RL2 - HALSA - GREMLIN Contacts

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RL2 - 50S ribosomal protein L2

UniProt:	Q9HPD1	Sequences: MGRRIQGQRRGRGTSTFRAPSHRYKAELSHKRTEDTDVLAGEVIDVEHDPARSAPVARVAFEDDDQRLVLASEGVGVGDTIEIGISATIEEGNTLPLAEIPEGVPVCNVESHPGDGGKFARAGGVNADLVTHERDATIVELPSGETKRLSPDCRATIGVVAGGGRTEKPFVKAGNKHHKMKARGTKWPRVRGVAMNAVDHPFGGGGRQHPGRPKSVSRDAAPGRKVGDIASKRTGRGGNE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	240 (227)
Sequences:	2553 (1012)
Seq/√Len:	67.1

ECOLI - RL2
BACSU - RL2
HALSA - RL2
SULSO - RL2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
41_G	59_V	3.328	1.00
115_D	118_K	3.238	1.00
37_D	154_R	3.200	1.00
44_I	60_A	3.047	1.00
137_T	151_P	2.862	1.00
129_L	137_T	2.772	1.00
17_F	189_R	2.739	1.00
120_A	127_A	2.612	1.00
108_N	117_G	2.447	1.00
104_V	157_I	2.447	1.00
106_V	129_L	2.443	1.00
106_V	139_V	2.442	1.00
98_A	152_D	2.420	1.00
185_T	189_R	2.370	1.00
73_E	163_G	2.360	1.00
207_R	210_P	2.304	1.00
231_S	234_T	2.296	1.00
109_V	127_A	2.249	1.00
22_H	182_A	2.243	1.00
206_G	210_P	2.234	1.00
53_S	165_R	2.091	1.00
8_Q	14_T	2.053	1.00
222_P	226_V	2.046	1.00
139_V	149_L	2.045	1.00
206_G	212_R	1.979	1.00
170_F	176_K	1.944	1.00
159_V	163_G	1.933	1.00
94_T	154_R	1.903	1.00
59_V	81_I	1.902	1.00
75_V	81_I	1.902	1.00
207_R	212_R	1.891	1.00
208_Q	212_R	1.870	1.00
76_G	79_D	1.859	1.00
138_I	146_T	1.808	1.00
193_V	209_H	1.800	1.00
35_D	63_D	1.766	1.00
18_R	185_T	1.760	1.00
43_V	75_V	1.743	1.00
210_P	214_K	1.733	1.00
70_L	117_G	1.714	1.00
210_P	224_R	1.682	0.99
135_D	150_S	1.679	0.99
212_R	216_V	1.651	0.99
34_E	67_R	1.643	0.99
100_I	157_I	1.625	0.99
170_F	183_R	1.620	0.99
60_A	66_Q	1.619	0.99
57_A	71_A	1.610	0.99
96_P	99_E	1.607	0.99
40_A	80_T	1.596	0.99
55_P	161_A	1.563	0.99
202_F	216_V	1.561	0.99
217_S	221_A	1.551	0.99
73_E	159_V	1.550	0.99
79_D	90_E	1.542	0.99
110_E	116_G	1.521	0.99
109_V	139_V	1.515	0.99
131_T	138_I	1.499	0.99
35_D	65_D	1.485	0.99
72_S	75_V	1.484	0.99
84_G	87_A	1.477	0.99
223_G	226_V	1.468	0.99
119_F	149_L	1.460	0.98
38_V	86_S	1.454	0.98
42_E	60_A	1.452	0.98
176_K	183_R	1.452	0.98
230_A	236_R	1.449	0.98
15_S	189_R	1.446	0.98
54_A	160_V	1.433	0.98
193_V	210_P	1.395	0.98
37_D	84_G	1.394	0.98
132_H	151_P	1.393	0.98
4_R	18_R	1.393	0.98
44_I	66_Q	1.391	0.98
221_A	226_V	1.383	0.98
136_A	150_S	1.367	0.98
111_S	119_F	1.336	0.97
95_L	100_I	1.324	0.97
37_D	83_I	1.318	0.97
40_A	62_E	1.304	0.97
38_V	84_G	1.293	0.97
233_R	236_R	1.285	0.96
73_E	161_A	1.281	0.96
42_E	80_T	1.277	0.96
43_V	59_V	1.275	0.96
98_A	151_P	1.264	0.96
87_A	95_L	1.224	0.95
193_V	208_Q	1.219	0.95
190_V	194_A	1.206	0.95
105_P	126_N	1.196	0.95
138_I	148_R	1.193	0.95
231_S	236_R	1.181	0.94
209_H	224_R	1.177	0.94
113_P	150_S	1.168	0.94
232_K	236_R	1.156	0.94
72_S	107_C	1.151	0.94
196_N	199_D	1.132	0.93
17_F	185_T	1.127	0.93
232_K	235_G	1.123	0.93
164_G	167_E	1.096	0.92
94_T	156_T	1.083	0.91
202_F	210_P	1.083	0.91
231_S	235_G	1.077	0.91
