100	0.126	Contact Map
3qoyA	1	1	100	0.126	Contact Map
3bboD	1	0.9784	100	0.128	Contact Map
3j3w5	1	0.5172	100	0.144	Contact Map
3j8g5	1	1	100	0.144	Contact Map
4lq4A	1	0.8664	100	0.252	Contact Map
3j21A	1	0.8879	100	0.253	Contact Map
4cxdu	1	0.8621	100	0.256	Contact Map
1mzpA	1	0.8836	100	0.263	Contact Map
4w27z	1	0.8836	100	0.287	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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