RL17 - ECOLI - GREMLIN Contacts

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RL17 - 50S ribosomal protein L17

UniProt:	P0AG44	Sequences: MRHRKSGRQLNRNSSHRQAMFRNMAGSLVRHEIIKTTLPKAKELRRVVEPLITLAKTDSVANRRLAFARTRDNEIVAKLFNELGPRFASRAGGYTRILKCGFRAGDNAPMAYIELVDRSEKAEAAAE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10878
Length:	127 (113)
Sequences:	2368 (1080)
Seq/√Len:	101.6

ECOLI - RL17
BACSU - RL17

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
8_R	43_E	2.946	1.00
38_L	111_A	2.892	1.00
32_E	78_K	2.792	1.00
33_I	114_E	2.709	1.00
44_L	113_I	2.563	1.00
30_R	72_D	2.428	1.00
52_I	115_L	2.311	1.00
16_H	23_N	2.286	1.00
29_V	48_V	2.074	1.00
25_A	48_V	2.052	1.00
96_R	114_E	2.003	1.00
66_A	80_F	1.982	1.00
28_L	48_V	1.945	1.00
29_V	115_L	1.940	1.00
77_A	81_N	1.857	1.00
38_L	99_K	1.799	1.00
32_E	86_R	1.772	1.00
67_F	76_V	1.685	1.00
61_A	65_L	1.649	1.00
35_K	112_Y	1.607	1.00
54_L	66_A	1.591	1.00
59_S	62_N	1.563	1.00
58_D	62_N	1.555	1.00
81_N	85_P	1.511	1.00
20_M	40_K	1.495	1.00
90_R	116_V	1.489	1.00
14_S	18_Q	1.469	1.00
23_N	27_S	1.447	1.00
25_A	47_V	1.446	1.00
20_M	24_M	1.372	0.99
65_L	69_R	1.343	0.99
35_K	100_C	1.330	0.99
33_I	112_Y	1.320	0.99
54_L	65_L	1.311	0.99
95_T	113_I	1.304	0.99
43_E	46_R	1.287	0.99
12_R	17_R	1.270	0.99
25_A	51_L	1.244	0.99
100_C	112_Y	1.240	0.99
78_K	82_E	1.224	0.99
60_V	64_R	1.204	0.99
36_T	41_A	1.202	0.99
55_A	84_G	1.196	0.99
16_H	20_M	1.192	0.99
12_R	40_K	1.182	0.98
97_I	111_A	1.132	0.98
10_L	43_E	1.131	0.98
102_F	107_N	1.128	0.98
26_G	75_I	1.121	0.98
55_A	79_L	1.114	0.98
57_T	62_N	1.100	0.98
26_G	71_R	1.098	0.97
29_V	75_I	1.084	0.97
22_R	26_G	1.065	0.97
32_E	83_L	1.058	0.97
70_T	75_I	1.047	0.97
13_N	16_H	1.045	0.97
22_R	71_R	1.040	0.97
51_L	69_R	1.031	0.96
62_N	65_L	1.030	0.96
20_M	27_S	1.028	0.96
38_L	109_P	1.008	0.96
65_L	68_A	1.008	0.96
100_C	110_M	1.003	0.96
63_R	80_F	0.985	0.95
49_E	97_I	0.982	0.95
35_K	110_M	0.980	0.95
67_F	77_A	0.968	0.95
46_R	50_P	0.966	0.95
17_R	43_E	0.964	0.95
102_F	109_P	0.935	0.94
51_L	79_L	0.896	0.92
85_P	88_A	0.893	0.92
12_R	20_M	0.879	0.92
27_S	30_R	0.873	0.91
46_R	49_E	0.866	0.91
21_F	47_V	0.858	0.91
50_P	54_L	0.857	0.90
26_G	72_D	0.852	0.90
66_A	76_V	0.851	0.90
45_R	113_I	0.838	0.89
45_R	49_E	0.823	0.89
37_T	108_A	0.821	0.89
26_G	70_T	0.802	0.87
29_V	83_L	0.801	0.87
79_L	83_L	0.801	0.87
