DUF1218 - PFAM28P - GREMLIN Contacts

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DUF1218 - Protein of unknown function (DUF1218)

PFAM:	PF06749	Sequences: AALLLLLAQVIANVAGGCFCCGKRLSPSGANRTLAVVFFVLSWITFAIAEALLLAGAARNAYHTKYRVYSCYTLRKGVFAAGAVLSLVTAI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	91 (90)
Sequences:	693 (435)
Seq/√Len:	45.8
META:	0.029

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
56_G	79_F	2.878	1.00
59_R	74_L	2.830	1.00
24_R	28_S	2.798	1.00
22_G	25_L	2.492	1.00
16_G	19_F	2.346	1.00
45_T	89_T	2.230	1.00
52_L	85_L	2.188	1.00
2_A	6_L	1.970	0.99
84_V	88_V	1.936	0.99
47_A	51_A	1.862	0.99
80_A	84_V	1.853	0.99
23_K	27_P	1.746	0.98
9_Q	43_W	1.675	0.98
22_G	27_P	1.622	0.97
53_L	82_G	1.602	0.97
82_G	90_A	1.597	0.97
66_Y	69_Y	1.453	0.95
17_G	20_C	1.446	0.95
14_V	51_A	1.443	0.94
9_Q	20_C	1.435	0.94
10_V	15_A	1.421	0.94
21_C	27_P	1.420	0.94
10_V	36_V	1.355	0.92
5_L	83_A	1.299	0.91
45_T	52_L	1.283	0.90
47_A	85_L	1.278	0.90
25_L	30_A	1.265	0.90
63_H	77_G	1.264	0.89
27_P	48_I	1.254	0.89
79_F	82_G	1.238	0.88
4_L	23_K	1.235	0.88
73_T	80_A	1.229	0.88
80_A	86_S	1.220	0.88
34_L	37_V	1.181	0.86
3_L	89_T	1.180	0.86
46_F	89_T	1.173	0.86
31_N	90_A	1.172	0.86
23_K	30_A	1.167	0.85
53_L	57_A	1.160	0.85
37_V	53_L	1.159	0.85
50_E	61_A	1.153	0.85
37_V	41_L	1.146	0.84
22_G	30_A	1.129	0.83
40_V	47_A	1.088	0.81
38_F	80_A	1.082	0.81
35_A	43_W	1.052	0.79
69_Y	76_K	1.017	0.76
44_I	47_A	1.012	0.76
21_C	42_S	1.000	0.75
18_C	57_A	0.991	0.74
77_G	87_L	0.984	0.74
3_L	50_E	0.977	0.73
26_S	29_G	0.975	0.73
13_N	39_F	0.963	0.72
25_L	28_S	0.961	0.72
26_S	47_A	0.948	0.71
78_V	85_L	0.939	0.70
26_S	30_A	0.918	0.69
26_S	37_V	0.909	0.68
12_A	15_A	0.903	0.67
73_T	76_K	0.888	0.66
16_G	20_C	0.887	0.66
62_Y	66_Y	0.881	0.65
58_A	76_K	0.880	0.65
57_A	60_N	0.865	0.64
11_I	90_A	0.854	0.63
12_A	16_G	0.850	0.63
31_N	35_A	0.846	0.62
32_R	38_F	0.832	0.61
24_R	27_P	0.827	0.60
52_L	77_G	0.821	0.60
40_V	43_W	0.819	0.60
10_V	75_R	0.814	0.59
77_G	81_A	0.811	0.59
42_S	47_A	0.808	0.59
26_S	78_V	0.795	0.57
18_C	82_G	0.794	0.57
75_R	78_V	0.793	0.57
2_A	50_E	0.788	0.57
26_S	41_L	0.784	0.56
66_Y	70_S	0.780	0.56
21_C	25_L	0.777	0.56
64_T	80_A	0.754	0.53
11_I	70_S	0.749	0.53
41_L	47_A	0.749	0.53
55_A	78_V	0.737	0.52
12_A	21_C	0.732	0.51
45_T	75_R	0.725	0.51
34_L	38_F	0.725	0.51
1_A	4_L	0.721	0.50
38_F	51_A	0.705	0.49
1_A	41_L	0.701	0.48
59_R	63_H	0.664	0.45
1_A	66_Y	0.661	0.44
56_G	61_A	0.648	0.43
13_N	87_L	0.647	0.43
35_A	40_V	0.647	0.43
12_A	20_C	0.639	0.42
75_R	83_A	0.637	0.42
11_I	21_C	0.636	0.42
3_L	25_L	0.633	0.42
62_Y	67_R	0.628	0.41
52_L	62_Y	0.626	0.41
33_T	41_L	0.622	0.41
9_Q	13_N	0.622	0.41
42_S	54_L	0.621	0.40
49_A	86_S	0.620	0.40
37_V	57_A	0.613	0.40
34_L	87_L	0.609	0.39
33_T	44_I	0.598	0.38
14_V	26_S	0.589	0.37
5_L	70_S	0.587	0.37
72_Y	85_L	0.577	0.36
20_C	35_A	0.573	0.36
62_Y	82_G	0.571	0.36
54_L	61_A	0.568	0.36
85_L	88_V	0.568	0.36
44_I	67_R	0.564	0.35
32_R	46_F	0.564	0.35
72_Y	76_K	0.561	0.35
28_S	37_V	0.560	0.35
16_G	90_A	0.557	0.35
20_C	27_P	0.537	0.33
12_A	56_G	0.534	0.33
55_A	63_H	0.533	0.32
33_T	37_V	0.531	0.32
5_L	86_S	0.530	0.32
21_C	30_A	0.529	0.32
33_T	48_I	0.527	0.32
13_N	17_G	0.527	0.32
18_C	35_A	0.520	0.31
39_F	81_A	0.517	0.31
33_T	77_G	0.506	0.30
18_C	60_N	0.504	0.30
55_A	73_T	0.500	0.30

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
3x29A	1	0.9231	41.2	0.852	Contact Map
4p79A	1	0.989	31.4	0.862	Contact Map
4he8J	1	0.2088	3.5	0.911	Contact Map
3pblA	1	0.9451	2.7	0.916	Contact Map
3lb6C	1	0	1.8	0.923	Contact Map
1v54K	1	0.2747	1.5	0.927	Contact Map
4mqsA	1	0.967	1.5	0.927	Contact Map
1cd1A	1	0	1.4	0.928	Contact Map
2ivdA	1	0.1868	1.4	0.929	Contact Map
3uonA	1	0.967	1.3	0.929	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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