DUF4087 - PFAM28P - GREMLIN Contacts

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DUF4087 - Protein of unknown function (DUF4087)

PFAM:	PF13316	Sequences: AAETRCGWFSNPTPANAWLTDRDGEWTIGVQGGYQAEGMDDWPDFSPGQWVETNGHYGYGCACLRVRVDRETHRVTRIKSARARPLSACRADPALK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	96 (94)
Sequences:	661 (460)
Seq/√Len:	47.4
META:	0.853

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
52_E	56_H	4.231	1.00
84_R	88_A	3.974	1.00
29_G	35_Q	3.337	1.00
66_V	75_V	2.778	1.00
50_W	60_G	2.603	1.00
9_F	17_A	2.577	1.00
9_F	42_W	2.364	1.00
9_F	62_A	2.337	1.00
16_N	31_Q	2.276	1.00
67_R	77_R	2.233	1.00
13_T	16_N	2.066	1.00
49_Q	83_A	2.036	1.00
4_T	65_R	1.820	0.99
28_I	78_I	1.777	0.99
67_R	79_K	1.742	0.98
17_A	42_W	1.637	0.98
45_F	60_G	1.633	0.98
24_G	73_H	1.628	0.98
60_G	83_A	1.604	0.97
45_F	49_Q	1.555	0.97
17_A	39_M	1.517	0.96
2_A	79_K	1.485	0.96
69_D	74_R	1.470	0.95
53_T	56_H	1.451	0.95
64_L	81_A	1.393	0.94
65_R	80_S	1.310	0.92
86_L	90_R	1.294	0.91
3_E	70_R	1.288	0.91
85_P	88_A	1.278	0.91
18_W	27_T	1.278	0.91
54_N	57_Y	1.261	0.90
31_Q	57_Y	1.211	0.88
51_V	59_Y	1.205	0.88
20_T	25_E	1.177	0.87
11_N	16_N	1.153	0.86
10_S	20_T	1.149	0.85
89_C	92_D	1.143	0.85
69_D	72_T	1.132	0.85
13_T	31_Q	1.105	0.83
68_V	76_T	1.102	0.83
22_R	81_A	1.101	0.83
12_P	16_N	1.061	0.81
18_W	30_V	1.040	0.79
22_R	73_H	1.026	0.78
66_V	79_K	1.004	0.77
87_S	91_A	0.975	0.75
46_S	81_A	0.948	0.72
36_A	40_D	0.935	0.71
29_G	72_T	0.915	0.70
37_E	77_R	0.913	0.70
37_E	76_T	0.891	0.68
4_T	82_R	0.887	0.67
52_E	57_Y	0.881	0.67
27_T	30_V	0.868	0.66
2_A	67_R	0.862	0.65
36_A	66_V	0.860	0.65
15_A	35_Q	0.835	0.63
87_S	90_R	0.835	0.63
17_A	40_D	0.833	0.62
15_A	29_G	0.830	0.62
28_I	39_M	0.830	0.62
12_P	57_Y	0.824	0.62
13_T	95_L	0.806	0.60
75_V	79_K	0.800	0.59
68_V	72_T	0.797	0.59
42_W	45_F	0.779	0.57
41_D	50_W	0.777	0.57
76_T	79_K	0.775	0.57
34_Y	67_R	0.767	0.56
18_W	25_E	0.765	0.56
12_P	18_W	0.762	0.56
48_G	94_A	0.743	0.54
9_F	81_A	0.742	0.54
66_V	80_S	0.741	0.53
65_R	71_E	0.732	0.53
12_P	31_Q	0.726	0.52
16_N	57_Y	0.724	0.52
3_E	6_C	0.704	0.50
5_R	8_W	0.699	0.49
42_W	83_A	0.699	0.49
24_G	81_A	0.696	0.49
22_R	68_V	0.689	0.48
29_G	82_R	0.682	0.48
72_T	84_R	0.677	0.47
20_T	68_V	0.671	0.47
49_Q	69_D	0.666	0.46
44_D	83_A	0.662	0.46
44_D	81_A	0.661	0.46
14_P	31_Q	0.660	0.45
71_E	76_T	0.653	0.45
43_P	62_A	0.650	0.44
19_L	62_A	0.636	0.43
10_S	28_I	0.636	0.43
37_E	93_P	0.632	0.43
68_V	75_V	0.630	0.42
30_V	34_Y	0.630	0.42
10_S	91_A	0.629	0.42
25_E	31_Q	0.627	0.42
70_R	87_S	0.623	0.42
33_G	36_A	0.615	0.41
90_R	95_L	0.611	0.41
25_E	40_D	0.605	0.40
10_S	73_H	0.604	0.40
21_D	92_D	0.599	0.39
15_A	30_V	0.593	0.39
51_V	58_G	0.591	0.39
67_R	70_R	0.589	0.39
13_T	18_W	0.585	0.38
12_P	59_Y	0.584	0.38
45_F	83_A	0.583	0.38
14_P	57_Y	0.575	0.37
20_T	30_V	0.571	0.37
74_R	82_R	0.567	0.36
75_V	83_A	0.566	0.36
22_R	93_P	0.566	0.36
61_C	89_C	0.562	0.36
64_L	82_R	0.557	0.36
30_V	66_V	0.556	0.35
20_T	23_D	0.554	0.35
70_R	74_R	0.552	0.35
42_W	59_Y	0.552	0.35
17_A	38_G	0.550	0.35
62_A	81_A	0.548	0.35
52_E	93_P	0.546	0.35
3_E	28_I	0.544	0.34
11_N	31_Q	0.543	0.34
27_T	34_Y	0.542	0.34
21_D	63_C	0.536	0.34
5_R	84_R	0.536	0.34
2_A	77_R	0.535	0.34
16_N	54_N	0.533	0.33
24_G	29_G	0.530	0.33
92_D	95_L	0.528	0.33
8_W	86_L	0.524	0.33
18_W	57_Y	0.522	0.32
74_R	94_A	0.514	0.32
64_L	75_V	0.513	0.32
50_W	58_G	0.504	0.31
37_E	82_R	0.501	0.31
33_G	43_P	0.501	0.31
65_R	79_K	0.500	0.31

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
1d4bA	1	0.5	10.6	0.939	Contact Map
3s5tA	2	0.3021	6.9	0.944	Contact Map
2yijA	2	0.4167	6.7	0.944	Contact Map
2d7uA	2	0.7917	6.2	0.945	Contact Map
3r7tA	4	0.8854	6.2	0.945	Contact Map
3ue9A	2	0.8854	5.8	0.946	Contact Map
4m9dA	2	0.8854	5.5	0.946	Contact Map
2v40A	2	0.8958	4.4	0.949	Contact Map
1p9bA	2	0.8854	4.2	0.949	Contact Map
3j38A	1	0	3.9	0.95	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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