RL5 - HALSA - GREMLIN Contacts

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RL5 - 50S ribosomal protein L5

UniProt:	P50558	Sequences: MSETDSTDFHEMREPRIEKVVVHMGVGQGGVELQNAETILEAITGQQTVRTKAKSPEPEFGLRQGDPIGAKVTLRDDTAVDFLERALPAADLDRRQFDNTGNVSFGIEEHTDFPSQEYDPNIGIYGMDVTVNLTRPGYRVAKRDQGTRQIPSNHRLNSEDAVSFLVSNFDVEVNE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	175 (140)
Sequences:	2392 (996)
Seq/√Len:	84.2

ECOLI - RL5
BACSU - RL5
HALSA - RL5
SULSO - RL5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
22_V	44_T	3.782	1.00
104_S	130_T	3.506	1.00
5_D	143_R	2.953	1.00
21_V	132_N	2.686	1.00
8_D	140_V	2.584	1.00
20_V	83_L	2.563	1.00
107_I	112_D	2.543	1.00
99_N	138_Y	2.429	1.00
84_E	88_P	2.299	1.00
24_M	36_A	2.288	1.00
17_I	131_V	2.287	1.00
51_T	71_K	2.263	1.00
41_E	47_Q	2.238	1.00
117_E	120_P	2.163	1.00
83_L	87_L	2.040	1.00
86_A	105_F	2.026	1.00
81_D	85_R	1.927	1.00
41_E	48_T	1.915	1.00
94_R	142_K	1.898	1.00
8_D	137_G	1.893	1.00
24_M	40_L	1.848	1.00
53_A	56_P	1.816	1.00
83_L	131_V	1.795	1.00
52_K	67_P	1.772	1.00
30_G	68_I	1.723	1.00
13_R	136_P	1.708	1.00
37_E	50_R	1.690	1.00
50_R	67_P	1.656	1.00
139_R	142_K	1.646	1.00
62_L	68_I	1.606	1.00
53_A	65_G	1.564	1.00
137_G	140_V	1.548	1.00
20_V	87_L	1.529	1.00
33_L	70_A	1.519	1.00
18_E	134_T	1.510	0.99
110_H	125_Y	1.464	0.99
22_V	127_M	1.451	0.99
40_L	70_A	1.416	0.99
51_T	69_G	1.387	0.99
26_V	36_A	1.384	0.99
111_T	118_Y	1.367	0.99
93_D	96_Q	1.335	0.99
37_E	41_E	1.333	0.99
39_I	125_Y	1.311	0.99
92_L	96_Q	1.304	0.98
71_K	128_D	1.293	0.98
96_Q	128_D	1.281	0.98
5_D	139_R	1.265	0.98
98_D	102_N	1.259	0.98
109_E	124_I	1.257	0.98
38_T	41_E	1.245	0.98
122_I	125_Y	1.237	0.98
35_N	39_I	1.218	0.98
74_L	82_F	1.210	0.98
92_L	105_F	1.206	0.97
26_V	33_L	1.189	0.97
24_M	125_Y	1.169	0.97
34_Q	38_T	1.169	0.97
17_I	83_L	1.159	0.97
18_E	21_V	1.148	0.97
81_D	84_E	1.146	0.97
56_P	64_Q	1.143	0.96
49_V	71_K	1.141	0.96
111_T	124_I	1.127	0.96
11_E	14_E	1.093	0.95
23_H	128_D	1.067	0.95
35_N	122_I	1.052	0.94
22_V	40_L	1.051	0.94
38_T	42_A	1.019	0.93
6_S	140_V	1.019	0.93
28_Q	123_G	1.011	0.93
37_E	70_A	1.007	0.93
4_T	7_T	1.003	0.93
24_M	70_A	0.983	0.92
36_A	70_A	0.971	0.92
100_T	138_Y	0.961	0.91
8_D	13_R	0.956	0.91
30_G	33_L	0.947	0.91
30_G	62_L	0.931	0.90
96_Q	105_F	0.928	0.90
6_S	143_R	0.921	0.89
26_V	41_E	0.916	0.89
35_N	118_Y	0.888	0.88
20_V	131_V	0.881	0.87
10_H	107_I	0.878	0.87
90_A	112_D	0.869	0.86
46_Q	78_T	0.864	0.86
41_E	44_T	0.860	0.86
118_Y	122_I	0.857	0.86
107_I	128_D	0.855	0.86
23_H	108_E	0.853	0.85
120_P	123_G	0.851	0.85
5_D	8_D	0.849	0.85
118_Y	125_Y	0.841	0.85
22_V	86_A	0.831	0.84
13_R	135_R	0.813	0.83
135_R	140_V	0.794	0.81
28_Q	125_Y	0.788	0.81
136_P	140_V	0.785	0.80
62_L	66_D	0.778	0.80
42_A	120_P	0.774	0.79
96_Q	103_V	0.771	0.79
95_R	139_R	0.765	0.79
125_Y	128_D	0.760	0.78
92_L	103_V	0.750	0.77
