DUF2849 - PFAM28P - GREMLIN Contacts

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DUF2849 - Protein of unknown function (DUF2849)

PFAM:	PF11011	Sequences: KVVTANRLRDGDVVYLTADGGWSEDLADAAVAEDEAEALLALAAAAAAANRVVGPYLIDVELGDGGPRPVHLRERIRAAGPTVRPD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	86 (83)
Sequences:	5804 (3560)
Seq/√Len:	390.7
META:	0.916

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
7_R	10_D	3.890	1.00
17_T	23_S	3.026	1.00
2_V	29_A	2.647	1.00
25_D	28_D	2.527	1.00
32_A	39_L	2.477	1.00
62_L	67_P	2.150	1.00
31_V	60_V	2.040	1.00
7_R	24_E	1.982	1.00
4_T	56_Y	1.897	1.00
23_S	28_D	1.775	1.00
17_T	21_G	1.761	1.00
76_I	82_T	1.719	1.00
12_D	24_E	1.684	1.00
46_A	51_R	1.630	1.00
44_A	47_A	1.597	1.00
2_V	60_V	1.551	1.00
61_E	70_V	1.527	1.00
36_A	57_L	1.525	1.00
72_L	76_I	1.434	1.00
34_D	37_E	1.375	1.00
32_A	41_A	1.374	1.00
63_G	68_R	1.373	1.00
37_E	40_L	1.367	1.00
46_A	49_A	1.363	1.00
40_L	44_A	1.353	1.00
56_Y	74_E	1.349	1.00
2_V	58_I	1.208	1.00
36_A	40_L	1.206	1.00
48_A	51_R	1.194	1.00
27_A	67_P	1.176	1.00
26_L	67_P	1.171	1.00
7_R	14_V	1.169	1.00
63_G	66_G	1.140	1.00
3_V	57_L	1.139	1.00
60_V	67_P	1.115	1.00
14_V	52_V	1.104	1.00
72_L	82_T	1.085	1.00
33_E	37_E	1.084	1.00
4_T	15_Y	1.080	1.00
42_L	46_A	1.072	1.00
59_D	71_H	1.054	1.00
75_R	79_A	1.006	1.00
4_T	77_R	0.988	1.00
15_Y	26_L	0.971	1.00
61_E	68_R	0.968	1.00
47_A	55_P	0.961	1.00
17_T	30_A	0.959	1.00
20_G	44_A	0.951	1.00
75_R	78_A	0.941	1.00
45_A	49_A	0.936	1.00
15_Y	78_A	0.936	1.00
68_R	75_R	0.930	1.00
76_I	83_V	0.920	1.00
3_V	16_L	0.895	1.00
59_D	70_V	0.893	1.00
41_A	44_A	0.874	1.00
71_H	76_I	0.872	1.00
42_L	45_A	0.840	1.00
8_L	53_V	0.827	1.00
47_A	54_G	0.826	1.00
39_L	43_A	0.825	1.00
40_L	43_A	0.823	1.00
3_V	40_L	0.814	1.00
71_H	75_R	0.814	1.00
3_V	43_A	0.809	1.00
39_L	42_L	0.794	1.00
30_A	42_L	0.790	1.00
7_R	51_R	0.784	1.00
52_V	55_P	0.784	1.00
69_P	78_A	0.780	1.00
35_E	39_L	0.777	1.00
37_E	41_A	0.748	1.00
4_T	58_I	0.744	1.00
79_A	84_R	0.744	1.00
17_T	28_D	0.731	1.00
9_R	12_D	0.725	1.00
32_A	35_E	0.720	1.00
30_A	38_A	0.702	1.00
3_V	32_A	0.692	0.99
39_L	46_A	0.689	0.99
27_A	66_G	0.689	0.99
44_A	48_A	0.681	0.99
44_A	54_G	0.673	0.99
62_L	65_G	0.662	0.99
61_E	75_R	0.660	0.99
49_A	52_V	0.655	0.99
46_A	54_G	0.653	0.99
35_E	38_A	0.652	0.99
30_A	41_A	0.642	0.99
6_N	13_V	0.633	0.99
7_R	12_D	0.633	0.99
16_L	48_A	0.617	0.99
43_A	47_A	0.613	0.99
26_L	78_A	0.613	0.99
12_D	84_R	0.613	0.99
34_D	42_L	0.608	0.99
71_H	78_A	0.603	0.99
74_E	77_R	0.603	0.99
54_G	73_R	0.591	0.98
18_A	30_A	0.591	0.98
31_V	62_L	0.591	0.98
10_D	24_E	0.581	0.98
43_A	55_P	0.578	0.98
16_L	32_A	0.575	0.98
41_A	48_A	0.574	0.98
2_V	26_L	0.569	0.98
38_A	57_L	0.567	0.98
16_L	30_A	0.566	0.98
21_G	24_E	0.559	0.98
15_Y	71_H	0.556	0.98
36_A	39_L	0.551	0.98
53_V	60_V	0.550	0.97
37_E	43_A	0.550	0.97
5_A	52_V	0.549	0.97
15_Y	57_L	0.548	0.97
26_L	60_V	0.545	0.97
15_Y	58_I	0.544	0.97
69_P	75_R	0.533	0.97
68_R	79_A	0.522	0.97
47_A	50_N	0.520	0.96
3_V	52_V	0.507	0.96
58_I	71_H	0.504	0.96
29_A	80_G	0.504	0.96
13_V	53_V	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
1dj2A	2	0.7907	10.1	0.904	Contact Map
4m9dA	2	0.8488	8.8	0.907	Contact Map
3r7tA	4	0.7674	8.1	0.908	Contact Map
3hidA	2	0.8256	7.8	0.909	Contact Map
2gk3A	5	0.5349	6.9	0.911	Contact Map
1g8mA	2	0.9302	6.7	0.912	Contact Map
3sozA	3	0.5233	6.5	0.912	Contact Map
3ue9A	2	0.8488	6.3	0.913	Contact Map
3zzmA	2	0.9186	5.8	0.914	Contact Map
2v0xA	2	0.1744	5.1	0.916	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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