DUF4869 - PFAM28P - GREMLIN Contacts

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DUF4869 - Domain of unknown function (DUF4869)

PFAM:	PF16163	Sequences: IYNTSVYFKNTYEDEWITDPLVKEMIKDVDKSEVIGPHLIDSPVLGPIPPEELSGGVKTLILMYNDPDKIFNASTCGDNCAKWILKIAKKKDITINLRHLMDFGDEPFEIKILNTGKIVHNMKELVPI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	128 (126)
Sequences:	551 (373)
Seq/√Len:	33.2
META:	0.768

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_L	47_P	3.995	1.00
27_K	33_E	3.923	1.00
86_K	89_K	3.562	1.00
63_M	84_I	3.537	1.00
63_M	93_I	3.126	1.00
22_V	61_I	2.839	1.00
24_E	86_K	2.756	1.00
25_M	57_V	2.747	1.00
28_D	82_K	2.568	1.00
3_N	6_V	2.482	1.00
28_D	83_W	2.394	0.99
45_L	48_I	2.209	0.99
56_G	79_N	2.178	0.99
4_T	75_T	2.157	0.99
20_P	23_K	2.152	0.99
109_E	120_H	2.121	0.99
111_K	116_G	2.085	0.98
84_I	93_I	2.027	0.98
49_P	52_E	1.907	0.97
33_E	41_D	1.882	0.97
32_S	40_I	1.869	0.97
120_H	124_E	1.862	0.97
122_M	125_L	1.736	0.95
112_I	125_L	1.699	0.94
25_M	61_I	1.696	0.94
35_I	39_L	1.619	0.93
22_V	65_N	1.610	0.93
67_P	91_K	1.581	0.92
59_T	76_C	1.431	0.87
112_I	119_V	1.426	0.87
32_S	42_S	1.412	0.87
40_I	53_L	1.356	0.84
53_L	57_V	1.318	0.83
59_T	71_F	1.301	0.82
73_A	95_I	1.292	0.81
54_S	57_V	1.279	0.81
20_P	24_E	1.272	0.80
84_I	95_I	1.268	0.80
18_T	23_K	1.254	0.79
21_L	64_Y	1.248	0.79
19_D	64_Y	1.246	0.79
109_E	121_N	1.223	0.78
84_I	110_I	1.221	0.77
22_V	64_Y	1.211	0.77
21_L	25_M	1.197	0.76
23_K	33_E	1.136	0.72
78_D	99_H	1.094	0.69
97_L	101_M	1.081	0.68
38_H	52_E	1.077	0.68
34_V	40_I	1.061	0.67
50_P	53_L	1.040	0.65
42_S	48_I	1.032	0.65
60_L	87_I	1.028	0.64
121_N	124_E	1.026	0.64
21_L	87_I	1.015	0.63
21_L	82_K	0.986	0.61
29_V	57_V	0.973	0.60
66_D	69_K	0.972	0.60
25_M	87_I	0.962	0.59
61_I	65_N	0.953	0.58
92_D	109_E	0.938	0.57
42_S	55_G	0.935	0.57
110_I	118_I	0.930	0.56
89_K	109_E	0.927	0.56
32_S	44_V	0.926	0.56
38_H	84_I	0.914	0.55
38_H	41_D	0.894	0.53
63_M	73_A	0.885	0.53
40_I	82_K	0.881	0.52
81_A	97_L	0.875	0.52
104_G	122_M	0.872	0.52
19_D	22_V	0.869	0.51
32_S	43_P	0.859	0.51
59_T	63_M	0.858	0.50
81_A	101_M	0.850	0.50
115_T	126_V	0.848	0.50
24_E	27_K	0.838	0.49
61_I	75_T	0.833	0.48
115_T	121_N	0.830	0.48
87_I	93_I	0.820	0.47
85_L	110_I	0.807	0.46
72_N	114_N	0.803	0.46
110_I	119_V	0.801	0.46
117_K	120_H	0.793	0.45
25_M	83_W	0.792	0.45
12_Y	16_W	0.791	0.45
5_S	52_E	0.787	0.45
28_D	57_V	0.785	0.44
16_W	80_C	0.778	0.44
107_P	121_N	0.770	0.43
18_T	22_V	0.753	0.42
6_V	10_N	0.743	0.41
5_S	47_P	0.743	0.41
6_V	20_P	0.741	0.41
57_V	83_W	0.740	0.41
17_I	22_V	0.729	0.40
