DUF4284 - PFAM28P - GREMLIN Contacts

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DUF4284 - Immunity protein 22

PFAM:	PF14112	Sequences: VSIWIGNFPSEEELEEYFEEDYDEDGDSIPSQFAKDFGIDWYDEDFIEANFLEEEPVPLEELLEGFSYSESFIPELKEKAKKKGLEKKANAVILLYDFEYDGEPKSVKNEYNGLKFIGSFEYE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	123 (121)
Sequences:	1024 (828)
Seq/√Len:	75.3
META:	0.72

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
17_Y	36_D	6.837	1.00
2_S	119_S	3.234	1.00
48_E	67_S	2.950	1.00
31_S	34_A	2.930	1.00
20_E	44_E	2.771	1.00
2_S	116_F	2.672	1.00
116_F	119_S	2.429	1.00
50_N	66_F	2.334	1.00
93_I	114_L	2.239	1.00
79_K	120_F	2.202	1.00
72_F	96_Y	2.139	1.00
10_S	13_E	2.081	1.00
6_G	90_N	1.829	1.00
14_L	91_A	1.806	1.00
65_G	69_S	1.798	1.00
58_P	61_E	1.742	1.00
14_L	18_F	1.642	1.00
48_E	94_L	1.602	0.99
3_I	76_L	1.599	0.99
5_I	89_A	1.588	0.99
62_L	65_G	1.581	0.99
76_L	120_F	1.550	0.99
26_G	29_I	1.550	0.99
72_F	76_L	1.497	0.99
63_L	76_L	1.449	0.99
2_S	98_F	1.444	0.99
75_E	78_E	1.426	0.99
48_E	68_Y	1.413	0.99
69_S	72_F	1.409	0.99
82_K	85_L	1.367	0.98
20_E	42_Y	1.361	0.98
27_D	30_P	1.352	0.98
18_F	49_A	1.346	0.98
100_Y	116_F	1.318	0.98
6_G	14_L	1.288	0.98
18_F	93_I	1.280	0.97
20_E	41_W	1.273	0.97
2_S	37_F	1.265	0.97
6_G	114_L	1.252	0.97
60_E	77_K	1.238	0.97
41_W	45_D	1.217	0.97
67_S	96_Y	1.202	0.96
36_D	62_L	1.177	0.96
37_F	100_Y	1.176	0.96
43_D	46_F	1.133	0.95
34_A	44_E	1.112	0.94
5_I	117_I	1.109	0.94
2_S	100_Y	1.098	0.94
26_G	30_P	1.096	0.94
79_K	82_K	1.080	0.93
23_D	40_D	1.075	0.93
37_F	98_F	1.060	0.93
23_D	28_S	1.050	0.92
104_P	107_V	1.048	0.92
41_W	44_E	1.045	0.92
80_A	89_A	1.038	0.92
71_S	120_F	1.001	0.91
51_F	91_A	0.995	0.90
102_G	105_K	0.995	0.90
10_S	79_K	0.986	0.90
3_I	94_L	0.967	0.89
47_I	95_L	0.962	0.89
22_Y	43_D	0.960	0.89
11_E	25_D	0.928	0.87
2_S	97_D	0.923	0.87
72_F	116_F	0.922	0.87
31_S	42_Y	0.920	0.86
23_D	27_D	0.919	0.86
43_D	90_N	0.913	0.86
100_Y	104_P	0.912	0.86
34_A	41_W	0.910	0.86
62_L	92_V	0.903	0.85
75_E	79_K	0.903	0.85
66_F	94_L	0.897	0.85
85_L	89_A	0.894	0.85
1_V	96_Y	0.892	0.85
2_S	96_Y	0.872	0.83
10_S	51_F	0.871	0.83
6_G	10_S	0.863	0.83
42_Y	101_D	0.858	0.82
73_I	77_K	0.854	0.82
51_F	90_N	0.850	0.82
1_V	94_L	0.843	0.81
77_K	80_A	0.827	0.80
6_G	33_F	0.826	0.80
34_A	42_Y	0.823	0.80
79_K	83_K	0.819	0.79
55_E	78_E	0.812	0.79
38_G	41_W	0.799	0.78
4_W	33_F	0.798	0.77
41_W	46_F	0.788	0.77
32_Q	38_G	0.787	0.76
11_E	19_E	0.780	0.76
