RL13 - HALSA - GREMLIN Contacts

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RL13 - 50S ribosomal protein L13

UniProt:	Q9HQJ3	Sequences: MSLAEFDADVVVDARDCIMGRVASNVAERALAGDRVAVVNAEQAVITGTEDDVFSTYRTRANLGSDRGPYYPKRPDGIFKRAIRGMLPYKQDDGREALDSVRVYVGNPMDEDGDVLDGTSLDRLSTIRFVTLSEVSEELGANVTW	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	145 (136)
Sequences:	430 (292)
Seq/√Len:	25.1

HALSA - RL13
SULSO - RL13

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
30_A	101_V	4.881	1.00
14_A	44_A	4.268	1.00
79_F	83_I	4.126	1.00
79_F	132_L	3.730	1.00
14_A	38_V	3.641	1.00
78_I	136_S	3.286	1.00
41_A	103_V	3.027	1.00
19_M	82_A	2.993	1.00
26_V	79_F	2.916	1.00
38_V	79_F	2.729	0.99
134_E	138_E	2.654	0.99
30_A	87_L	2.564	0.99
83_I	101_V	2.563	0.99
31_L	97_A	2.445	0.99
46_I	135_V	2.273	0.98
57_Y	82_A	2.166	0.97
10_V	36_V	1.981	0.95
104_Y	111_E	1.829	0.92
58_R	62_N	1.739	0.90
29_R	32_A	1.716	0.89
15_R	43_Q	1.590	0.85
64_G	67_R	1.578	0.85
35_R	100_S	1.566	0.84
19_M	57_Y	1.470	0.80
37_A	111_E	1.364	0.75
53_V	130_V	1.358	0.74
46_I	53_V	1.326	0.73
118_G	122_D	1.318	0.72
44_A	57_Y	1.291	0.71
87_L	98_L	1.288	0.70
38_V	137_E	1.254	0.68
10_V	13_D	1.237	0.67
27_A	97_A	1.232	0.67
38_V	90_K	1.226	0.66
52_D	56_T	1.207	0.65
21_R	40_N	1.194	0.64
119_T	123_R	1.182	0.64
109_M	132_L	1.173	0.63
29_R	36_V	1.164	0.62
130_V	135_V	1.147	0.61
135_V	139_L	1.147	0.61
27_A	31_L	1.138	0.61
22_V	79_F	1.137	0.61
28_E	31_L	1.136	0.60
40_N	43_Q	1.132	0.60
80_K	87_L	1.089	0.57
61_A	70_Y	1.089	0.57
50_E	134_E	1.070	0.56
84_R	106_G	1.064	0.55
24_S	43_Q	1.058	0.55
8_A	12_V	1.056	0.55
85_G	106_G	1.047	0.54
45_V	119_T	1.015	0.52
104_Y	110_D	1.011	0.52
72_P	107_N	1.008	0.51
39_V	111_E	1.008	0.51
50_E	55_S	1.008	0.51
13_D	134_E	1.003	0.51
13_D	40_N	1.001	0.51
49_T	53_V	0.975	0.49
60_R	65_S	0.974	0.49
11_V	107_N	0.964	0.48
64_G	68_G	0.959	0.48
60_R	71_Y	0.949	0.47
19_M	46_I	0.938	0.46
68_G	71_Y	0.937	0.46
87_L	129_F	0.917	0.45
71_Y	141_A	0.913	0.44
13_D	73_K	0.898	0.43
61_A	65_S	0.884	0.42
12_V	36_V	0.873	0.42
46_I	80_K	0.871	0.41
107_N	115_V	0.868	0.41
47_T	141_A	0.866	0.41
56_T	98_L	0.863	0.41
136_S	141_A	0.851	0.40
81_R	84_R	0.847	0.40
137_E	143_V	0.845	0.40
136_S	140_G	0.842	0.39
42_E	85_G	0.834	0.39
42_E	106_G	0.820	0.38
39_V	107_N	0.820	0.38
43_Q	131_T	0.817	0.38
44_A	130_V	0.816	0.38
33_G	140_G	0.809	0.37
44_A	66_D	0.808	0.37
14_A	87_L	0.806	0.37
64_G	71_Y	0.801	0.37
92_D	95_R	0.800	0.37
25_N	29_R	0.800	0.37
9_D	61_A	0.796	0.36
134_E	137_E	0.781	0.35
78_I	82_A	0.781	0.35
35_R	102_R	0.778	0.35
59_T	64_G	0.778	0.35
21_R	106_G	0.775	0.35
61_A	128_R	0.773	0.35
53_V	56_T	0.770	0.35
72_P	80_K	0.768	0.34
47_T	51_D	0.757	0.34
21_R	81_R	0.757	0.34
36_V	134_E	0.753	0.33
87_L	126_T	0.753	0.33
