DUF4418 - PFAM28P - GREMLIN Contacts

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DUF4418 - Domain of unknown function (DUF4418)

PFAM:	PF14387	Sequences: FIVLGLLIALGPQFLFPVCESMGDLGKMMKCHWTARAEIGIGILIAALGILLLFFKDKKTRLGLSIGIILLGILAILIPTVLIGVCAMPTMACRTVTFPALIVLGILLIVLSLINIFL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	118 (114)
Sequences:	1132 (938)
Seq/√Len:	87.8
META:	0.863

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
34_T	78_I	3.079	1.00
18_V	35_A	2.667	1.00
85_V	98_F	2.642	1.00
9_A	42_G	2.441	1.00
40_G	82_L	2.257	1.00
63_G	67_G	2.191	1.00
16_F	100_A	2.151	1.00
80_T	102_I	2.010	1.00
10_L	14_F	2.010	1.00
38_E	75_A	2.001	1.00
41_I	78_I	1.917	1.00
32_H	36_R	1.916	1.00
11_G	14_F	1.849	1.00
40_G	74_L	1.825	1.00
85_V	94_R	1.803	1.00
48_L	67_G	1.803	1.00
37_A	83_I	1.802	1.00
65_S	115_N	1.787	1.00
76_I	105_G	1.778	1.00
38_E	101_L	1.762	1.00
8_I	101_L	1.715	1.00
12_P	42_G	1.706	1.00
75_A	105_G	1.688	1.00
33_W	83_I	1.648	1.00
94_R	98_F	1.633	1.00
9_A	46_A	1.631	1.00
72_G	105_G	1.558	1.00
88_M	91_M	1.523	1.00
45_I	68_I	1.492	1.00
77_L	81_V	1.482	0.99
5_G	42_G	1.453	0.99
34_T	84_G	1.451	0.99
6_L	10_L	1.447	0.99
102_I	106_I	1.434	0.99
72_G	108_L	1.428	0.99
37_A	78_I	1.356	0.99
16_F	19_C	1.355	0.99
18_V	97_T	1.354	0.99
76_I	109_I	1.340	0.99
110_V	114_I	1.329	0.99
11_G	16_F	1.301	0.99
33_W	36_R	1.291	0.99
72_G	109_I	1.288	0.99
92_A	96_V	1.269	0.98
76_I	102_I	1.253	0.98
30_K	33_W	1.159	0.97
52_L	64_L	1.158	0.97
60_T	63_G	1.150	0.97
52_L	61_R	1.126	0.97
68_I	112_S	1.110	0.96
98_F	102_I	1.105	0.96
80_T	85_V	1.102	0.96
21_S	28_M	1.101	0.96
100_A	104_L	1.082	0.96
2_I	49_G	1.080	0.96
10_L	15_L	1.077	0.96
34_T	79_P	1.054	0.95
8_I	75_A	1.046	0.95
47_A	51_L	1.042	0.95
74_L	78_I	1.041	0.95
40_G	63_G	1.039	0.95
2_I	53_L	1.014	0.94
89_P	94_R	1.008	0.94
21_S	24_D	1.006	0.94
24_D	91_M	1.003	0.94
4_L	107_L	0.986	0.93
103_V	107_L	0.958	0.92
48_L	64_L	0.952	0.92
29_M	86_C	0.938	0.91
39_I	43_I	0.936	0.91
70_L	73_I	0.933	0.91
6_L	66_I	0.905	0.90
85_V	102_I	0.904	0.90
78_I	83_I	0.882	0.88
13_Q	39_I	0.875	0.88
13_Q	35_A	0.875	0.88
35_A	38_E	0.866	0.87
18_V	21_S	0.848	0.86
4_L	7_L	0.835	0.85
40_G	83_I	0.829	0.85
33_W	40_G	0.821	0.84
80_T	84_G	0.812	0.84
18_V	32_H	0.800	0.83
4_L	108_L	0.797	0.83
50_I	54_F	0.794	0.82
41_I	71_L	0.779	0.81
30_K	88_M	0.775	0.81
