RL6 - BACSU - GREMLIN Contacts

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RL6 - 50S ribosomal protein L6

UniProt:	P46898	Sequences: MSRVGKKLLEIPSDVTVTLNDNNTVAVKGPKGELTRTFHPDMEIKVEDNVLTVARPSDQKEHRALHGTTRSLLGNMVEGVSKGFERGLELVGVGYRASKSGNKLVLNVGYSHPVEIVPEEGIEIEVPSQTKVVVKGTDKERVGAIAANIRAVRSPEPYKGKGIRYEGEVVRRKEGKSAK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	179 (176)
Sequences:	3800 (2090)
Seq/√Len:	157.5

ECOLI - RL6
BACSU - RL6
HALSA - RL6
SULSO - RL6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
78_E	82_K	3.182	1.00
74_G	78_E	3.023	1.00
118_P	124_I	2.699	1.00
28_K	33_E	2.675	1.00
45_K	54_A	2.525	1.00
125_E	135_K	2.432	1.00
85_E	135_K	2.396	1.00
103_K	117_V	2.301	1.00
103_K	115_E	2.201	1.00
16_T	28_K	2.191	1.00
87_G	166_E	2.128	1.00
108_V	152_V	2.120	1.00
144_A	148_N	2.106	1.00
53_V	73_L	2.079	1.00
57_S	62_H	2.067	1.00
164_R	170_V	2.016	1.00
134_V	142_V	1.956	1.00
36_R	140_E	1.907	1.00
26_A	33_E	1.905	1.00
91_V	164_R	1.894	1.00
128_S	131_K	1.893	1.00
116_I	145_I	1.843	1.00
136_G	142_V	1.757	1.00
123_E	135_K	1.749	1.00
99_K	126_V	1.744	1.00
24_T	35_T	1.724	1.00
41_D	62_H	1.722	1.00
116_I	152_V	1.717	1.00
87_G	133_V	1.676	1.00
36_R	76_M	1.634	1.00
87_G	131_K	1.604	1.00
24_T	37_T	1.589	1.00
89_E	167_G	1.574	1.00
138_D	141_R	1.574	1.00
26_A	35_T	1.546	1.00
100_S	105_V	1.542	1.00
19_L	25_V	1.521	1.00
46_V	51_L	1.509	1.00
99_K	118_P	1.480	1.00
105_V	115_E	1.469	1.00
10_E	50_V	1.447	1.00
29_G	32_G	1.445	1.00
174_E	177_S	1.440	1.00
102_N	120_E	1.436	1.00
55_R	66_H	1.422	1.00
43_E	54_A	1.416	1.00
108_V	163_I	1.390	1.00
121_G	141_R	1.383	1.00
11_I	17_V	1.378	1.00
68_T	72_L	1.369	1.00
19_L	46_V	1.349	1.00
114_V	152_V	1.340	1.00
131_K	166_E	1.326	1.00
116_I	148_N	1.324	1.00
11_I	46_V	1.322	1.00
25_V	73_L	1.300	1.00
127_P	133_V	1.294	1.00
100_S	103_K	1.288	1.00
82_K	85_E	1.282	1.00
36_R	72_L	1.276	1.00
31_K	137_T	1.268	1.00
43_E	56_P	1.228	1.00
65_L	69_T	1.224	1.00
122_I	145_I	1.221	1.00
38_F	44_I	1.219	1.00
124_I	145_I	1.219	1.00
110_Y	114_V	1.200	1.00
150_R	155_P	1.178	1.00
5_G	66_H	1.169	1.00
27_V	76_M	1.162	1.00
89_E	166_E	1.152	1.00
97_A	132_V	1.124	1.00
55_R	63_R	1.108	1.00
102_N	117_V	1.108	1.00
10_E	49_N	1.107	1.00
31_K	135_K	1.096	0.99
61_E	64_A	1.095	0.99
145_I	149_I	1.094	0.99
97_A	106_L	1.093	0.99
