RL23 - HALSA - GREMLIN Contacts

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RL23 - 50S ribosomal protein L23P

UniProt:	Q06842	Sequences: MSSIIDYPLVTEKAMDEMDFQNKLQFIVDIDAAKPEIRDVVESEYDVTVVDVNTQITPEAEKKATVKLSAEDDAQDVASRIGVF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	84 (80)
Sequences:	566 (293)
Seq/√Len:	32.8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
42_E	48_T	4.077	1.00
33_A	36_E	3.616	1.00
16_D	20_F	2.928	1.00
40_V	44_E	2.532	1.00
24_L	77_V	2.496	1.00
64_A	76_D	1.986	0.98
39_D	43_S	1.981	0.98
23_K	60_A	1.836	0.96
34_K	37_I	1.790	0.96
10_V	83_V	1.728	0.95
39_D	50_V	1.712	0.94
53_N	56_I	1.636	0.93
18_M	24_L	1.627	0.93
12_E	41_V	1.596	0.92
41_V	66_V	1.581	0.92
9_L	14_A	1.502	0.89
13_K	65_T	1.455	0.88
5_I	44_E	1.449	0.88
10_V	72_D	1.442	0.87
6_D	61_E	1.419	0.87
8_P	26_F	1.383	0.85
17_E	73_D	1.308	0.82
28_V	74_A	1.295	0.81
9_L	43_S	1.285	0.80
22_N	53_N	1.262	0.79
12_E	22_N	1.243	0.78
7_Y	61_E	1.229	0.77
19_D	83_V	1.228	0.77
28_V	49_V	1.183	0.75
61_E	67_K	1.176	0.74
67_K	82_G	1.175	0.74
6_D	10_V	1.133	0.71
18_M	67_K	1.123	0.71
28_V	76_D	1.092	0.68
45_Y	77_V	1.074	0.67
15_M	83_V	1.073	0.67
5_I	41_V	1.070	0.67
20_F	24_L	1.033	0.64
75_Q	79_S	1.023	0.63
47_V	68_L	1.020	0.63
19_D	82_G	1.008	0.62
36_E	39_D	1.003	0.62
14_A	29_D	0.987	0.60
67_K	71_E	0.983	0.60
13_K	83_V	0.968	0.59
49_V	65_T	0.959	0.58
19_D	32_A	0.957	0.58
11_T	80_R	0.955	0.58
46_D	61_E	0.928	0.56
8_P	32_A	0.927	0.56
40_V	58_P	0.923	0.55
17_E	38_R	0.916	0.55
26_F	74_A	0.914	0.55
47_V	56_I	0.887	0.52
73_D	79_S	0.882	0.52
10_V	75_Q	0.861	0.50
16_D	75_Q	0.853	0.50
42_E	73_D	0.830	0.48
8_P	78_A	0.830	0.48
49_V	69_S	0.809	0.46
37_I	54_T	0.800	0.45
16_D	83_V	0.798	0.45
21_Q	33_A	0.785	0.44
75_Q	83_V	0.779	0.43
54_T	76_D	0.779	0.43
46_D	51_D	0.779	0.43
39_D	52_V	0.774	0.43
42_E	69_S	0.762	0.42
10_V	14_A	0.762	0.42
22_N	62_K	0.762	0.42
48_T	69_S	0.748	0.41
52_V	64_A	0.735	0.40
30_I	57_T	0.726	0.39
41_V	80_R	0.726	0.39
22_N	45_Y	0.709	0.38
12_E	24_L	0.688	0.36
46_D	71_E	0.681	0.36
26_F	78_A	0.674	0.35
17_E	70_A	0.673	0.35
39_D	61_E	0.666	0.35
39_D	48_T	0.660	0.34
26_F	46_D	0.657	0.34
26_F	40_V	0.656	0.34
22_N	47_V	0.654	0.34
27_I	30_I	0.650	0.33
39_D	69_S	0.646	0.33
25_Q	53_N	0.642	0.33
79_S	83_V	0.631	0.32
46_D	50_V	0.622	0.31
62_K	78_A	0.620	0.31
32_A	54_T	0.618	0.31
15_M	46_D	0.616	0.31
51_D	77_V	0.615	0.31
13_K	27_I	0.608	0.30
49_V	61_E	0.606	0.30
19_D	55_Q	0.603	0.30
75_Q	78_A	0.600	0.30
35_P	49_V	0.597	0.30
38_R	52_V	0.593	0.29
12_E	47_V	0.583	0.29
17_E	71_E	0.576	0.28
17_E	72_D	0.569	0.28
8_P	45_Y	0.556	0.27
58_P	78_A	0.554	0.27
6_D	67_K	0.544	0.26
4_I	61_E	0.536	0.26
26_F	32_A	0.534	0.25
4_I	35_P	0.529	0.25
52_V	76_D	0.527	0.25
35_P	48_T	0.517	0.24
31_D	36_E	0.516	0.24
60_A	77_V	0.515	0.24
9_L	80_R	0.514	0.24
34_K	58_P	0.514	0.24
28_V	71_E	0.513	0.24
17_E	79_S	0.509	0.24
6_D	31_D	0.509	0.24
27_I	63_K	0.508	0.24
34_K	64_A	0.505	0.24
18_M	78_A	0.500	0.23

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
3zf7X	1	1	100	0.178	Contact Map
3j39X	1	1	100	0.178	Contact Map
4ujrK	1	1	100	0.185	Contact Map
4a17R	1	1	100	0.186	Contact Map
4w20X	1	1	100	0.189	Contact Map
3bboV	1	1	100	0.192	Contact Map
2go54	1	0.9643	100	0.192	Contact Map
1vx7Y	1	0.9762	100	0.199	Contact Map
3j21T	1	1	100	0.207	Contact Map
1vq8S	1	0.0119	100	0.21	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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