32_Q	35_K	0.778	0.76
104_P	109_N	0.771	0.75
21_D	43_D	0.761	0.74
117_I	120_F	0.759	0.74
9_P	13_E	0.756	0.74
89_A	115_K	0.755	0.73
62_L	89_A	0.752	0.73
18_F	91_A	0.746	0.73
102_G	109_N	0.746	0.73
36_D	112_N	0.744	0.72
14_L	93_I	0.742	0.72
5_I	83_K	0.735	0.71
65_G	92_V	0.728	0.71
59_L	84_G	0.722	0.70
68_Y	76_L	0.719	0.70
108_K	111_Y	0.716	0.69
14_L	90_N	0.713	0.69
18_F	47_I	0.710	0.69
18_F	74_P	0.708	0.69
67_S	72_F	0.707	0.68
65_G	93_I	0.702	0.68
37_F	96_Y	0.700	0.68
61_E	84_G	0.690	0.67
22_Y	67_S	0.688	0.66
78_E	82_K	0.683	0.66
52_L	61_E	0.677	0.65
109_N	112_N	0.673	0.65
103_E	107_V	0.670	0.64
46_F	97_D	0.667	0.64
11_E	15_E	0.667	0.64
3_I	88_K	0.663	0.64
68_Y	122_Y	0.658	0.63
32_Q	36_D	0.652	0.62
44_E	47_I	0.650	0.62
6_G	91_A	0.649	0.62
38_G	121_E	0.643	0.61
81_K	86_E	0.642	0.61
14_L	51_F	0.641	0.61
10_S	14_L	0.638	0.61
4_W	117_I	0.635	0.60
71_S	74_P	0.633	0.60
18_F	34_A	0.626	0.59
36_D	49_A	0.626	0.59
48_E	72_F	0.621	0.59
33_F	51_F	0.621	0.59
9_P	57_V	0.620	0.58
5_I	34_A	0.618	0.58
14_L	47_I	0.617	0.58
116_F	121_E	0.614	0.58
19_E	28_S	0.608	0.57
31_S	72_F	0.605	0.57
1_V	98_F	0.603	0.56
23_D	74_P	0.589	0.55
23_D	29_I	0.587	0.54
48_E	92_V	0.587	0.54
93_I	97_D	0.582	0.54
76_L	92_V	0.572	0.52
3_I	69_S	0.571	0.52
12_E	86_E	0.564	0.51
6_G	13_E	0.556	0.50
113_G	116_F	0.554	0.50
29_I	63_L	0.552	0.50
28_S	38_G	0.550	0.50
22_Y	95_L	0.548	0.49
36_D	109_N	0.545	0.49
16_E	82_K	0.544	0.49
108_K	117_I	0.543	0.49
16_E	21_D	0.542	0.49
40_D	119_S	0.542	0.49
22_Y	25_D	0.540	0.48
76_L	80_A	0.539	0.48
1_V	4_W	0.539	0.48
7_N	85_L	0.539	0.48
48_E	96_Y	0.534	0.48
70_E	117_I	0.533	0.48
34_A	37_F	0.532	0.47
58_P	89_A	0.529	0.47
12_E	15_E	0.521	0.46
77_K	89_A	0.520	0.46
95_L	98_F	0.519	0.46
73_I	81_K	0.518	0.46
3_I	65_G	0.517	0.46
55_E	62_L	0.513	0.45
38_G	110_E	0.511	0.45
101_D	120_F	0.509	0.45
1_V	71_S	0.508	0.44
31_S	90_N	0.505	0.44
20_E	51_F	0.502	0.44
8_F	91_A	0.500	0.43

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
1na6A	2	0.9431	8.2	0.915	Contact Map
1gccA	1	0.3008	6.2	0.92	Contact Map
1el6A	3	0.6992	3.4	0.929	Contact Map
4y66A	1	0.3496	3	0.931	Contact Map
1tr0A	7	0.3659	2.6	0.933	Contact Map
3fmbA	2	0.3577	2.4	0.935	Contact Map
3bguA	2	0.3577	2.3	0.935	Contact Map
1pyaB	3	0.8862	2.2	0.936	Contact Map
3sggA	1	0.3333	2.2	0.936	Contact Map
1d0nA	5	0.6098	2.2	0.936	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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