RL44E - HALSA - GREMLIN Contacts

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RL44E - 50S ribosomal protein L44e

UniProt:	Q9HRT6	Sequences: MEMPRRFNSYCPNCDEHHQLEAEKVRSGRSSGMKWDARRTKRANASIGNHGRFSKVPVGNKPTNRTDLKYRCSECGNAHLREGWRAGRLVLQE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	93 (89)
Sequences:	371 (174)
Seq/√Len:	18.5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
27_S	30_S	4.684	1.00
30_S	37_A	3.698	1.00
71_R	78_A	3.034	0.99
11_C	75_C	2.861	0.99
37_A	41_K	2.487	0.96
9_S	20_L	2.197	0.93
11_C	14_C	2.148	0.92
14_C	75_C	2.014	0.89
66_T	89_L	1.977	0.88
40_T	43_A	1.853	0.85
6_R	19_Q	1.826	0.84
32_G	37_A	1.772	0.82
21_E	26_R	1.760	0.82
43_A	52_R	1.664	0.78
41_K	52_R	1.613	0.75
39_R	54_S	1.575	0.74
40_T	52_R	1.527	0.71
15_D	77_N	1.491	0.69
85_R	90_V	1.431	0.66
74_E	81_R	1.397	0.64
31_S	35_W	1.371	0.63
11_C	17_H	1.364	0.62
31_S	37_A	1.326	0.60
15_D	19_Q	1.308	0.59
12_P	77_N	1.302	0.59
16_E	74_E	1.300	0.58
44_N	50_H	1.286	0.58
18_H	76_G	1.245	0.55
76_G	80_L	1.172	0.51
42_R	88_R	1.169	0.50
2_E	5_R	1.113	0.47
10_Y	16_E	1.112	0.47
38_R	72_C	1.093	0.46
3_M	68_L	1.092	0.46
73_S	82_E	1.084	0.45
36_D	40_T	1.084	0.45
13_N	74_E	1.074	0.44
37_A	51_G	1.070	0.44
24_K	58_V	1.057	0.43
42_R	45_A	1.041	0.42
10_Y	19_Q	1.024	0.41
3_M	9_S	1.023	0.41
36_D	39_R	1.004	0.40
15_D	18_H	1.003	0.40
67_D	91_L	0.999	0.40
61_K	64_N	0.998	0.40
36_D	54_S	0.996	0.40
70_Y	79_H	0.993	0.40
62_P	78_A	0.983	0.39
3_M	6_R	0.969	0.38
36_D	49_N	0.962	0.38
49_N	54_S	0.955	0.37
14_C	61_K	0.946	0.37
51_G	56_V	0.880	0.33
49_N	56_V	0.879	0.33
38_R	61_K	0.866	0.32
49_N	57_P	0.862	0.32
38_R	75_C	0.862	0.32
5_R	91_L	0.860	0.32
2_E	88_R	0.859	0.32
12_P	81_R	0.855	0.32
55_K	77_N	0.849	0.31
29_R	90_V	0.838	0.31
69_K	78_A	0.837	0.31
40_T	44_N	0.837	0.31
5_R	68_L	0.833	0.30
44_N	51_G	0.832	0.30
77_N	80_L	0.830	0.30
11_C	63_T	0.824	0.30
42_R	90_V	0.814	0.29
70_Y	82_E	0.813	0.29
17_H	22_A	0.813	0.29
48_G	52_R	0.813	0.29
19_Q	80_L	0.793	0.28
25_V	78_A	0.790	0.28
42_R	47_I	0.771	0.27
21_E	71_R	0.768	0.27
37_A	42_R	0.765	0.27
8_N	77_N	0.759	0.27
58_V	89_L	0.744	0.26
68_L	71_R	0.716	0.25
2_E	64_N	0.715	0.25
38_R	48_G	0.712	0.24
22_A	68_L	0.705	0.24
31_S	34_K	0.698	0.24
55_K	59_G	0.692	0.24
43_A	50_H	0.691	0.24
18_H	80_L	0.681	0.23
8_N	69_K	0.679	0.23
19_Q	79_H	0.676	0.23
16_E	89_L	0.668	0.23
14_C	17_H	0.667	0.22
56_V	59_G	0.665	0.22
40_T	51_G	0.665	0.22
6_R	82_E	0.664	0.22
28_G	65_R	0.646	0.22
79_H	83_G	0.632	0.21
5_R	14_C	0.632	0.21
73_S	79_H	0.627	0.21
11_C	38_R	0.627	0.21
61_K	72_C	0.618	0.20
80_L	88_R	0.609	0.20
67_D	71_R	0.607	0.20
19_Q	73_S	0.601	0.20
39_R	42_R	0.598	0.20
12_P	79_H	0.597	0.20
69_K	74_E	0.587	0.19
12_P	33_M	0.585	0.19
3_M	10_Y	0.584	0.19
6_R	89_L	0.584	0.19
18_H	78_A	0.580	0.19
35_W	52_R	0.577	0.19
72_C	90_V	0.574	0.19
57_P	77_N	0.562	0.18
41_K	44_N	0.559	0.18
21_E	45_A	0.555	0.18
20_L	33_M	0.554	0.18
49_N	59_G	0.535	0.17
42_R	52_R	0.532	0.17
36_D	46_S	0.531	0.17
43_A	51_G	0.529	0.17
44_N	52_R	0.528	0.17
61_K	85_R	0.527	0.17
71_R	76_G	0.527	0.17
70_Y	80_L	0.523	0.17
62_P	66_T	0.519	0.17
60_N	65_R	0.519	0.17
34_K	60_N	0.518	0.17
79_H	91_L	0.515	0.17
13_N	55_K	0.515	0.17
10_Y	33_M	0.507	0.16
2_E	63_T	0.507	0.16
40_T	50_H	0.504	0.16
73_S	77_N	0.500	0.16

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
3j21j	1	0.9892	100	0.09	Contact Map
4a18C	1	0.9892	100	0.093	Contact Map
1vx7i	1	0.9892	100	0.097	Contact Map
1vq83	1	0.9785	100	0.098	Contact Map
3j39o	1	0.9892	100	0.101	Contact Map
3zf7t	1	0.9892	100	0.105	Contact Map
4ujrb	1	0.9892	100	0.116	Contact Map
1vw4X	1	0.4301	84.4	0.89	Contact Map
4rb66	1	0.2688	61	0.909	Contact Map
4tp91	1	0.2581	59.6	0.909	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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