RL20 - BACSU - GREMLIN Contacts

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RL20 - 50S ribosomal protein L20

UniProt:	P55873	Sequences: MPRVKGGTVTRKRRKKVLKLAKGYFGSKHTLYKVANQQVMKSGNYAFRDRRQKKRDFRKLWITRINAAARMNGLSYSRLMHGLKLSGIEVNRKMLADLAVNDLTAFNQLADAAKAQLNK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	119 (114)
Sequences:	2243 (933)
Seq/√Len:	87.4

ECOLI - RL20
BACSU - RL20

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
21_A	39_V	3.826	1.00
69_A	79_L	2.899	1.00
81_H	85_L	2.867	1.00
6_G	10_T	2.683	1.00
66_N	70_R	2.672	1.00
96_A	100_V	2.662	1.00
52_Q	55_R	2.601	1.00
28_K	38_Q	2.540	1.00
72_N	107_N	2.510	1.00
102_D	105_A	2.242	1.00
38_Q	42_S	2.166	1.00
49_D	52_Q	2.133	1.00
27_S	31_L	2.114	1.00
31_L	34_V	2.092	1.00
53_K	56_D	2.045	1.00
97_D	101_N	2.006	1.00
20_L	43_G	1.854	1.00
27_S	30_T	1.852	1.00
108_Q	111_D	1.799	1.00
75_S	78_R	1.781	1.00
48_R	52_Q	1.768	1.00
34_V	37_Q	1.723	1.00
83_L	109_L	1.702	1.00
107_N	111_D	1.670	1.00
32_Y	36_N	1.648	1.00
36_N	40_M	1.610	1.00
94_M	97_D	1.564	1.00
111_D	114_K	1.514	1.00
88_I	112_A	1.463	0.99
52_Q	56_D	1.432	0.99
37_Q	41_K	1.411	0.99
108_Q	112_A	1.394	0.99
9_V	12_K	1.356	0.99
8_T	12_K	1.329	0.99
104_T	107_N	1.322	0.99
24_Y	38_Q	1.311	0.99
65_I	96_A	1.288	0.99
41_K	45_Y	1.278	0.98
91_N	94_M	1.260	0.98
90_V	94_M	1.226	0.98
18_L	35_A	1.225	0.98
25_F	31_L	1.193	0.98
78_R	81_H	1.152	0.97
69_A	72_N	1.108	0.96
71_M	103_L	1.099	0.96
60_L	64_R	1.092	0.96
11_R	14_R	1.091	0.96
86_S	113_A	1.084	0.96
27_S	34_V	1.079	0.96
98_L	105_A	1.076	0.96
103_L	107_N	1.075	0.96
8_T	14_R	1.070	0.95
74_L	114_K	1.068	0.95
58_R	80_M	1.053	0.95
6_G	9_V	1.041	0.95
9_V	13_R	1.033	0.94
82_G	113_A	0.999	0.93
26_G	29_H	0.997	0.93
69_A	74_L	0.970	0.92
40_M	43_G	0.967	0.92
9_V	14_R	0.962	0.92
98_L	102_D	0.957	0.92
58_R	62_I	0.950	0.92
53_K	57_F	0.942	0.91
58_R	92_R	0.921	0.90
59_K	63_T	0.907	0.90
38_Q	41_K	0.904	0.89
25_F	28_K	0.901	0.89
56_D	59_K	0.900	0.89
98_L	109_L	0.897	0.89
4_V	7_G	0.878	0.88
28_K	42_S	0.868	0.87
82_G	86_S	0.857	0.87
14_R	32_Y	0.856	0.87
74_L	78_R	0.854	0.87
82_G	85_L	0.854	0.87
17_V	35_A	0.828	0.85
65_I	80_M	0.808	0.83
31_L	36_N	0.806	0.83
14_R	18_L	0.795	0.82
17_V	36_N	0.794	0.82
77_S	81_H	0.785	0.82
25_F	42_S	0.781	0.81
104_T	108_Q	0.771	0.80
85_L	89_E	0.770	0.80
48_R	55_R	0.769	0.80
74_L	82_G	0.768	0.80
