DUF4825 - PFAM28P - GREMLIN Contacts

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DUF4825 - Domain of unknown function (DUF4825)

PFAM:	PF16107	Sequences: LYKYKTPYVGDNSAVGNIINALPLPEGLGYYGIELQTDEEPYGLTVNYETTDESINEEELEEAFLYNAILLFALIDNLDEVTFNFTDDGGENEYTYTFT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	99 (88)
Sequences:	1034 (833)
Seq/√Len:	88.8
META:	0.707

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
16_G	33_I	3.685	1.00
43_G	80_E	3.487	1.00
7_P	76_D	3.128	1.00
6_T	15_V	2.769	1.00
40_E	79_D	2.625	1.00
72_F	78_L	2.181	1.00
19_I	71_L	2.151	1.00
6_T	14_A	2.044	1.00
68_A	83_F	2.007	1.00
23_P	48_Y	1.999	1.00
37_T	41_P	1.946	1.00
36_Q	45_T	1.858	1.00
32_G	47_N	1.679	1.00
12_N	15_V	1.656	1.00
35_L	41_P	1.650	1.00
9_V	44_L	1.633	1.00
10_G	77_N	1.628	1.00
9_V	78_L	1.614	1.00
78_L	81_V	1.576	1.00
34_E	45_T	1.566	1.00
44_L	71_L	1.547	1.00
19_I	46_V	1.437	0.99
4_Y	21_A	1.421	0.99
4_Y	17_N	1.395	0.99
66_Y	70_L	1.383	0.99
64_F	85_F	1.378	0.99
47_N	84_N	1.351	0.99
43_G	82_T	1.334	0.99
36_Q	79_D	1.330	0.99
33_I	44_L	1.275	0.99
71_L	78_L	1.257	0.98
24_L	48_Y	1.226	0.98
4_Y	14_A	1.224	0.98
14_A	17_N	1.219	0.98
11_D	14_A	1.211	0.98
15_V	75_I	1.127	0.97
41_P	79_D	1.125	0.97
65_L	69_I	1.113	0.96
37_T	79_D	1.098	0.96
6_T	18_I	1.085	0.96
44_L	78_L	1.083	0.96
12_N	33_I	1.070	0.96
12_N	16_G	1.040	0.95
45_T	82_T	1.019	0.94
18_I	75_I	1.012	0.94
10_G	35_L	0.988	0.93
64_F	83_F	0.986	0.93
70_L	73_A	0.950	0.92
34_E	47_N	0.936	0.91
31_Y	49_E	0.918	0.90
28_L	85_F	0.913	0.90
19_I	33_I	0.881	0.89
52_D	56_N	0.876	0.88
17_N	20_N	0.866	0.88
35_L	77_N	0.863	0.88
59_E	76_D	0.842	0.86
9_V	43_G	0.838	0.86
49_E	86_T	0.838	0.86
57_E	61_E	0.825	0.85
64_F	81_V	0.820	0.85
19_I	44_L	0.809	0.84
16_G	20_N	0.804	0.84
16_G	32_G	0.802	0.83
51_T	58_E	0.771	0.81
16_G	19_I	0.760	0.80
7_P	11_D	0.756	0.80
53_E	62_E	0.751	0.79
34_E	37_T	0.742	0.78
10_G	13_S	0.738	0.78
53_E	56_N	0.731	0.77
15_V	44_L	0.726	0.77
37_T	42_Y	0.721	0.76
37_T	45_T	0.718	0.76
35_L	40_E	0.717	0.76
8_Y	77_N	0.716	0.76
14_A	18_I	0.702	0.74
7_P	32_G	0.701	0.74
17_N	21_A	0.699	0.74
9_V	37_T	0.698	0.74
61_E	82_T	0.693	0.73
69_I	73_A	0.691	0.73
66_Y	75_I	0.683	0.72
36_Q	80_E	0.669	0.71
3_K	13_S	0.667	0.71
1_L	4_Y	0.663	0.70
5_K	55_I	0.655	0.69
45_T	84_N	0.650	0.69
71_L	75_I	0.645	0.68
1_L	74_L	0.641	0.68
42_Y	79_D	0.639	0.67
26_E	50_T	0.638	0.67
3_K	59_E	0.638	0.67
30_Y	72_F	0.636	0.67
23_P	66_Y	0.626	0.66
23_P	67_N	0.620	0.65
9_V	15_V	0.615	0.64
62_E	88_D	0.601	0.63
6_T	76_D	0.600	0.63
12_N	77_N	0.599	0.62
31_Y	46_V	0.597	0.62
44_L	75_I	0.592	0.61
7_P	24_L	0.581	0.60
3_K	57_E	0.581	0.60
40_E	43_G	0.580	0.60
15_V	33_I	0.579	0.60
54_S	58_E	0.577	0.60
32_G	48_Y	0.573	0.59
54_S	87_D	0.564	0.58
42_Y	78_L	0.563	0.58
5_K	79_D	0.561	0.57
71_L	81_V	0.560	0.57
57_E	60_L	0.557	0.57
18_I	21_A	0.554	0.56
19_I	83_F	0.553	0.56
4_Y	72_F	0.549	0.56
24_L	72_F	0.546	0.55
25_P	50_T	0.546	0.55
9_V	71_L	0.543	0.55
26_E	59_E	0.542	0.55
24_L	51_T	0.539	0.54
7_P	18_I	0.538	0.54
4_Y	18_I	0.538	0.54
16_G	46_V	0.535	0.54
44_L	81_V	0.526	0.53
18_I	23_P	0.523	0.52
20_N	46_V	0.521	0.52
3_K	58_E	0.520	0.52
29_G	40_E	0.517	0.51
67_N	74_L	0.511	0.51
55_I	66_Y	0.511	0.51
14_A	73_A	0.509	0.50
29_G	69_I	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
3enuA	2	0.3636	5.2	0.916	Contact Map
3r2nA	4	0.2424	2.9	0.926	Contact Map
3htnA	3	0.6768	2.9	0.926	Contact Map
1zxhA	1	0.4949	2.6	0.927	Contact Map
1l8nA	2	1	2.6	0.928	Contact Map
1pn5A	1	0.0101	2.5	0.928	Contact Map
2z16A	1	0.7071	2.4	0.929	Contact Map
4qeyA	3	0.8384	2.4	0.929	Contact Map
3hwuA	3	0.697	2.2	0.93	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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