RL1 - ECOLI - GREMLIN Contacts

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RL1 - 50S ribosomal protein L1

UniProt:	P0A7L0	Sequences: MAKLTKRMRVIREKVDATKQYDINEAIALLKELATAKFVESVDVAVNLGIDARKSDQNVRGATVLPHGTGRSVRVAVFTQGANAEAAKAAGAELVGMEDLADQIKKGEMNFDVVIASPDAMRVVGQLGQVLGPRGLMPNPKVGTVTPNVAEAVKNAKAGQVRYRNDKNGIIHTTIGKVDFDADKLKENLEALLVALKKAKPTQAKGVYIKKVSISTTMGAGVAVDQAGLSASVN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10864
Length:	234 (224)
Sequences:	3147 (1467)
Seq/√Len:	98.0

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
181_D	184_K	3.807	1.00
175_I	189_L	3.537	1.00
85_E	89_A	3.276	1.00
67_H	187_E	3.267	1.00
67_H	184_K	3.094	1.00
14_K	32_E	3.081	1.00
115_I	156_A	3.044	1.00
39_V	179_D	3.041	1.00
83_N	86_A	3.034	1.00
50_I	165_N	2.908	1.00
10_V	13_E	2.857	1.00
148_N	151_E	2.824	1.00
28_A	32_E	2.676	1.00
85_E	88_K	2.622	1.00
28_A	182_A	2.534	1.00
46_V	196_L	2.345	1.00
102_D	106_K	2.297	1.00
4_L	8_M	2.266	1.00
195_A	199_A	2.193	1.00
103_Q	108_E	2.186	1.00
30_L	216_T	2.164	1.00
24_N	186_K	2.126	1.00
213_S	221_G	2.084	1.00
78_F	114_V	2.037	1.00
173_T	192_L	1.946	1.00
9_R	13_E	1.944	1.00
42_V	178_V	1.907	1.00
105_K	126_Q	1.885	1.00
5_T	8_M	1.865	1.00
76_A	94_L	1.844	1.00
41_S	174_T	1.844	1.00
36_A	40_E	1.843	1.00
94_L	108_E	1.842	1.00
7_R	35_T	1.836	1.00
88_K	95_V	1.816	1.00
98_E	123_V	1.803	1.00
31_K	181_D	1.789	1.00
52_A	165_N	1.757	1.00
49_G	204_A	1.748	1.00
101_A	123_V	1.746	1.00
44_V	189_L	1.729	1.00
176_G	185_L	1.685	1.00
150_A	154_K	1.681	1.00
4_L	9_R	1.637	1.00
23_I	189_L	1.599	1.00
183_D	187_E	1.590	1.00
46_V	193_L	1.585	1.00
97_M	120_A	1.583	1.00
151_E	155_N	1.555	1.00
38_F	218_M	1.551	1.00
155_N	160_Q	1.546	1.00
79_T	84_A	1.492	1.00
76_A	114_V	1.456	1.00
44_V	192_L	1.454	1.00
14_K	33_L	1.448	1.00
34_A	40_E	1.422	1.00
45_A	215_S	1.365	0.99
42_V	216_T	1.363	0.99
27_I	214_I	1.356	0.99
27_I	185_L	1.340	0.99
82_A	85_E	1.330	0.99
163_Y	199_A	1.321	0.99
22_D	25_E	1.312	0.99
8_M	12_R	1.300	0.99
46_V	212_V	1.295	0.99
19_K	25_E	1.272	0.99
84_A	95_V	1.265	0.99
15_V	29_L	1.264	0.99
16_D	19_K	1.250	0.99
30_L	222_V	1.241	0.99
76_A	100_L	1.232	0.99
30_L	178_V	1.230	0.99
27_I	182_A	1.221	0.99
216_T	219_G	1.216	0.99
76_A	108_E	1.215	0.99
7_R	10_V	1.212	0.99
186_K	190_E	1.199	0.98
197_K	209_I	1.198	0.98
74_R	110_N	1.189	0.98
86_A	150_A	1.187	0.98
80_Q	123_V	1.186	0.98
34_A	178_V	1.174	0.98
80_Q	119_D	1.173	0.98
22_D	225_D	1.168	0.98
30_L	34_A	1.157	0.98
45_A	172_H	1.154	0.98
7_R	11_I	1.138	0.98
15_V	21_Y	1.131	0.98
83_N	147_P	1.129	0.98
33_L	219_G	1.127	0.98
27_I	186_K	1.121	0.98
96_G	99_D	1.121	0.98
93_E	157_K	1.110	0.97
77_V	115_I	1.110	0.97
102_D	105_K	1.110	0.97
154_K	158_A	1.108	0.97
212_V	224_V	1.106	0.97
10_V	14_K	1.103	0.97
170_I	211_K	1.089	0.97
111_F	114_V	1.072	0.97
98_E	102_D	1.068	0.97
195_A	198_K	1.067	0.97
80_Q	97_M	1.065	0.97