20_L	39_V	0.768	0.80
33_K	37_Q	0.766	0.80
32_Y	35_A	0.758	0.79
71_M	107_N	0.745	0.78
68_A	72_N	0.740	0.78
33_K	40_M	0.738	0.77
72_N	103_L	0.735	0.77
6_G	14_R	0.727	0.76
10_T	32_Y	0.722	0.76
64_R	100_V	0.711	0.75
37_Q	40_M	0.696	0.73
22_K	51_R	0.688	0.72
63_T	91_N	0.684	0.72
45_Y	110_A	0.683	0.72
110_A	113_A	0.677	0.71
17_V	40_M	0.673	0.71
105_A	108_Q	0.669	0.70
42_S	45_Y	0.665	0.70
2_P	9_V	0.649	0.68
18_L	32_Y	0.647	0.68
78_R	82_G	0.647	0.68
5_K	9_V	0.640	0.67
24_Y	43_G	0.639	0.67
90_V	109_L	0.637	0.66
79_L	109_L	0.632	0.66
47_F	51_R	0.622	0.65
84_K	89_E	0.621	0.65
45_Y	48_R	0.619	0.64
10_T	14_R	0.615	0.64
107_N	110_A	0.614	0.64
91_N	112_A	0.611	0.63
74_L	110_A	0.590	0.61
68_A	110_A	0.589	0.60
43_G	51_R	0.589	0.60
83_L	88_I	0.586	0.60
24_Y	39_V	0.583	0.60
36_N	109_L	0.575	0.59
97_D	100_V	0.573	0.58
7_G	10_T	0.572	0.58
16_K	20_L	0.571	0.58
12_K	59_K	0.571	0.58
68_A	106_F	0.571	0.58
27_S	38_Q	0.567	0.58
80_M	84_K	0.566	0.57
40_M	44_N	0.564	0.57
19_K	25_F	0.562	0.57
70_R	73_G	0.561	0.57
62_I	76_Y	0.561	0.57
72_N	110_A	0.560	0.57
30_T	36_N	0.553	0.56
6_G	11_R	0.553	0.56
12_K	27_S	0.550	0.55
4_V	12_K	0.548	0.55
21_A	24_Y	0.547	0.55
87_G	101_N	0.545	0.55
69_A	75_S	0.542	0.54
84_K	90_V	0.539	0.54
21_A	99_A	0.539	0.54
17_V	39_V	0.539	0.54
79_L	110_A	0.538	0.54
68_A	99_A	0.538	0.54
109_L	112_A	0.538	0.54
70_R	75_S	0.537	0.54
38_Q	45_Y	0.533	0.53
23_G	47_F	0.533	0.53
5_K	14_R	0.532	0.53
41_K	44_N	0.531	0.53
45_Y	94_M	0.530	0.53
90_V	98_L	0.529	0.52
107_N	114_K	0.527	0.52
81_H	84_K	0.527	0.52
13_R	101_N	0.523	0.52
9_V	16_K	0.519	0.51
47_F	108_Q	0.519	0.51
68_A	103_L	0.514	0.50
4_V	9_V	0.514	0.50
53_K	100_V	0.514	0.50
54_K	93_K	0.511	0.50
17_V	20_L	0.510	0.50
28_K	101_N	0.506	0.49
42_S	63_T	0.504	0.49
4_V	37_Q	0.504	0.49
52_Q	59_K	0.501	0.49
74_L	79_L	0.500	0.49

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
2zjrN	1	0.9832	100	0.008	Contact Map
4rb6U	1	0.9748	100	0.01	Contact Map
3j3wQ	1	0.9832	100	0.013	Contact Map
4tp9Q	1	0.9832	100	0.034	Contact Map
3bboS	1	0.9832	100	0.049	Contact Map
2ghjA	4	0.8403	100	0.051	Contact Map
3j7yR	1	0.9832	100	0.075	Contact Map
1vx7J	1	0.8824	61.6	0.916	Contact Map
4w20G	1	0.9916	49.6	0.922	Contact Map
3j39G	1	0.9916	43.2	0.925	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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