57_A	75_V	1.072	0.91
86_S	99_E	1.066	0.91
119_F	141_L	1.062	0.91
176_K	185_T	1.055	0.90
24_Y	51_A	1.053	0.90
111_S	149_L	1.046	0.90
70_L	160_V	1.044	0.90
135_D	151_P	1.042	0.90
112_H	115_D	1.040	0.90
100_I	155_A	1.038	0.89
13_G	17_F	1.024	0.89
18_R	189_R	1.017	0.89
132_H	137_T	1.012	0.88
45_D	77_V	1.004	0.88
45_D	57_A	1.002	0.88
42_E	62_E	0.998	0.88
16_T	195_M	0.997	0.88
189_R	202_F	0.992	0.87
5_I	18_R	0.990	0.87
29_S	56_V	0.987	0.87
202_F	223_G	0.986	0.87
214_K	224_R	0.981	0.87
193_V	214_K	0.960	0.85
100_I	129_L	0.959	0.85
175_N	183_R	0.948	0.85
217_S	224_R	0.944	0.84
70_L	108_N	0.931	0.84
58_R	68_L	0.925	0.83
15_S	18_R	0.898	0.81
170_F	175_N	0.897	0.81
230_A	233_R	0.894	0.81
53_S	71_A	0.891	0.81
17_F	190_V	0.888	0.81
45_D	58_R	0.885	0.80
168_K	175_N	0.873	0.80
39_L	62_E	0.870	0.79
221_A	224_R	0.869	0.79
9_R	14_T	0.860	0.79
86_S	95_L	0.841	0.77
39_L	65_D	0.838	0.77
46_V	55_P	0.833	0.76
217_S	223_G	0.833	0.76
216_V	222_P	0.829	0.76
225_K	228_D	0.824	0.75
85_I	99_E	0.823	0.75
83_I	94_T	0.820	0.75
193_V	212_R	0.818	0.75
40_A	82_E	0.806	0.74
107_C	156_T	0.797	0.73
192_G	202_F	0.793	0.73
209_H	214_K	0.792	0.73
82_E	88_T	0.789	0.72
218_R	230_A	0.788	0.72
191_R	194_A	0.782	0.72
35_D	39_L	0.780	0.71
21_S	24_Y	0.776	0.71
109_V	120_A	0.776	0.71
44_I	59_V	0.773	0.71
206_G	209_H	0.768	0.70
27_E	30_H	0.765	0.70
41_G	61_F	0.765	0.70
197_A	206_G	0.763	0.70
69_V	72_S	0.762	0.70
75_V	107_C	0.756	0.69
46_V	56_V	0.755	0.69
128_D	140_E	0.748	0.68
198_V	224_R	0.748	0.68
108_N	156_T	0.747	0.68
45_D	161_A	0.747	0.68
19_A	24_Y	0.745	0.68
49_D	52_R	0.742	0.68
8_Q	12_R	0.742	0.68
7_G	13_G	0.741	0.67
59_V	67_R	0.739	0.67
193_V	216_V	0.737	0.67
45_D	66_Q	0.736	0.67
85_I	98_A	0.735	0.67
129_L	151_P	0.734	0.67
217_S	222_P	0.728	0.66
210_P	223_G	0.719	0.65
220_A	224_R	0.719	0.65
209_H	212_R	0.718	0.65
74_G	144_G	0.713	0.64
202_F	209_H	0.713	0.64
17_F	195_M	0.712	0.64
50_P	121_R	0.712	0.64
9_R	13_G	0.712	0.64
110_E	114_G	0.712	0.64
29_S	45_D	0.711	0.64
47_E	68_L	0.709	0.64
8_Q	13_G	0.708	0.64
46_V	57_A	0.707	0.64
202_F	224_R	0.700	0.63
120_A	139_V	0.700	0.63
17_F	186_K	0.700	0.63
45_D	55_P	0.699	0.63
120_A	142_P	0.697	0.63
84_G	154_R	0.695	0.63
26_A	51_A	0.694	0.62
75_V	91_E	0.693	0.62
216_V	223_G	0.690	0.62
195_M	199_D	0.687	0.62
3_R	18_R	0.686	0.62
41_G	81_I	0.677	0.60
102_E	227_G	0.674	0.60
107_C	160_V	0.673	0.60
33_T	107_C	0.672	0.60
89_I	95_L	0.669	0.60
212_R	224_R	0.667	0.59
120_A	125_V	0.667	0.59
39_L	61_F	0.665	0.59
41_G	67_R	0.663	0.59
230_A	234_T	0.662	0.59
205_G	209_H	0.661	0.59
106_V	127_A	0.660	0.59
9_R	12_R	0.657	0.58
198_V	214_K	0.657	0.58
102_E	132_H	0.654	0.58
38_V	82_E	0.652	0.58
129_L	132_H	0.651	0.58
89_I	157_I	0.651	0.58
202_F	217_S	0.650	0.57
97_L	139_V	0.649	0.57
62_E	80_T	0.649	0.57
55_P	142_P	0.649	0.57
73_E	167_E	0.647	0.57
13_G	16_T	0.647	0.57
208_Q	224_R	0.643	0.57
214_K	223_G	0.643	0.57
83_I	154_R	0.642	0.56