78_F	100_L	1.056	0.96
96_G	100_L	1.042	0.96
31_K	182_A	1.041	0.96
103_Q	106_K	1.038	0.96
94_L	103_Q	1.035	0.96
94_L	100_L	1.035	0.96
5_T	9_R	1.033	0.96
151_E	154_K	1.026	0.96
190_E	194_V	1.026	0.96
171_I	196_L	1.022	0.96
184_K	187_E	1.014	0.96
41_S	177_K	1.012	0.95
43_D	174_T	1.010	0.95
200_K	204_A	1.002	0.95
146_T	152_A	1.000	0.95
24_N	28_A	0.996	0.95
104_I	111_F	0.990	0.95
52_A	169_G	0.985	0.95
89_A	150_A	0.967	0.94
84_A	97_M	0.960	0.94
26_A	224_V	0.956	0.94
72_S	93_E	0.950	0.94
182_A	186_K	0.948	0.94
78_F	124_V	0.939	0.93
47_N	210_K	0.937	0.93
82_A	147_P	0.935	0.93
30_L	33_L	0.929	0.93
163_Y	195_A	0.928	0.93
15_V	18_T	0.916	0.92
43_D	215_S	0.913	0.92
149_V	153_V	0.912	0.92
94_L	109_M	0.905	0.92
58_N	165_N	0.892	0.91
78_F	116_A	0.879	0.91
21_Y	29_L	0.871	0.90
165_N	169_G	0.871	0.90
64_V	155_N	0.871	0.90
211_K	223_A	0.866	0.90
123_V	126_Q	0.864	0.90
5_T	11_I	0.851	0.89
117_S	147_P	0.846	0.89
20_Q	226_Q	0.845	0.89
25_E	28_A	0.842	0.89
113_V	156_A	0.839	0.89
84_A	88_K	0.831	0.88
83_N	119_D	0.826	0.88
193_L	209_I	0.824	0.88
31_K	34_A	0.820	0.88
183_D	186_K	0.817	0.87
124_V	128_G	0.817	0.87
40_E	178_V	0.814	0.87
63_T	195_A	0.812	0.87
109_M	114_V	0.810	0.87
175_I	214_I	0.807	0.87
59_V	204_A	0.805	0.87
163_Y	192_L	0.804	0.86
44_V	173_T	0.797	0.86
78_F	101_A	0.792	0.86
200_K	208_Y	0.781	0.85
113_V	166_D	0.781	0.85
16_D	21_Y	0.780	0.85
61_G	163_Y	0.776	0.84
114_V	124_V	0.771	0.84
33_L	222_V	0.771	0.84
212_V	226_Q	0.768	0.84
50_I	55_S	0.767	0.84
127_L	130_V	0.767	0.84
50_I	59_V	0.767	0.84
81_G	84_A	0.765	0.84
196_L	209_I	0.759	0.83
150_A	153_V	0.757	0.83
101_A	124_V	0.756	0.83
87_A	90_A	0.755	0.83
20_Q	225_D	0.754	0.83
42_V	185_L	0.754	0.83
52_A	58_N	0.750	0.82
124_V	127_L	0.749	0.82
43_D	177_K	0.745	0.82
161_V	173_T	0.744	0.82
78_F	104_I	0.740	0.82
97_M	123_V	0.737	0.81
79_T	117_S	0.737	0.81
189_L	214_I	0.733	0.81
104_I	108_E	0.732	0.81
82_A	86_A	0.729	0.81
35_T	178_V	0.717	0.80
193_L	212_V	0.711	0.79
8_M	11_I	0.709	0.79
114_V	127_L	0.707	0.79
94_L	110_N	0.706	0.78
45_A	173_T	0.704	0.78
87_A	91_G	0.702	0.78
11_I	35_T	0.698	0.78
7_R	12_R	0.698	0.78
186_K	189_L	0.697	0.78
165_N	171_I	0.697	0.78
72_S	158_A	0.695	0.77
29_L	33_L	0.691	0.77
46_V	209_I	0.690	0.77
101_A	127_L	0.688	0.77
33_L	40_E	0.687	0.77
24_N	183_D	0.678	0.76
194_V	198_K	0.677	0.76
29_L	222_V	0.672	0.75
76_A	109_M	0.671	0.75
44_V	193_L	0.668	0.75
15_V	19_K	0.667	0.74
23_I	186_K	0.664	0.74
156_A	160_Q	0.663	0.74
166_D	170_I	0.662	0.74
62_A	142_V	0.658	0.73
86_A	89_A	0.657	0.73
23_I	190_E	0.657	0.73
79_T	116_A	0.652	0.73
7_R	37_K	0.651	0.73
36_A	218_M	0.650	0.73
215_S	221_G	0.649	0.72
27_I	189_L	0.643	0.72
22_D	27_I	0.642	0.72
50_I	58_N	0.639	0.71
55_S	122_R	0.638	0.71
25_E	29_L	0.637	0.71
86_A	147_P	0.632	0.70
14_K	216_T	0.631	0.70
46_V	192_L	0.625	0.70
14_K	28_A	0.625	0.70
45_A	142_V	0.621	0.69
121_M	140_P	0.617	0.69
