DUF3567 - PFAM28P - GREMLIN Contacts

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DUF3567 - Protein of unknown function (DUF3567)

PFAM:	PF12091	Sequences: MQMLYNSDSFAVVEFDAPAAAAAAAAPARGGFEIVDKFARKEIFLDGALAESFQQGVEALIENEPSEEEVDDFLEGYAGLAQQPVVLH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	88 (88)
Sequences:	1303 (630)
Seq/√Len:	67.1
META:	0.928

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
70_V	74_L	2.986	1.00
58_E	62_E	2.985	1.00
29_R	46_D	2.965	1.00
51_E	55_Q	2.649	1.00
20_A	24_A	2.293	1.00
75_E	78_A	2.039	1.00
74_L	82_Q	1.938	1.00
18_P	23_A	1.851	1.00
11_A	35_V	1.850	1.00
51_E	54_Q	1.809	1.00
83_Q	86_V	1.769	1.00
51_E	58_E	1.669	0.99
20_A	23_A	1.570	0.99
59_A	62_E	1.554	0.99
22_A	25_A	1.511	0.99
23_A	27_P	1.505	0.99
3_M	6_N	1.460	0.98
38_F	41_K	1.402	0.98
61_I	74_L	1.396	0.98
72_D	75_E	1.393	0.98
28_A	79_G	1.391	0.98
21_A	25_A	1.387	0.98
67_E	72_D	1.331	0.97
21_A	24_A	1.314	0.97
85_V	88_H	1.284	0.96
20_A	26_A	1.280	0.96
65_P	69_E	1.273	0.96
22_A	27_P	1.269	0.96
18_P	24_A	1.265	0.96
8_D	11_A	1.263	0.96
61_I	65_P	1.258	0.96
23_A	26_A	1.234	0.96
4_L	14_E	1.214	0.95
15_F	42_E	1.196	0.95
19_A	25_A	1.193	0.95
32_F	54_Q	1.182	0.94
29_R	35_V	1.164	0.94
61_I	81_A	1.157	0.94
24_A	27_P	1.150	0.94
32_F	42_E	1.147	0.93
32_F	61_I	1.138	0.93
11_A	15_F	1.136	0.93
52_S	55_Q	1.123	0.93
75_E	81_A	1.122	0.93
57_V	60_L	1.101	0.92
10_F	55_Q	1.098	0.92
14_E	54_Q	1.088	0.92
20_A	27_P	1.074	0.91
62_E	69_E	1.073	0.91
2_Q	35_V	1.049	0.90
15_F	60_L	0.995	0.87
20_A	25_A	0.987	0.87
6_N	68_E	0.987	0.87
22_A	26_A	0.980	0.87
12_V	49_L	0.973	0.86
10_F	78_A	0.944	0.84
73_F	76_G	0.931	0.84
19_A	26_A	0.913	0.82
45_L	53_F	0.911	0.82
16_D	44_F	0.910	0.82
3_M	56_G	0.892	0.81
40_R	57_V	0.870	0.79
66_S	69_E	0.864	0.79
19_A	28_A	0.860	0.79
19_A	24_A	0.846	0.77
17_A	20_A	0.838	0.77
60_L	69_E	0.833	0.76
31_G	42_E	0.828	0.76
30_G	60_L	0.809	0.74
49_L	61_I	0.797	0.73
56_G	74_L	0.796	0.73
35_V	85_V	0.786	0.72
8_D	35_V	0.782	0.72
40_R	52_S	0.782	0.72
39_A	68_E	0.774	0.71
21_A	27_P	0.774	0.71
44_F	51_E	0.773	0.71
73_F	77_Y	0.766	0.70
63_N	69_E	0.764	0.70
2_Q	27_P	0.745	0.68
14_E	70_V	0.743	0.68
1_M	7_S	0.741	0.67
22_A	45_L	0.732	0.67
64_E	67_E	0.729	0.66
49_L	79_G	0.725	0.66
49_L	52_S	0.721	0.65
27_P	62_E	0.718	0.65
40_R	43_I	0.699	0.63
61_I	70_V	0.696	0.63
56_G	73_F	0.686	0.62
70_V	79_G	0.679	0.61
13_V	17_A	0.669	0.60
69_E	72_D	0.664	0.59
13_V	76_G	0.661	0.59
64_E	70_V	0.656	0.58
2_Q	11_A	0.655	0.58
50_A	57_V	0.649	0.57
12_V	54_Q	0.646	0.57
1_M	4_L	0.637	0.56
44_F	71_D	0.634	0.56
4_L	29_R	0.632	0.55
20_A	76_G	0.627	0.55
8_D	38_F	0.623	0.54
56_G	59_A	0.622	0.54
52_S	77_Y	0.615	0.53
41_K	62_E	0.613	0.53
72_D	77_Y	0.594	0.51
61_I	64_E	0.593	0.51
34_I	69_E	0.588	0.50
52_S	58_E	0.580	0.49
9_S	77_Y	0.579	0.49
12_V	53_F	0.572	0.48
18_P	28_A	0.570	0.48
43_I	66_S	0.569	0.48
35_V	46_D	0.569	0.48
61_I	71_D	0.564	0.47
10_F	87_L	0.561	0.47
45_L	81_A	0.560	0.47
16_D	28_A	0.559	0.47
67_E	71_D	0.558	0.47
3_M	13_V	0.557	0.46
48_A	52_S	0.543	0.45
84_P	88_H	0.538	0.44
68_E	73_F	0.534	0.44
1_M	5_Y	0.534	0.44
14_E	28_A	0.526	0.43
46_D	54_Q	0.510	0.41
9_S	85_V	0.505	0.40
14_E	78_A	0.504	0.40
39_A	49_L	0.502	0.40
14_E	81_A	0.502	0.40
16_D	68_E	0.500	0.40

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
1wyuA	2	0.8068	24.8	0.917	Contact Map
1kijA	2	0.625	13.8	0.926	Contact Map
3ly1A	2	0.7614	12.2	0.928	Contact Map
1u8vA	3	0.7045	9.7	0.931	Contact Map
2xvlA	1	0.9205	9	0.932	Contact Map
3getA	2	0.7273	8.6	0.933	Contact Map
4lnjA	4	0.7386	7.2	0.935	Contact Map
3n0aA	1	0.8182	6.8	0.935	Contact Map
3v0dA	1	0.9545	6.8	0.936	Contact Map
3b5iA	2	0.9773	6.7	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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