106_L	152_V	1.091	0.99
68_T	71_S	1.079	0.99
140_E	144_A	1.063	0.99
45_K	52_T	1.061	0.99
56_P	62_H	1.060	0.99
151_A	154_S	1.049	0.99
23_N	37_T	1.049	0.99
16_T	33_E	1.048	0.99
150_R	168_E	1.044	0.99
124_I	134_V	1.042	0.99
18_T	26_A	1.041	0.99
22_N	37_T	1.034	0.99
118_P	145_I	1.026	0.99
59_Q	62_H	1.024	0.99
104_L	124_I	1.022	0.99
105_V	113_P	1.021	0.99
51_L	73_L	1.021	0.99
70_R	74_G	1.020	0.99
164_R	172_R	0.999	0.99
155_P	161_K	0.993	0.99
125_E	133_V	0.993	0.99
32_G	80_V	0.991	0.99
42_M	56_P	0.987	0.99
141_R	145_I	0.971	0.99
91_V	170_V	0.969	0.99
85_E	133_V	0.967	0.99
100_S	115_E	0.966	0.99
20_N	24_T	0.960	0.99
39_H	65_L	0.952	0.99
127_P	131_K	0.947	0.98
118_P	134_V	0.944	0.98
89_E	131_K	0.939	0.98
55_R	58_D	0.933	0.98
134_V	149_I	0.931	0.98
17_V	51_L	0.931	0.98
104_L	149_I	0.922	0.98
156_E	170_V	0.914	0.98
110_Y	152_V	0.913	0.98
103_K	118_P	0.910	0.98
98_S	105_V	0.907	0.98
116_I	124_I	0.906	0.98
64_A	71_S	0.904	0.98
42_M	62_H	0.904	0.98
102_N	123_E	0.899	0.98
90_L	97_A	0.898	0.98
41_D	57_S	0.895	0.98
89_E	164_R	0.893	0.98
36_R	69_T	0.887	0.98
157_P	172_R	0.883	0.98
122_I	136_G	0.883	0.98
34_L	76_M	0.882	0.98
107_N	113_P	0.882	0.98
98_S	107_N	0.881	0.98
144_A	151_A	0.880	0.98
31_K	83_G	0.865	0.97
120_E	141_R	0.852	0.97
99_K	124_I	0.841	0.97
29_G	80_V	0.837	0.97
95_Y	153_R	0.830	0.97
41_D	56_P	0.817	0.96
13_S	49_N	0.808	0.96
7_K	70_R	0.801	0.96
121_G	136_G	0.801	0.96
86_R	167_G	0.798	0.96
31_K	123_E	0.798	0.96
119_E	141_R	0.795	0.96
61_E	65_L	0.794	0.96
110_Y	153_R	0.791	0.95
63_R	66_H	0.784	0.95
164_R	167_G	0.782	0.95
108_V	112_H	0.772	0.95
38_F	73_L	0.765	0.95
27_V	81_S	0.765	0.95
150_R	165_Y	0.761	0.94
96_R	129_Q	0.754	0.94
146_A	165_Y	0.752	0.94
18_T	28_K	0.749	0.94
66_H	177_S	0.746	0.94
11_I	51_L	0.737	0.93
42_M	53_V	0.737	0.93
42_M	65_L	0.735	0.93
39_H	69_T	0.729	0.93
12_P	15_V	0.728	0.93
15_V	81_S	0.726	0.93
53_V	69_T	0.719	0.93
47_E	50_V	0.719	0.93
91_V	167_G	0.718	0.92
32_G	137_T	0.715	0.92
34_L	137_T	0.712	0.92
104_L	132_V	0.712	0.92
41_D	61_E	0.711	0.92
39_H	61_E	0.709	0.92
47_E	52_T	0.702	0.92
64_A	68_T	0.701	0.92
4_V	71_S	0.700	0.91
80_V	137_T	0.699	0.91
88_L	132_V	0.697	0.91
90_L	108_V	0.696	0.91
141_R	148_N	0.695	0.91
145_I	148_N	0.694	0.91
39_H	42_M	0.692	0.91
122_I	134_V	0.688	0.91
9_L	77_V	0.685	0.91
44_I	53_V	0.671	0.90