14_D	18_T	0.728	0.40
63_M	67_P	0.727	0.40
104_G	111_K	0.727	0.40
36_G	39_L	0.720	0.39
2_Y	99_H	0.717	0.39
5_S	9_K	0.716	0.39
96_N	99_H	0.713	0.39
60_L	80_C	0.708	0.38
68_D	125_L	0.704	0.38
42_S	45_L	0.700	0.37
39_L	49_P	0.688	0.37
13_E	44_V	0.683	0.36
11_T	22_V	0.682	0.36
21_L	116_G	0.671	0.35
85_L	89_K	0.667	0.35
61_I	84_I	0.664	0.35
25_M	38_H	0.658	0.34
6_V	65_N	0.656	0.34
42_S	46_G	0.656	0.34
30_D	77_G	0.652	0.34
17_I	26_I	0.651	0.34
64_Y	87_I	0.650	0.34
9_K	51_E	0.649	0.34
22_V	87_I	0.648	0.34
72_N	99_H	0.643	0.33
94_T	113_L	0.641	0.33
109_E	118_I	0.641	0.33
4_T	11_T	0.629	0.32
52_E	68_D	0.627	0.32
117_K	121_N	0.621	0.32
67_P	92_D	0.621	0.32
62_L	75_T	0.619	0.31
31_K	116_G	0.611	0.31
59_T	119_V	0.610	0.31
5_S	75_T	0.609	0.31
14_D	37_P	0.604	0.30
43_P	46_G	0.604	0.30
67_P	118_I	0.603	0.30
64_Y	91_K	0.603	0.30
108_F	112_I	0.599	0.30
22_V	25_M	0.594	0.30
42_S	73_A	0.594	0.30
4_T	62_L	0.593	0.30
122_M	126_V	0.591	0.29
38_H	51_E	0.588	0.29
104_G	125_L	0.587	0.29
26_I	40_I	0.583	0.29
34_V	50_P	0.581	0.29
76_C	97_L	0.575	0.28
111_K	118_I	0.574	0.28
100_L	126_V	0.569	0.28
25_M	29_V	0.567	0.28
86_K	90_K	0.565	0.28
117_K	122_M	0.565	0.28
24_E	36_G	0.564	0.28
7_Y	66_D	0.564	0.28
7_Y	69_K	0.564	0.28
115_T	120_H	0.563	0.28
55_G	80_C	0.561	0.27
87_I	103_F	0.561	0.27
13_E	64_Y	0.559	0.27
36_G	47_P	0.557	0.27
65_N	91_K	0.556	0.27
23_K	27_K	0.555	0.27
85_L	100_L	0.553	0.27
93_I	112_I	0.553	0.27
63_M	71_F	0.553	0.27
117_K	125_L	0.552	0.27
39_L	82_K	0.547	0.26
47_P	50_P	0.545	0.26
73_A	81_A	0.540	0.26
33_E	68_D	0.538	0.26
57_V	61_I	0.537	0.26
71_F	74_S	0.536	0.26
28_D	88_A	0.534	0.26
59_T	70_I	0.533	0.26
40_I	50_P	0.532	0.25
123_K	126_V	0.527	0.25
31_K	44_V	0.527	0.25
72_N	78_D	0.525	0.25
30_D	79_N	0.521	0.25
43_P	57_V	0.521	0.25
40_I	73_A	0.521	0.25
5_S	100_L	0.520	0.25
18_T	31_K	0.518	0.25
69_K	117_K	0.516	0.24
97_L	103_F	0.514	0.24
30_D	54_S	0.513	0.24
3_N	9_K	0.512	0.24
11_T	65_N	0.511	0.24
15_E	41_D	0.507	0.24
35_I	47_P	0.501	0.24
100_L	125_L	0.500	0.24

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
4ry2A	2	0.9688	56.1	0.917	Contact Map
4a82A	2	0.9688	32.4	0.928	Contact Map
4pl0A	2	0.9688	31.7	0.928	Contact Map
4q9hA	1	0.9609	30.1	0.929	Contact Map
4q4hB	1	0.9688	29.5	0.93	Contact Map
4f4cA	1	0.9688	28.7	0.93	Contact Map
3b60A	2	0.9688	21.4	0.934	Contact Map
4mrsA	2	0.9688	20.6	0.935	Contact Map
3nh6A	1	0.9688	19.2	0.936	Contact Map
2ghiA	1	0.9688	18.5	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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