RL23 - BACSU - GREMLIN Contacts

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RL23 - 50S ribosomal protein L23

UniProt:	P42924	Sequences: MKDPRDVLKRPVITERSADLMTEKKYTFEVDVRANKTEVKDAVESIFGVKVDKVNIMNYKGKSKRVGRYTGMTSRRRKAIVKLTADSKEIEIFEA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	95 (89)
Sequences:	2440 (1326)
Seq/√Len:	140.6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
39_V	56_I	3.415	1.00
10_R	29_E	3.158	1.00
32_V	58_N	2.582	1.00
61_G	75_R	2.542	1.00
57_M	80_I	2.434	1.00
52_D	84_T	2.422	1.00
59_Y	76_R	2.405	1.00
29_E	76_R	2.115	1.00
50_K	88_K	2.104	1.00
56_I	77_R	2.062	1.00
25_K	80_I	1.899	1.00
63_S	72_M	1.890	1.00
50_K	84_T	1.878	1.00
84_T	87_S	1.843	1.00
9_K	31_D	1.733	1.00
17_S	27_T	1.679	1.00
52_D	82_K	1.641	1.00
59_Y	78_K	1.624	1.00
63_S	70_T	1.610	1.00
12_V	29_E	1.572	1.00
66_V	69_Y	1.561	1.00
55_N	82_K	1.488	1.00
4_P	45_S	1.482	1.00
35_N	38_E	1.407	1.00
37_T	41_D	1.393	1.00
32_V	75_R	1.362	1.00
5_R	46_I	1.360	1.00
41_D	45_S	1.351	1.00
8_L	46_I	1.343	1.00
38_E	41_D	1.295	1.00
30_V	39_V	1.262	1.00
9_K	29_E	1.240	1.00
61_G	72_M	1.221	1.00
24_K	88_K	1.205	1.00
26_Y	90_I	1.168	1.00
72_M	75_R	1.157	0.99
58_N	75_R	1.138	0.99
24_K	89_E	1.112	0.99
12_V	27_T	1.105	0.99
44_E	50_K	1.073	0.99
83_L	88_K	1.065	0.99
37_T	40_K	1.057	0.99
27_T	80_I	1.055	0.99
65_R	70_T	1.053	0.99
24_K	87_S	1.052	0.99
14_T	18_A	1.023	0.99
29_E	74_S	0.986	0.98
25_K	82_K	0.984	0.98
8_L	43_V	0.965	0.98
84_T	88_K	0.965	0.98
13_I	18_A	0.958	0.98
20_L	27_T	0.953	0.98
48_G	88_K	0.939	0.98
25_K	55_N	0.931	0.98
51_V	54_V	0.858	0.96
18_A	21_M	0.852	0.96
57_M	78_K	0.851	0.96
43_V	51_V	0.849	0.96
52_D	85_A	0.837	0.95
4_P	7_V	0.828	0.95
29_E	78_K	0.824	0.95
60_K	76_R	0.815	0.95
48_G	87_S	0.808	0.94
32_V	74_S	0.803	0.94
66_V	71_G	0.795	0.94
45_S	48_G	0.784	0.93
43_V	81_V	0.784	0.93
28_F	90_I	0.782	0.93
52_D	55_N	0.759	0.92
16_R	19_D	0.758	0.92
25_K	53_K	0.749	0.92
29_E	32_V	0.743	0.92
20_L	25_K	0.740	0.91
38_E	42_A	0.739	0.91
18_A	93_F	0.728	0.91
35_N	54_V	0.725	0.91
19_D	22_T	0.724	0.90
6_D	9_K	0.712	0.90
60_K	75_R	0.705	0.89
44_E	51_V	0.700	0.89
42_A	79_A	0.679	0.87
43_V	54_V	0.674	0.87
26_Y	89_E	0.672	0.87
21_M	93_F	0.668	0.87
63_S	66_V	0.662	0.86
43_V	46_I	0.655	0.85
11_P	49_V	0.654	0.85
52_D	83_L	0.652	0.85
64_K	71_G	0.648	0.85
60_K	74_S	0.645	0.85
19_D	91_E	0.644	0.85
62_K	73_T	0.644	0.85
85_A	88_K	0.641	0.84
21_M	92_I	0.639	0.84
40_K	44_E	0.624	0.83
17_S	65_R	0.617	0.82
90_I	93_F	0.617	0.82
61_G	73_T	0.614	0.82
4_P	41_D	0.610	0.81
24_K	52_D	0.609	0.81
20_L	23_E	0.606	0.81
19_D	23_E	0.603	0.80
17_S	46_I	0.600	0.80
20_L	80_I	0.598	0.80
5_R	9_K	0.586	0.79
5_R	41_D	0.585	0.78
35_N	41_D	0.576	0.77
36_K	65_R	0.571	0.77
67_G	71_G	0.566	0.76
12_V	17_S	0.566	0.76
34_A	42_A	0.565	0.76
59_Y	73_T	0.562	0.76
43_V	90_I	0.560	0.75
15_E	91_E	0.548	0.74
88_K	91_E	0.545	0.73
69_Y	91_E	0.543	0.73
33_R	77_R	0.540	0.73
52_D	88_K	0.538	0.72
7_V	43_V	0.536	0.72
38_E	45_S	0.532	0.72
54_V	81_V	0.531	0.72
26_Y	93_F	0.529	0.71
56_I	79_A	0.526	0.71
7_V	42_A	0.523	0.70
57_M	60_K	0.522	0.70
44_E	54_V	0.521	0.70
89_E	92_I	0.520	0.70
18_A	27_T	0.520	0.70
60_K	63_S	0.519	0.70
66_V	70_T	0.511	0.69
64_K	73_T	0.509	0.68
11_P	67_G	0.504	0.68
13_I	16_R	0.501	0.67
24_K	84_T	0.500	0.67

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
2zjrQ	1	0.9684	100	0.128	Contact Map
3j3wT	1	0.9895	100	0.133	Contact Map
4btdX	1	0.9579	100	0.151	Contact Map
4tp9T	1	0.9368	100	0.174	Contact Map
3j39X	1	0.8526	99.9	0.292	Contact Map
4a17R	1	0.8632	99.9	0.299	Contact Map
1vx7Y	1	0.8526	99.9	0.304	Contact Map
4ujrK	1	0.8632	99.9	0.309	Contact Map
2go54	1	0.8211	99.9	0.309	Contact Map
3zf7X	1	0.8632	99.9	0.313	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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