DUF1820 - PFAM28P - GREMLIN Contacts

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DUF1820 - Domain of unknown function (DUF1820)

PFAM:	PF08850	Sequences: QIYKVIFLNQGKVYEIYARSVSQSDLYGFVEVEELVFGERSSVVVDPSEEKLKSEFAGVKRTYIPMHSVIRIDEVEKEGVAKISDAEGGGNVTPFPM	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	97 (95)
Sequences:	2626 (1368)
Seq/√Len:	140.3
META:	0.922

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
2_I	36_V	3.603	1.00
60_K	76_E	2.611	1.00
20_S	33_E	2.470	1.00
22_S	25_D	2.446	1.00
9_N	70_I	2.312	1.00
30_V	72_I	2.218	1.00
19_R	34_E	2.167	1.00
17_Y	81_A	2.162	1.00
22_S	27_Y	2.157	1.00
60_K	74_E	2.084	1.00
13_V	70_I	2.071	1.00
27_Y	30_V	1.912	1.00
32_V	64_I	1.899	1.00
18_A	35_L	1.870	1.00
38_G	49_E	1.798	1.00
19_R	36_V	1.760	1.00
34_E	60_K	1.743	1.00
18_A	32_V	1.731	1.00
14_Y	55_E	1.688	1.00
16_I	35_L	1.682	1.00
58_G	76_E	1.670	1.00
35_L	62_T	1.668	1.00
62_T	73_D	1.652	1.00
33_E	61_R	1.617	1.00
39_E	42_S	1.609	1.00
45_V	50_E	1.563	1.00
25_D	31_E	1.480	1.00
25_D	63_Y	1.447	1.00
8_L	70_I	1.382	1.00
59_V	73_D	1.337	1.00
16_I	81_A	1.290	1.00
63_Y	74_E	1.269	1.00
12_K	51_K	1.262	1.00
61_R	74_E	1.250	1.00
52_L	64_I	1.186	1.00
22_S	33_E	1.173	1.00
44_V	47_P	1.151	0.99
5_V	32_V	1.151	0.99
16_I	32_V	1.129	0.99
26_L	63_Y	1.103	0.99
42_S	82_K	1.097	0.99
49_E	53_K	1.067	0.99
6_I	70_I	1.050	0.99
22_S	31_E	1.037	0.99
30_V	69_V	1.018	0.99
24_S	31_E	1.004	0.98
27_Y	67_H	0.985	0.98
75_V	79_G	0.974	0.98
40_R	51_K	0.948	0.98
86_A	90_G	0.925	0.97
12_K	42_S	0.918	0.97
31_E	61_R	0.909	0.97
23_Q	52_L	0.902	0.97
27_Y	66_M	0.893	0.97
8_L	86_A	0.891	0.97
37_F	49_E	0.884	0.97
23_Q	27_Y	0.880	0.96
50_E	53_K	0.876	0.96
11_G	23_Q	0.873	0.96
31_E	71_R	0.838	0.95
56_F	70_I	0.836	0.95
23_Q	30_V	0.826	0.95
14_Y	59_V	0.824	0.95
85_D	88_G	0.809	0.94
6_I	13_V	0.803	0.94
38_G	41_S	0.803	0.94
24_S	27_Y	0.802	0.94
28_G	65_P	0.801	0.94
60_K	84_S	0.797	0.94
14_Y	83_I	0.787	0.94
15_E	29_F	0.782	0.93
5_V	18_A	0.782	0.93
22_S	63_Y	0.771	0.93
23_Q	26_L	0.762	0.92
51_K	85_D	0.754	0.92
37_F	50_E	0.748	0.92
84_S	91_N	0.748	0.92
4_K	17_Y	0.741	0.91
80_V	85_D	0.738	0.91
12_K	85_D	0.733	0.91
10_Q	13_V	0.731	0.91
8_L	13_V	0.729	0.91
55_E	71_R	0.725	0.90
16_I	28_G	0.710	0.90
36_V	39_E	0.704	0.89
8_L	27_Y	0.703	0.89
25_D	28_G	0.701	0.89
27_Y	51_K	0.700	0.89
8_L	12_K	0.697	0.89
22_S	62_T	0.693	0.88
42_S	54_S	0.688	0.88
74_E	78_E	0.685	0.88
64_I	73_D	0.679	0.87
90_G	93_T	0.677	0.87
45_V	53_K	0.676	0.87
85_D	89_G	0.668	0.87
29_F	46_D	0.658	0.86
18_A	74_E	0.657	0.86
87_E	90_G	0.657	0.86
40_R	46_D	0.655	0.85
60_K	95_F	0.643	0.84
52_L	81_A	0.634	0.84
48_S	53_K	0.634	0.84
54_S	57_A	0.633	0.83
88_G	94_P	0.627	0.83
44_V	50_E	0.620	0.82
51_K	83_I	0.619	0.82
4_K	75_V	0.616	0.82
80_V	86_A	0.608	0.81
31_E	63_Y	0.607	0.81
61_R	90_G	0.604	0.81
9_N	55_E	0.603	0.80
91_N	94_P	0.603	0.80
20_S	34_E	0.600	0.80
43_V	80_V	0.596	0.80
3_Y	63_Y	0.596	0.80
84_S	87_E	0.591	0.79
91_N	95_F	0.590	0.79
21_V	24_S	0.589	0.79
64_I	69_V	0.578	0.78
89_G	93_T	0.573	0.77
24_S	35_L	0.570	0.77
85_D	90_G	0.561	0.75
78_E	81_A	0.561	0.75
77_K	91_N	0.553	0.74
23_Q	66_M	0.552	0.74
34_E	62_T	0.543	0.73
81_A	84_S	0.532	0.72
8_L	11_G	0.526	0.71
16_I	78_E	0.526	0.71
62_T	69_V	0.525	0.71
43_V	47_P	0.524	0.70
23_Q	63_Y	0.519	0.70
12_K	35_L	0.515	0.69
44_V	51_K	0.510	0.68
46_D	75_V	0.509	0.68
12_K	27_Y	0.508	0.68
20_S	25_D	0.506	0.68
27_Y	55_E	0.505	0.68
26_L	70_I	0.502	0.67
17_Y	52_L	0.502	0.67
2_I	6_I	0.500	0.67

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
3ay2A	1	0.3402	15	0.923	Contact Map
1nynA	1	0.9072	9.8	0.929	Contact Map
4hczA	1	0.2784	8.2	0.931	Contact Map
3ef4A	1	0.6186	6.3	0.934	Contact Map
2i4lA	2	0.866	5.7	0.936	Contact Map
1bxvA	1	0.3299	5	0.938	Contact Map
2ux6A	1	0.6289	5	0.938	Contact Map
3j26A	9	0.9691	4.9	0.938	Contact Map
3a32A	2	0.8763	4.8	0.938	Contact Map
3uh0A	2	0.9588	4.4	0.939	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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