96_R	107_N	0.664	0.89
156_E	172_R	0.663	0.89
15_V	80_V	0.661	0.89
156_E	159_K	0.656	0.89
8_L	50_V	0.654	0.88
20_N	26_A	0.647	0.88
17_V	27_V	0.646	0.88
14_D	30_P	0.643	0.88
8_L	70_R	0.637	0.87
99_K	125_E	0.636	0.87
60_K	64_A	0.628	0.86
16_T	46_V	0.626	0.86
8_L	52_T	0.624	0.86
88_L	134_V	0.622	0.86
20_N	23_N	0.619	0.86
165_Y	168_E	0.615	0.85
9_L	74_G	0.614	0.85
160_G	172_R	0.613	0.85
19_L	51_L	0.613	0.85
87_G	127_P	0.610	0.85
70_R	77_V	0.609	0.85
88_L	146_A	0.608	0.85
71_S	75_N	0.607	0.85
6_K	54_A	0.601	0.84
110_Y	154_S	0.600	0.84
86_R	165_Y	0.600	0.84
148_N	152_V	0.599	0.84
155_P	170_V	0.595	0.83
11_I	14_D	0.595	0.83
153_R	163_I	0.593	0.83
25_V	46_V	0.592	0.83
99_K	105_V	0.586	0.82
5_G	175_G	0.586	0.82
23_N	43_E	0.585	0.82
9_L	70_R	0.583	0.82
58_D	61_E	0.583	0.82
65_L	68_T	0.582	0.82
114_V	163_I	0.581	0.82
156_E	174_E	0.578	0.82
27_V	36_R	0.578	0.82
2_S	5_G	0.577	0.81
91_V	130_T	0.576	0.81
145_I	152_V	0.576	0.81
6_K	55_R	0.574	0.81
92_G	162_G	0.555	0.79
142_V	146_A	0.554	0.79
104_L	126_V	0.552	0.79
34_L	80_V	0.551	0.78
34_L	138_D	0.549	0.78
11_I	77_V	0.548	0.78
122_I	141_R	0.543	0.77
57_S	66_H	0.543	0.77
6_K	63_R	0.541	0.77
58_D	66_H	0.541	0.77
18_T	46_V	0.540	0.77
71_S	74_G	0.538	0.77
172_R	175_G	0.534	0.76
86_R	169_V	0.534	0.76
85_E	166_E	0.533	0.76
68_T	177_S	0.531	0.76
37_T	76_M	0.530	0.76
144_A	147_A	0.525	0.75
126_V	132_V	0.525	0.75
74_G	82_K	0.523	0.75
38_F	69_T	0.523	0.75
164_R	169_V	0.522	0.75
84_F	142_V	0.521	0.74
118_P	122_I	0.519	0.74
148_N	151_A	0.518	0.74
103_K	124_I	0.516	0.74
156_E	160_G	0.516	0.74
106_L	132_V	0.515	0.74
10_E	13_S	0.514	0.74
27_V	34_L	0.514	0.74
118_P	142_V	0.511	0.73
53_V	70_R	0.509	0.73
91_V	154_S	0.507	0.73
42_M	55_R	0.506	0.72
19_L	44_I	0.502	0.72
113_P	126_V	0.502	0.72
93_V	161_K	0.500	0.71

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
4rb6H	1	0.9721	100	0.009	Contact Map
2zjrE	1	0.9553	100	0.009	Contact Map
3bboI	1	0.9944	100	0.01	Contact Map
1nkwE	1	0.9721	100	0.01	Contact Map
1rl6A	1	0.9162	100	0.033	Contact Map
4tp9G	1	0.9832	100	0.035	Contact Map
1vw4F	1	0.9441	100	0.045	Contact Map
3j21F	1	0.9832	100	0.181	Contact Map
1vq8E	1	0.9162	100	0.191	Contact Map
4a17E	1	0.9665	100	0.217	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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