DUF3007 - PFAM28P - GREMLIN Contacts

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DUF3007 - Protein of unknown function (DUF3007)

PFAM:	PF11460	Sequences: MTRIDVILIGLGVFLLGGLGYLGLQAAGLDGFSAGIWSQALLVLGLLGWVSTYLFRVVTGKMTYMQQRKDYEEAVLQKRLEELSPEELAKLQAEIE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	96 (96)
Sequences:	589 (365)
Seq/√Len:	37.3
META:	0.701

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
68_R	75_V	4.446	1.00
77_Q	81_E	4.236	1.00
6_V	10_G	4.172	1.00
80_L	88_L	2.910	1.00
66_Q	70_D	2.432	1.00
72_E	79_R	2.212	0.99
24_L	29_L	2.027	0.99
88_L	92_Q	1.989	0.99
76_L	91_L	1.954	0.98
51_S	55_F	1.841	0.98
64_Y	68_R	1.810	0.97
57_V	91_L	1.738	0.96
68_R	72_E	1.688	0.96
69_K	73_E	1.624	0.95
14_F	18_G	1.623	0.95
60_G	65_M	1.607	0.95
57_V	61_K	1.509	0.92
78_K	82_E	1.498	0.92
2_T	5_D	1.496	0.92
65_M	83_L	1.478	0.92
60_G	68_R	1.471	0.91
9_I	13_V	1.455	0.91
38_S	50_V	1.440	0.91
85_P	89_A	1.328	0.87
12_G	16_L	1.310	0.86
34_A	39_Q	1.307	0.86
76_L	80_L	1.305	0.86
39_Q	43_V	1.294	0.85
65_M	72_E	1.277	0.84
4_I	7_I	1.260	0.83
47_L	51_S	1.226	0.82
17_G	38_S	1.222	0.82
50_V	57_V	1.186	0.80
65_M	75_V	1.160	0.78
57_V	60_G	1.145	0.77
47_L	89_A	1.125	0.76
89_A	93_A	1.120	0.75
15_L	44_L	1.106	0.75
89_A	92_Q	1.092	0.74
65_M	68_R	1.080	0.73
25_Q	90_K	1.077	0.73
78_K	87_E	1.070	0.72
9_I	86_E	1.057	0.71
10_G	95_I	1.044	0.70
79_R	82_E	1.041	0.70
42_L	47_L	1.040	0.70
15_L	18_G	1.023	0.69
82_E	88_L	0.997	0.67
38_S	44_L	0.987	0.66
3_R	7_I	0.984	0.66
84_S	87_E	0.984	0.66
48_G	51_S	0.975	0.65
7_I	74_A	0.971	0.65
7_I	11_L	0.967	0.64
44_L	48_G	0.951	0.63
43_V	52_T	0.940	0.62
5_D	8_L	0.930	0.61
92_Q	96_E	0.930	0.61
16_L	43_V	0.927	0.61
13_V	19_L	0.917	0.60
36_I	39_Q	0.904	0.59
15_L	19_L	0.903	0.59
8_L	12_G	0.899	0.58
12_G	48_G	0.884	0.57
75_V	82_E	0.880	0.57
40_A	69_K	0.874	0.56
16_L	20_G	0.871	0.56
42_L	46_L	0.864	0.55
72_E	75_V	0.839	0.53
48_G	54_L	0.831	0.53
43_V	46_L	0.824	0.52
20_G	40_A	0.822	0.52
90_K	94_E	0.816	0.51
66_Q	81_E	0.805	0.50
44_L	54_L	0.791	0.49
29_L	41_L	0.790	0.49
18_G	39_Q	0.769	0.47
15_L	27_A	0.758	0.46
73_E	83_L	0.737	0.44
27_A	44_L	0.726	0.43
57_V	62_M	0.725	0.43
14_F	36_I	0.723	0.43
31_G	87_E	0.712	0.42
91_L	95_I	0.712	0.42
47_L	86_E	0.708	0.42
70_D	75_V	0.706	0.42
38_S	64_Y	0.705	0.41
84_S	95_I	0.688	0.40
64_Y	72_E	0.687	0.40
3_R	38_S	0.687	0.40
37_W	59_T	0.684	0.40
11_L	15_L	0.682	0.40
61_K	66_Q	0.681	0.39
31_G	43_V	0.676	0.39
55_F	58_V	0.674	0.39
47_L	50_V	0.674	0.39
84_S	92_Q	0.668	0.38
81_E	96_E	0.665	0.38
16_L	23_G	0.655	0.37
3_R	9_I	0.655	0.37
16_L	45_G	0.654	0.37
66_Q	72_E	0.644	0.36
23_G	48_G	0.642	0.36
1_M	18_G	0.629	0.35
75_V	78_K	0.626	0.35
24_L	38_S	0.624	0.35
20_G	46_L	0.619	0.34
4_I	9_I	0.609	0.34
60_G	64_Y	0.608	0.33
29_L	34_A	0.605	0.33
3_R	40_A	0.602	0.33
1_M	14_F	0.599	0.33
23_G	33_S	0.595	0.32
20_G	29_L	0.593	0.32
33_S	54_L	0.581	0.31
58_V	83_L	0.571	0.31
67_Q	71_Y	0.571	0.31
17_G	28_G	0.567	0.30
5_D	9_I	0.562	0.30
14_F	35_G	0.557	0.30
12_G	45_G	0.556	0.29
25_Q	85_P	0.553	0.29
63_T	79_R	0.553	0.29
73_E	76_L	0.546	0.29
45_G	83_L	0.542	0.28
86_E	89_A	0.542	0.28
47_L	54_L	0.537	0.28
36_I	61_K	0.532	0.28
31_G	90_K	0.532	0.28
69_K	91_L	0.528	0.27
11_L	41_L	0.521	0.27
3_R	74_A	0.520	0.27
23_G	27_A	0.520	0.27
32_F	68_R	0.520	0.27
11_L	90_K	0.520	0.27
18_G	24_L	0.517	0.27
29_L	38_S	0.516	0.27
18_G	22_L	0.506	0.26
8_L	15_L	0.506	0.26
57_V	83_L	0.504	0.26
26_A	89_A	0.502	0.26
25_Q	74_A	0.501	0.26
27_A	34_A	0.501	0.26
86_E	93_A	0.500	0.26

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
2yqcA	1	0.3438	66.7	0.896	Contact Map
1jv1A	2	0.3646	60	0.9	Contact Map
4bmaA	1	0.3646	34.3	0.915	Contact Map
2i5kA	5	0.2917	30.4	0.917	Contact Map
1dgsA	1	0.4688	28.9	0.918	Contact Map
3ogzA	1	0.375	26.9	0.919	Contact Map
2a61A	2	1	24.7	0.921	Contact Map
4bqhA	1	0.4062	22.6	0.922	Contact Map
2owoA	1	0.4375	22.3	0.922	Contact Map
3nqoA	2	1	21.8	0.923	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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