56_P	65_G	0.741	0.76
39_I	110_H	0.737	0.76
40_L	44_T	0.736	0.76
37_E	48_T	0.736	0.76
15_P	133_L	0.733	0.76
119_D	128_D	0.733	0.76
109_E	119_D	0.728	0.75
24_M	128_D	0.727	0.75
90_A	107_I	0.722	0.74
104_S	128_D	0.719	0.74
134_T	142_K	0.717	0.74
25_G	69_G	0.716	0.74
51_T	57_E	0.709	0.73
16_R	80_V	0.706	0.73
24_M	39_I	0.705	0.73
110_H	131_V	0.704	0.73
82_F	113_F	0.703	0.72
57_E	104_S	0.697	0.72
28_Q	32_E	0.694	0.72
100_T	139_R	0.690	0.71
51_T	119_D	0.686	0.71
18_E	132_N	0.679	0.70
30_G	66_D	0.678	0.70
99_N	133_L	0.677	0.70
40_L	72_V	0.675	0.69
30_G	104_S	0.669	0.69
77_D	81_D	0.669	0.69
44_T	48_T	0.662	0.68
60_F	82_F	0.659	0.68
92_L	95_R	0.659	0.68
15_P	90_A	0.653	0.67
31_V	59_E	0.648	0.66
12_M	24_M	0.648	0.66
139_R	143_R	0.645	0.66
11_E	43_I	0.645	0.66
77_D	80_V	0.645	0.66
17_I	20_V	0.635	0.65
21_V	71_K	0.631	0.64
97_F	102_N	0.627	0.64
31_V	107_I	0.626	0.64
26_V	29_G	0.619	0.63
103_V	110_H	0.618	0.63
23_H	104_S	0.613	0.62
97_F	103_V	0.612	0.62
12_M	111_T	0.611	0.62
27_G	63_R	0.610	0.62
26_V	68_I	0.599	0.60
59_E	62_L	0.597	0.60
94_R	139_R	0.593	0.59
93_D	97_F	0.593	0.59
133_L	141_A	0.589	0.59
10_H	14_E	0.587	0.59
42_A	76_D	0.587	0.59
53_A	66_D	0.587	0.59
123_G	143_R	0.586	0.59
17_I	132_N	0.577	0.57
29_G	33_L	0.576	0.57
44_T	110_H	0.575	0.57
18_E	71_K	0.575	0.57
33_L	110_H	0.573	0.57
39_I	122_I	0.572	0.57
32_E	81_D	0.571	0.57
24_M	53_A	0.570	0.56
26_V	51_T	0.569	0.56
5_D	9_F	0.567	0.56
76_D	83_L	0.567	0.56
59_E	118_Y	0.564	0.56
76_D	105_F	0.563	0.56
22_V	66_D	0.557	0.55
104_S	132_N	0.555	0.55
49_V	80_V	0.555	0.55
104_S	112_D	0.554	0.54
20_V	79_A	0.548	0.54
76_D	92_L	0.546	0.53
64_Q	87_L	0.546	0.53
107_I	127_M	0.543	0.53
12_M	77_D	0.540	0.53
26_V	77_D	0.539	0.52
108_E	118_Y	0.538	0.52
83_L	136_P	0.538	0.52
9_F	13_R	0.537	0.52
110_H	121_N	0.537	0.52
26_V	70_A	0.535	0.52
104_S	118_Y	0.534	0.52
29_G	32_E	0.532	0.51
22_V	107_I	0.530	0.51
118_Y	123_G	0.527	0.51
36_A	125_Y	0.525	0.51
76_D	101_G	0.520	0.50
26_V	71_K	0.519	0.50
57_E	62_L	0.519	0.50
20_V	82_F	0.519	0.50
95_R	111_T	0.517	0.49
57_E	60_F	0.517	0.49
15_P	82_F	0.512	0.49
105_F	114_P	0.511	0.49
23_H	96_Q	0.510	0.49
15_P	98_D	0.509	0.48
29_G	68_I	0.508	0.48
10_H	88_P	0.505	0.48
56_P	66_D	0.504	0.48
36_A	40_L	0.503	0.48
30_G	34_Q	0.502	0.47
30_G	111_T	0.500	0.47
135_R	141_A	0.500	0.47

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
1vq8D	1	0.8	100	0.115	Contact Map
3j21E	1	0.9943	100	0.124	Contact Map
3zf7L	1	0.9486	100	0.127	Contact Map
4a17D	1	0.9543	100	0.133	Contact Map
1vx7G	1	0.7086	100	0.135	Contact Map
4ujqM	1	0.9486	100	0.141	Contact Map
1iq4A	1	0.88	100	0.239	Contact Map
4tp9F	1	0.8743	100	0.239	Contact Map
4rb6G	1	0.88	100	0.24	Contact Map
3bboH	1	0.8686	100	0.247	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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