52_I	87_F	0.801	0.87
28_L	113_I	0.797	0.87
57_T	61_A	0.797	0.87
32_E	87_F	0.797	0.87
48_V	95_T	0.795	0.87
27_S	31_H	0.795	0.87
101_G	109_P	0.791	0.87
45_R	97_I	0.789	0.86
21_F	24_M	0.773	0.85
60_V	67_F	0.772	0.85
9_Q	13_N	0.765	0.85
87_F	115_L	0.764	0.85
21_F	44_L	0.758	0.84
30_R	75_I	0.753	0.84
25_A	69_R	0.735	0.82
82_E	85_P	0.734	0.82
90_R	117_D	0.710	0.80
54_L	80_F	0.709	0.80
47_V	69_R	0.708	0.80
24_M	44_L	0.708	0.80
58_D	63_R	0.707	0.80
86_R	117_D	0.704	0.80
7_G	46_R	0.700	0.79
103_R	110_M	0.698	0.79
25_A	44_L	0.691	0.78
24_M	27_S	0.679	0.77
104_A	110_M	0.673	0.76
63_R	76_V	0.670	0.76
53_T	94_Y	0.668	0.76
56_K	91_A	0.666	0.76
83_L	87_F	0.662	0.75
66_A	79_L	0.661	0.75
32_E	82_E	0.657	0.75
39_P	109_P	0.656	0.75
101_G	110_M	0.648	0.74
18_Q	22_R	0.637	0.72
8_R	39_P	0.635	0.72
105_G	115_L	0.635	0.72
30_R	73_N	0.631	0.72
87_F	117_D	0.629	0.71
55_A	66_A	0.617	0.70
67_F	73_N	0.615	0.70
23_N	49_E	0.613	0.70
30_R	74_E	0.608	0.69
28_L	44_L	0.608	0.69
19_A	71_R	0.601	0.68
103_R	106_D	0.600	0.68
44_L	47_V	0.599	0.68
45_R	95_T	0.597	0.68
107_N	110_M	0.593	0.67
60_V	63_R	0.589	0.67
53_T	92_G	0.585	0.66
58_D	66_A	0.584	0.66
10_L	20_M	0.581	0.65
5_K	43_E	0.579	0.65
78_K	87_F	0.578	0.65
103_R	108_A	0.577	0.65
16_H	40_K	0.577	0.65
51_L	89_S	0.573	0.64
31_H	40_K	0.573	0.64
9_Q	104_A	0.571	0.64
95_T	115_L	0.569	0.64
11_N	39_P	0.559	0.62
53_T	56_K	0.555	0.62
29_V	79_L	0.553	0.62
63_R	67_F	0.553	0.62
16_H	19_A	0.553	0.62
20_M	34_I	0.545	0.61
67_F	70_T	0.541	0.60
73_N	77_A	0.539	0.60
39_P	108_A	0.538	0.60
42_K	97_I	0.534	0.59
67_F	71_R	0.532	0.59
13_N	40_K	0.529	0.58
25_A	49_E	0.529	0.58
76_V	80_F	0.511	0.56
36_T	40_K	0.510	0.56
74_E	78_K	0.509	0.55
96_R	116_V	0.505	0.55
7_G	21_F	0.505	0.55
17_R	20_M	0.505	0.55
26_G	67_F	0.502	0.54
22_R	51_L	0.501	0.54
18_Q	69_R	0.500	0.54

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
4tp9N	1	0.9449	100	0.03	Contact Map
3bboP	1	0.9055	100	0.036	Contact Map
1gd8A	1	0.8189	100	0.042	Contact Map
3j7yO	1	1	100	0.045	Contact Map
2zjrK	1	0.8898	100	0.048	Contact Map
1vw4L	1	0.9843	100	0.088	Contact Map
3j3wN	1	0.8819	100	0.105	Contact Map
3h0dA	2	0.6929	6.7	0.951	Contact Map
2bkmA	1	0.4252	6.3	0.952	Contact Map
4yfkF	1	0	4.8	0.954	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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