98_L	139_L	0.751	0.33
34_D	49_T	0.747	0.33
102_R	110_D	0.741	0.33
89_Y	98_L	0.739	0.33
62_N	70_Y	0.738	0.32
18_I	47_T	0.738	0.32
49_T	52_D	0.736	0.32
61_A	64_G	0.731	0.32
84_R	89_Y	0.731	0.32
118_G	123_R	0.725	0.32
56_T	133_S	0.722	0.31
14_A	22_V	0.721	0.31
95_R	99_D	0.718	0.31
30_A	137_E	0.718	0.31
10_V	32_A	0.718	0.31
75_P	141_A	0.717	0.31
51_D	55_S	0.710	0.31
17_C	37_A	0.708	0.31
67_R	98_L	0.705	0.30
11_V	39_V	0.698	0.30
29_R	34_D	0.697	0.30
27_A	100_S	0.695	0.30
19_M	79_F	0.693	0.30
15_R	132_L	0.691	0.30
35_R	135_V	0.691	0.30
66_D	87_L	0.686	0.29
8_A	34_D	0.685	0.29
45_V	53_V	0.683	0.29
99_D	132_L	0.682	0.29
18_I	51_D	0.676	0.29
74_R	141_A	0.675	0.29
24_S	99_D	0.675	0.29
35_R	96_E	0.673	0.28
43_Q	87_L	0.672	0.28
44_A	83_I	0.672	0.28
29_R	35_R	0.669	0.28
11_V	78_I	0.669	0.28
130_V	137_E	0.667	0.28
50_E	137_E	0.662	0.28
87_L	135_V	0.658	0.28
30_A	83_I	0.650	0.27
93_D	97_A	0.643	0.27
64_G	78_I	0.641	0.27
61_A	67_R	0.639	0.27
95_R	101_V	0.635	0.26
70_Y	87_L	0.635	0.26
74_R	105_V	0.634	0.26
18_I	80_K	0.633	0.26
47_T	123_R	0.633	0.26
18_I	55_S	0.630	0.26
104_Y	124_L	0.630	0.26
85_G	88_P	0.628	0.26
54_F	138_E	0.624	0.26
55_S	82_A	0.622	0.26
106_G	140_G	0.619	0.25
25_N	28_E	0.619	0.25
94_G	97_A	0.614	0.25
123_R	129_F	0.609	0.25
8_A	58_R	0.609	0.25
50_E	135_V	0.609	0.25
81_R	90_K	0.602	0.24
22_V	132_L	0.601	0.24
34_D	110_D	0.601	0.24
17_C	22_V	0.601	0.24
10_V	29_R	0.599	0.24
39_V	110_D	0.598	0.24
68_G	81_R	0.596	0.24
27_A	81_R	0.594	0.24
43_Q	142_N	0.582	0.23
75_P	136_S	0.580	0.23
70_Y	99_D	0.580	0.23
11_V	29_R	0.578	0.23
93_D	116_L	0.570	0.23
82_A	113_G	0.559	0.22
57_Y	131_T	0.558	0.22
120_S	135_V	0.556	0.22
46_I	107_N	0.554	0.22
17_C	47_T	0.550	0.22
65_S	70_Y	0.542	0.21
46_I	130_V	0.541	0.21
59_T	62_N	0.538	0.21
87_L	132_L	0.538	0.21
107_N	114_D	0.537	0.21
103_V	142_N	0.535	0.21
25_N	109_M	0.535	0.21
71_Y	127_I	0.534	0.21
47_T	124_L	0.533	0.21
17_C	141_A	0.532	0.21
15_R	40_N	0.528	0.21
11_V	116_L	0.527	0.21
37_A	102_R	0.521	0.20
30_A	103_V	0.518	0.20
133_S	139_L	0.514	0.20
95_R	102_R	0.509	0.20
18_I	123_R	0.508	0.20
133_S	142_N	0.508	0.20
12_V	26_V	0.507	0.20
45_V	51_D	0.507	0.20
36_V	115_V	0.502	0.20
55_S	135_V	0.500	0.19
89_Y	127_I	0.500	0.19

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
1vq8J	1	0.9793	100	0.28	Contact Map
4cuwO	1	0.9655	100	0.301	Contact Map
4ujrB	1	0.9655	100	0.304	Contact Map
3j39O	1	0.9931	100	0.306	Contact Map
4w20O	1	0.9655	100	0.312	Contact Map
3j61O	1	1	100	0.312	Contact Map
4a17I	1	0.9724	100	0.317	Contact Map
1vx7K	1	0.9724	100	0.319	Contact Map
3zf7O	1	0.9586	100	0.335	Contact Map
1j3aA	1	0.8483	100	0.345	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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