20_Q	23_I	0.616	0.68
36_A	178_V	0.615	0.68
33_L	216_T	0.613	0.68
142_V	162_R	0.613	0.68
63_T	191_A	0.612	0.68
67_H	183_D	0.607	0.67
134_R	217_T	0.606	0.67
191_A	195_A	0.604	0.67
35_T	40_E	0.604	0.67
129_Q	163_Y	0.604	0.67
189_L	193_L	0.602	0.67
67_H	181_D	0.600	0.66
116_A	119_D	0.598	0.66
30_L	214_I	0.596	0.66
104_I	109_M	0.595	0.66
4_L	12_R	0.594	0.66
55_S	165_N	0.591	0.65
12_R	15_V	0.590	0.65
37_K	190_E	0.584	0.64
49_G	200_K	0.582	0.64
10_V	33_L	0.581	0.64
23_I	175_I	0.581	0.64
80_Q	120_A	0.577	0.63
122_R	125_G	0.576	0.63
103_Q	109_M	0.576	0.63
94_L	104_I	0.575	0.63
182_A	214_I	0.575	0.63
29_L	32_E	0.573	0.63
46_V	59_V	0.572	0.63
40_E	216_T	0.572	0.63
116_A	120_A	0.571	0.63
27_I	42_V	0.570	0.63
9_R	12_R	0.568	0.62
51_D	70_G	0.568	0.62
154_K	184_K	0.567	0.62
54_K	58_N	0.567	0.62
79_T	83_N	0.567	0.62
55_S	58_N	0.566	0.62
54_K	203_Q	0.564	0.62
69_T	180_F	0.557	0.61
105_K	127_L	0.555	0.61
62_A	195_A	0.552	0.60
212_V	215_S	0.552	0.60
30_L	219_G	0.552	0.60
27_I	31_K	0.551	0.60
37_K	167_K	0.551	0.60
23_I	214_I	0.550	0.60
141_K	149_V	0.550	0.60
97_M	117_S	0.549	0.60
7_R	13_E	0.549	0.60
5_T	13_E	0.547	0.59
59_V	195_A	0.547	0.59
213_S	223_A	0.546	0.59
51_D	57_Q	0.545	0.59
45_A	168_N	0.544	0.59
100_L	124_V	0.544	0.59
216_T	221_G	0.544	0.59
107_G	111_F	0.543	0.59
47_N	170_I	0.539	0.58
171_I	192_L	0.538	0.58
40_E	218_M	0.538	0.58
51_D	68_G	0.537	0.58
132_G	135_G	0.535	0.58
7_R	40_E	0.534	0.58
94_L	111_F	0.533	0.57
10_V	22_D	0.533	0.57
128_G	169_G	0.533	0.57
74_R	134_R	0.532	0.57
52_A	171_I	0.531	0.57
79_T	95_V	0.531	0.57
81_G	95_V	0.531	0.57
184_K	209_I	0.531	0.57
7_R	36_A	0.530	0.57
113_V	140_P	0.530	0.57
87_A	149_V	0.529	0.57
7_R	34_A	0.529	0.57
64_V	158_A	0.525	0.56
77_V	84_A	0.525	0.56
44_V	175_I	0.525	0.56
20_Q	224_V	0.524	0.56
102_D	126_Q	0.524	0.56
28_A	181_D	0.519	0.55
45_A	169_G	0.519	0.55
201_P	208_Y	0.517	0.55
27_I	30_L	0.517	0.55
91_G	95_V	0.516	0.55
39_V	177_K	0.515	0.55
81_G	87_A	0.515	0.55
105_K	130_V	0.514	0.55
127_L	189_L	0.513	0.55
16_D	223_A	0.513	0.55
122_R	147_P	0.511	0.54
63_T	173_T	0.509	0.54
124_V	147_P	0.509	0.54
122_R	126_Q	0.508	0.54
26_A	220_A	0.508	0.54
49_G	206_G	0.507	0.54
107_G	130_V	0.506	0.54
45_A	170_I	0.506	0.54
49_G	52_A	0.505	0.53
15_V	33_L	0.504	0.53
126_Q	196_L	0.501	0.53
5_T	10_V	0.501	0.53
142_V	160_Q	0.500	0.53
12_R	16_D	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
3qoyA	1	1	100	0.127	Contact Map
4reoA	1	0.9402	100	0.133	Contact Map
3bboD	1	0.9701	100	0.135	Contact Map
3j8g5	1	1	100	0.136	Contact Map
3j3w5	1	0.5128	100	0.152	Contact Map
4lq4A	1	0.859	100	0.268	Contact Map
3j21A	1	0.8803	100	0.269	Contact Map
4cxdu	1	0.8547	100	0.272	Contact Map
1mzpA	1	0.8761	100	0.276	Contact Map
4w27z	1	0.8803	100	0.296	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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