RL21 - HALSA - GREMLIN Contacts

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RL21 - 50S ribosomal protein L21e

UniProt:	Q9HQG8	Sequences: MPNSNGPLSNSGGKLQNDPRDRGTSPPQRAIADYDDGESVHLTLDPSVQDGRFHPRFSGLTGTVVGTQGDAFKVEVNDGGMDKTLIVGAAHLRTQRQEE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	99 (96)
Sequences:	489 (271)
Seq/√Len:	27.6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
2_P	10_N	2.936	1.00
2_P	5_N	2.827	1.00
3_N	9_S	2.648	0.99
17_N	45_D	2.601	0.99
72_F	92_L	2.257	0.98
12_G	88_G	2.164	0.98
32_A	94_T	2.156	0.98
79_G	82_D	2.128	0.97
29_R	45_D	2.086	0.97
8_L	62_G	2.009	0.96
43_T	58_S	1.991	0.96
2_P	9_S	1.886	0.95
34_Y	94_T	1.858	0.94
40_V	59_G	1.734	0.92
5_N	9_S	1.724	0.92
65_V	86_I	1.693	0.91
10_N	13_G	1.650	0.90
39_S	94_T	1.640	0.89
9_S	63_T	1.614	0.89
59_G	62_G	1.556	0.87
39_S	63_T	1.547	0.86
66_G	86_I	1.524	0.86
17_N	46_P	1.489	0.84
41_H	61_T	1.481	0.84
18_D	21_D	1.476	0.84
4_S	71_A	1.472	0.84
42_L	60_L	1.400	0.80
4_S	9_S	1.397	0.80
75_E	86_I	1.381	0.79
3_N	44_L	1.343	0.77
15_L	62_G	1.334	0.77
66_G	92_L	1.285	0.74
3_N	49_Q	1.249	0.72
36_D	70_D	1.230	0.71
60_L	63_T	1.197	0.69
23_G	74_V	1.183	0.68
30_A	89_A	1.182	0.68
73_K	86_I	1.133	0.64
71_A	77_N	1.111	0.63
23_G	37_G	1.102	0.62
46_P	63_T	1.100	0.62
40_V	91_H	1.093	0.61
41_H	95_Q	1.091	0.61
70_D	84_T	1.078	0.60
43_T	93_R	1.059	0.59
80_G	84_T	1.048	0.58
35_D	38_E	1.048	0.58
14_K	55_P	1.041	0.58
17_N	53_F	1.020	0.56
37_G	40_V	1.013	0.56
39_S	49_Q	0.997	0.54
25_S	48_V	0.991	0.54
25_S	28_Q	0.974	0.53
88_G	91_H	0.961	0.52
1_M	6_G	0.959	0.51
26_P	48_V	0.956	0.51
20_R	23_G	0.927	0.49
47_S	74_V	0.921	0.49
21_D	33_D	0.917	0.48
1_M	4_S	0.908	0.48
11_S	58_S	0.904	0.47
68_Q	86_I	0.893	0.46
5_N	10_N	0.883	0.46
59_G	91_H	0.879	0.45
68_Q	92_L	0.870	0.45
50_D	91_H	0.867	0.44
3_N	10_N	0.861	0.44
29_R	93_R	0.858	0.44
35_D	75_E	0.853	0.43
25_S	46_P	0.852	0.43
21_D	24_T	0.851	0.43
17_N	26_P	0.844	0.43
45_D	56_R	0.807	0.40
21_D	72_F	0.806	0.40
8_L	42_L	0.785	0.38
37_G	88_G	0.779	0.38
14_K	96_R	0.774	0.38
40_V	52_R	0.760	0.37
36_D	69_G	0.760	0.37
35_D	60_L	0.753	0.36
3_N	55_P	0.747	0.36
18_D	75_E	0.746	0.36
16_Q	72_F	0.742	0.35
19_P	88_G	0.733	0.35
14_K	76_V	0.733	0.35
36_D	44_L	0.724	0.34
78_D	83_K	0.722	0.34
12_G	74_V	0.722	0.34
66_G	83_K	0.722	0.34
43_T	57_F	0.717	0.34
12_G	47_S	0.715	0.33
25_S	31_I	0.711	0.33
40_V	87_V	0.702	0.33
56_R	79_G	0.697	0.32
29_R	55_P	0.695	0.32
11_S	15_L	0.690	0.32
77_N	85_L	0.682	0.31
42_L	50_D	0.681	0.31
73_K	84_T	0.664	0.30
29_R	32_A	0.659	0.30
28_Q	36_D	0.647	0.29
48_V	70_D	0.646	0.29
78_D	95_Q	0.642	0.29
41_H	50_D	0.639	0.29
51_G	59_G	0.630	0.28
2_P	50_D	0.627	0.28
5_N	82_D	0.625	0.28
33_D	36_D	0.623	0.28
17_N	29_R	0.621	0.27
36_D	63_T	0.620	0.27
52_R	57_F	0.619	0.27
33_D	46_P	0.618	0.27
90_A	95_Q	0.616	0.27
28_Q	31_I	0.611	0.27
39_S	96_R	0.610	0.27
40_V	53_F	0.606	0.27
15_L	72_F	0.600	0.26
68_Q	73_K	0.598	0.26
44_L	94_T	0.598	0.26
13_G	85_L	0.595	0.26
33_D	79_G	0.580	0.25
22_R	79_G	0.579	0.25
18_D	67_T	0.578	0.25
39_S	67_T	0.574	0.25
80_G	87_V	0.567	0.24
70_D	77_N	0.567	0.24
51_G	61_T	0.549	0.23
78_D	87_V	0.549	0.23
10_N	38_E	0.546	0.23
15_L	64_V	0.544	0.23
57_F	78_D	0.543	0.23
8_L	59_G	0.538	0.23
40_V	51_G	0.536	0.23
53_F	58_S	0.536	0.23
12_G	83_K	0.533	0.22
52_R	91_H	0.530	0.22
11_S	61_T	0.530	0.22
7_P	47_S	0.529	0.22
2_P	14_K	0.529	0.22
64_V	70_D	0.518	0.22
25_S	30_A	0.513	0.21
73_K	80_G	0.511	0.21
50_D	82_D	0.510	0.21
22_R	64_V	0.500	0.21

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
3zf7U	1	0.9899	100	0.04	Contact Map
3j61T	1	1	100	0.046	Contact Map
1vq8Q	1	0.9596	100	0.049	Contact Map
4w20T	1	0.9899	100	0.051	Contact Map
4a17P	1	0.9899	100	0.051	Contact Map
1vx7V	1	0.9798	100	0.059	Contact Map
3j21R	1	0.9596	100	0.062	Contact Map
3jywQ	1	0.9899	100	0.065	Contact Map
4ujrG	1	0.9899	100	0.066	Contact Map
2do3A	1	0.697	47.6	0.919	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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