33_W	63_G	0.763	0.80
20_E	23_G	0.757	0.79
43_I	74_L	0.753	0.79
3_V	71_L	0.747	0.78
5_G	49_G	0.745	0.78
18_V	22_M	0.741	0.78
73_I	107_L	0.737	0.77
34_T	97_T	0.721	0.76
2_I	46_A	0.720	0.76
16_F	38_E	0.714	0.75
44_L	71_L	0.713	0.75
50_I	89_P	0.704	0.74
50_I	113_L	0.704	0.74
8_I	68_I	0.703	0.74
22_M	27_K	0.698	0.74
12_P	15_L	0.696	0.73
28_M	36_R	0.692	0.73
18_V	44_L	0.689	0.73
44_L	51_L	0.689	0.73
14_F	17_P	0.682	0.72
97_T	101_L	0.682	0.72
11_G	15_L	0.679	0.72
31_C	86_C	0.679	0.72
34_T	37_A	0.675	0.71
8_I	12_P	0.667	0.70
87_A	92_A	0.667	0.70
7_L	18_V	0.666	0.70
55_F	59_K	0.656	0.69
5_G	12_P	0.655	0.69
49_G	68_I	0.655	0.69
96_V	99_P	0.653	0.69
9_A	12_P	0.648	0.68
36_R	41_I	0.646	0.68
60_T	66_I	0.644	0.68
28_M	33_W	0.643	0.67
41_I	75_A	0.642	0.67
80_T	98_F	0.642	0.67
32_H	91_M	0.638	0.67
49_G	85_V	0.638	0.67
34_T	85_V	0.635	0.66
50_I	56_K	0.634	0.66
73_I	109_I	0.634	0.66
51_L	59_K	0.633	0.66
104_L	111_L	0.628	0.66
77_L	82_L	0.624	0.65
35_A	39_I	0.623	0.65
10_L	13_Q	0.619	0.64
13_Q	17_P	0.616	0.64
11_G	96_V	0.616	0.64
11_G	100_A	0.615	0.64
16_F	99_P	0.602	0.62
7_L	104_L	0.600	0.62
74_L	82_L	0.590	0.61
30_K	83_I	0.587	0.60
23_G	87_A	0.580	0.59
12_P	97_T	0.575	0.59
88_M	114_I	0.574	0.59
5_G	9_A	0.574	0.59
4_L	104_L	0.570	0.58
8_I	108_L	0.567	0.58
56_K	109_I	0.564	0.57
47_A	70_L	0.560	0.57
104_L	115_N	0.558	0.57
11_G	17_P	0.550	0.55
46_A	50_I	0.549	0.55
5_G	11_G	0.548	0.55
45_I	108_L	0.541	0.54
36_R	78_I	0.539	0.54
59_K	62_L	0.537	0.54
29_M	95_T	0.536	0.54
51_L	55_F	0.534	0.53
24_D	28_M	0.533	0.53
28_M	53_L	0.532	0.53
101_L	105_G	0.531	0.53
24_D	27_K	0.528	0.53
35_A	85_V	0.528	0.53
61_R	81_V	0.525	0.52
44_L	57_D	0.521	0.52
31_C	93_C	0.518	0.51
53_L	114_I	0.510	0.50
43_I	113_L	0.504	0.49
52_L	56_K	0.502	0.49
96_V	100_A	0.500	0.49
33_W	67_G	0.500	0.49

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
4i0uA	4	0.4915	4.9	0.926	Contact Map
4o6yA	2	0.8814	4.7	0.927	Contact Map
4ev6A	3	0.4915	4.1	0.929	Contact Map
2jwaA	2	0.339	2.4	0.937	Contact Map
3b5dA	2	0.6271	1.5	0.944	Contact Map
2ks1B	1	0.2712	0.9	0.95	Contact Map
3ux4A	3	0.6017	0.8	0.952	Contact Map
3x29A	1	0.7627	0.7	0.954	Contact Map
2a65A	2	0.7542	0.7	0.955	Contact Map
2xq2A	2	0.6949	0.7	0.955	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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