DUF2164 - PFAM28P - GREMLIN Contacts

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DUF2164 - Uncharacterized conserved protein (DUF2164)

PFAM:	PF09932	Sequences: IELSKEERAQLIASIQRYFAEELDEEIGDLAAELLLDFFLEEIGPYIYNQAVADAQAYLQERVEDLDGEIYELE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	74 (73)
Sequences:	5021 (3324)
Seq/√Len:	389.1
META:	0.885

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
40_L	47_I	2.745	1.00
19_F	27_I	2.554	1.00
14_S	42_E	2.532	1.00
48_Y	54_D	2.201	1.00
19_F	25_E	2.078	1.00
8_R	33_E	1.918	1.00
60_Q	64_E	1.839	1.00
17_R	21_E	1.771	1.00
51_A	55_A	1.769	1.00
62_R	65_D	1.766	1.00
4_S	7_E	1.700	1.00
30_L	34_L	1.664	1.00
47_I	51_A	1.655	1.00
16_Q	29_D	1.627	1.00
23_L	31_A	1.581	1.00
15_I	36_L	1.520	1.00
18_Y	34_L	1.511	1.00
20_A	26_E	1.500	1.00
5_K	9_A	1.401	1.00
18_Y	35_L	1.391	1.00
11_L	43_I	1.361	1.00
7_E	50_Q	1.345	1.00
19_F	23_L	1.324	1.00
56_Q	60_Q	1.321	1.00
68_G	71_Y	1.320	1.00
35_L	39_F	1.306	1.00
15_I	39_F	1.202	1.00
52_V	70_I	1.185	1.00
65_D	68_G	1.143	1.00
44_G	47_I	1.138	1.00
10_Q	14_S	1.137	1.00
12_I	33_E	1.125	1.00
3_L	11_L	1.106	1.00
50_Q	54_D	1.102	1.00
6_E	9_A	1.097	1.00
57_A	61_E	1.089	1.00
60_Q	67_D	1.071	1.00
28_G	31_A	1.061	1.00
18_Y	38_F	1.055	1.00
59_L	63_V	1.052	1.00
37_D	41_E	1.045	1.00
13_A	16_Q	0.980	1.00
25_E	31_A	0.970	1.00
19_F	35_L	0.969	1.00
16_Q	20_A	0.967	1.00
61_E	65_D	0.967	1.00
53_A	56_Q	0.953	1.00
31_A	34_L	0.928	1.00
10_Q	13_A	0.908	1.00
7_E	46_Y	0.908	1.00
50_Q	53_A	0.901	1.00
8_R	37_D	0.895	1.00
13_A	17_R	0.887	1.00
56_Q	67_D	0.881	1.00
57_A	60_Q	0.878	1.00
69_E	72_E	0.866	1.00
18_Y	22_E	0.852	1.00
64_E	67_D	0.844	1.00
9_A	13_A	0.830	1.00
58_Y	61_E	0.823	1.00
6_E	10_Q	0.820	1.00
61_E	64_E	0.811	1.00
12_I	36_L	0.806	1.00
18_Y	23_L	0.803	1.00
62_R	69_E	0.798	1.00
14_S	17_R	0.787	1.00
5_K	8_R	0.784	1.00
52_V	55_A	0.764	1.00
58_Y	69_E	0.760	1.00
11_L	39_F	0.759	1.00
58_Y	70_I	0.696	1.00
43_I	46_Y	0.683	0.99
2_E	5_K	0.679	0.99
8_R	12_I	0.673	0.99
51_A	70_I	0.667	0.99
39_F	47_I	0.667	0.99
3_L	46_Y	0.663	0.99
3_L	7_E	0.660	0.99
69_E	73_L	0.659	0.99
63_V	66_L	0.658	0.99
16_Q	30_L	0.655	0.99
17_R	20_A	0.646	0.99
58_Y	62_R	0.641	0.99
15_I	27_I	0.619	0.99
27_I	31_A	0.616	0.99
7_E	10_Q	0.613	0.99
53_A	57_A	0.611	0.99
68_G	72_E	0.592	0.98
14_S	38_F	0.585	0.98
3_L	40_L	0.575	0.98
67_D	71_Y	0.575	0.98
16_Q	26_E	0.572	0.98
65_D	69_E	0.572	0.98
63_V	67_D	0.567	0.98
34_L	39_F	0.558	0.98
68_G	73_L	0.554	0.98
38_F	42_E	0.553	0.98
48_Y	51_A	0.542	0.97
60_Q	63_V	0.534	0.97
12_I	32_A	0.534	0.97
11_L	46_Y	0.531	0.97
7_E	11_L	0.527	0.97
14_S	40_L	0.526	0.97
36_L	43_I	0.524	0.97
3_L	44_G	0.520	0.96
34_L	37_D	0.518	0.96
29_D	33_E	0.518	0.96
30_L	37_D	0.508	0.96
27_I	32_A	0.505	0.96
9_A	29_D	0.500	0.96

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
4nguA	1	0.6216	20.1	0.863	Contact Map
2mjgA	2	0.3108	18.3	0.865	Contact Map
3m1gA	2	1	10.4	0.879	Contact Map
4n4uA	1	0.5811	8.1	0.885	Contact Map
3ppuA	2	1	7.7	0.886	Contact Map
4g0iA	2	1	7.3	0.887	Contact Map
4pfiA	1	0.527	6.8	0.889	Contact Map
1af7A	1	0.6892	6.4	0.89	Contact Map
1fxkA	2	0.9324	5.8	0.892	Contact Map
3le1A	1	0.3378	5.8	0.892	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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