64_D	116_G	0.640	0.56
126_N	159_V	0.638	0.56
59_V	161_A	0.628	0.55
197_A	216_V	0.625	0.54
102_E	131_T	0.625	0.54
69_V	107_C	0.623	0.54
35_D	61_F	0.622	0.54
14_T	17_F	0.621	0.54
55_P	73_E	0.618	0.54
97_L	149_L	0.613	0.53
208_Q	214_K	0.612	0.53
9_R	15_S	0.611	0.53
71_A	161_A	0.610	0.53
10_R	13_G	0.607	0.52
85_I	95_L	0.607	0.52
85_I	96_P	0.606	0.52
193_V	207_R	0.606	0.52
127_A	139_V	0.605	0.52
105_P	159_V	0.604	0.52
202_F	215_S	0.600	0.52
98_A	137_T	0.598	0.51
163_G	166_T	0.598	0.51
88_T	166_T	0.597	0.51
122_A	125_V	0.596	0.51
30_H	33_T	0.590	0.50
29_S	134_R	0.589	0.50
171_V	175_N	0.588	0.50
106_V	109_V	0.586	0.50
105_P	128_D	0.586	0.50
131_T	134_R	0.582	0.49
87_A	99_E	0.582	0.49
193_V	205_G	0.580	0.49
226_V	231_S	0.579	0.49
88_T	154_R	0.578	0.49
84_G	95_L	0.577	0.49
131_T	142_P	0.575	0.49
161_A	166_T	0.574	0.48
10_R	14_T	0.573	0.48
47_E	56_V	0.571	0.48
17_F	218_R	0.571	0.48
15_S	190_V	0.570	0.48
53_S	168_K	0.570	0.48
33_T	94_T	0.569	0.48
111_S	153_C	0.568	0.48
27_E	50_P	0.566	0.47
58_R	66_Q	0.565	0.47
46_V	66_Q	0.565	0.47
77_V	130_V	0.564	0.47
177_H	186_K	0.562	0.47
189_R	218_R	0.562	0.47
206_G	211_G	0.561	0.47
55_P	164_G	0.561	0.47
111_S	139_V	0.559	0.47
170_F	194_A	0.556	0.46
20_P	23_R	0.556	0.46
123_G	165_R	0.555	0.46
13_G	20_P	0.553	0.46
218_R	223_G	0.552	0.46
53_S	161_A	0.551	0.46
16_T	20_P	0.549	0.45
15_S	55_P	0.548	0.45
85_I	154_R	0.547	0.45
34_E	65_D	0.547	0.45
45_D	142_P	0.545	0.45
96_P	152_D	0.544	0.45
198_V	210_P	0.544	0.45
13_G	189_R	0.543	0.45
104_V	128_D	0.541	0.45
126_N	163_G	0.540	0.44
123_G	171_V	0.539	0.44
39_L	82_E	0.536	0.44
7_G	20_P	0.535	0.44
110_E	153_C	0.534	0.44
4_R	24_Y	0.533	0.44
35_D	67_R	0.532	0.43
70_L	107_C	0.530	0.43
5_I	15_S	0.528	0.43
55_P	168_K	0.528	0.43
133_E	144_G	0.526	0.43
38_V	85_I	0.525	0.43
45_D	56_V	0.525	0.43
194_A	216_V	0.525	0.43
13_G	190_V	0.524	0.43
4_R	15_S	0.523	0.42
137_T	149_L	0.522	0.42
26_A	29_S	0.522	0.42
193_V	224_R	0.520	0.42
175_N	182_A	0.519	0.42
97_L	129_L	0.518	0.42
226_V	234_T	0.518	0.42
136_A	148_R	0.516	0.42
142_P	167_E	0.513	0.41
97_L	105_P	0.512	0.41
62_E	67_R	0.511	0.41
8_Q	21_S	0.511	0.41
45_D	59_V	0.510	0.41
18_R	21_S	0.508	0.41
4_R	102_E	0.507	0.41
193_V	206_G	0.504	0.40
194_A	205_G	0.503	0.40
225_K	229_I	0.503	0.40
127_A	141_L	0.502	0.40
119_F	127_A	0.502	0.40
14_T	113_P	0.502	0.40
205_G	208_Q	0.501	0.40
165_R	168_K	0.500	0.40
38_V	61_F	0.500	0.40

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
3j3wC	1	0.975	100	0.046	Contact Map
4tp9C	1	0.0083	100	0.053	Contact Map
4rb6D	1	0.9708	100	0.057	Contact Map
3bboE	1	0.975	100	0.062	Contact Map
1vw3B	1	0.9708	100	0.063	Contact Map
3j21B	1	0.9792	100	0.083	Contact Map
1vq8A	1	0.9708	100	0.089	Contact Map
4ujqD	1	0.9875	100	0.12	Contact Map
3zf7e	1	0.7333	100	0.122	Contact Map
1vx7D	1	0.9833	100	0.122	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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