DUF4936 - PFAM28P - GREMLIN Contacts

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DUF4936 - Domain of unknown function (DUF4936)

PFAM:	PF16290	Sequences: YVYYRVAPADAAAARAAVRALQAALAARTGVRGRLLRRRDDPEARDGLQTWMEVYEGVADAAAFEAALAAAVAAAGLAALLAGPRHVERFV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	91 (84)
Sequences:	1920 (1445)
Seq/√Len:	157.7
META:	0.938

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
38_R	50_T	3.191	1.00
34_R	56_E	3.029	1.00
15_R	19_R	2.811	1.00
10_D	13_A	2.540	1.00
64_F	68_L	2.349	1.00
7_A	10_D	2.283	1.00
11_A	51_W	2.142	1.00
77_L	81_L	1.956	1.00
6_V	14_A	1.917	1.00
41_D	50_T	1.841	1.00
1_Y	36_L	1.601	1.00
69_A	73_A	1.592	1.00
4_Y	18_V	1.567	1.00
24_A	27_A	1.542	1.00
22_Q	25_L	1.537	1.00
85_R	90_F	1.516	1.00
1_Y	54_V	1.495	1.00
35_L	51_W	1.422	1.00
68_L	72_V	1.407	1.00
13_A	17_A	1.383	1.00
67_A	71_A	1.334	1.00
18_V	77_L	1.289	1.00
66_A	70_A	1.280	1.00
12_A	16_A	1.272	1.00
36_L	54_V	1.266	1.00
72_V	77_L	1.260	1.00
18_V	35_L	1.235	1.00
24_A	74_A	1.210	1.00
65_E	69_A	1.209	1.00
5_R	86_H	1.204	1.00
76_G	79_A	1.196	1.00
26_A	32_R	1.189	1.00
15_R	35_L	1.169	1.00
15_R	37_R	1.164	1.00
17_A	80_L	1.121	1.00
71_A	75_A	1.107	1.00
30_G	33_G	1.096	0.99
78_A	84_P	1.072	0.99
23_A	26_A	1.069	0.99
79_A	85_R	1.069	0.99
21_L	25_L	1.057	0.99
41_D	49_Q	1.044	0.99
58_V	64_F	1.043	0.99
70_A	74_A	1.000	0.99
22_Q	33_G	0.993	0.99
4_Y	51_W	0.986	0.99
5_R	14_A	0.975	0.99
37_R	40_D	0.975	0.99
20_A	24_A	0.968	0.99
3_Y	37_R	0.946	0.98
11_A	35_L	0.933	0.98
15_R	51_W	0.929	0.98
85_R	88_E	0.928	0.98
22_Q	80_L	0.920	0.98
20_A	23_A	0.913	0.98
18_V	22_Q	0.903	0.98
2_V	22_Q	0.892	0.98
25_L	31_V	0.876	0.97
64_F	72_V	0.872	0.97
6_V	49_Q	0.848	0.97
21_L	75_A	0.834	0.97
24_A	28_R	0.832	0.97
24_A	75_A	0.829	0.97
39_R	89_R	0.822	0.96
39_R	65_E	0.822	0.96
62_A	65_E	0.820	0.96
28_R	31_V	0.813	0.96
29_T	33_G	0.807	0.96
3_Y	8_P	0.800	0.96
27_A	71_A	0.796	0.96
62_A	66_A	0.795	0.96
16_A	19_R	0.788	0.95
63_A	72_V	0.783	0.95
22_Q	55_Y	0.779	0.95
65_E	68_L	0.773	0.95
17_A	77_L	0.772	0.95
2_V	38_R	0.767	0.95
4_Y	36_L	0.763	0.94
20_A	74_A	0.751	0.94
50_T	86_H	0.751	0.94
31_V	57_G	0.749	0.94
42_P	76_G	0.741	0.94
83_G	86_H	0.727	0.93
5_R	41_D	0.726	0.93
8_P	13_A	0.716	0.92
19_R	26_A	0.715	0.92
73_A	78_A	0.715	0.92
15_R	36_L	0.714	0.92
57_G	60_D	0.703	0.92
3_Y	22_Q	0.696	0.91
12_A	78_A	0.685	0.91
69_A	78_A	0.678	0.90
64_F	70_A	0.669	0.90
26_A	59_A	0.661	0.89
26_A	61_A	0.648	0.88
7_A	12_A	0.648	0.88
31_V	56_E	0.646	0.88
37_R	49_Q	0.642	0.88
11_A	84_P	0.640	0.87
63_A	66_A	0.638	0.87
77_L	82_A	0.629	0.87
22_Q	35_L	0.624	0.86
51_W	82_A	0.624	0.86
67_A	70_A	0.612	0.85
81_L	84_P	0.591	0.83
31_V	58_V	0.590	0.83
39_R	61_A	0.586	0.82
14_A	70_A	0.585	0.82
19_R	23_A	0.583	0.82
62_A	69_A	0.578	0.82
73_A	87_V	0.578	0.82
40_D	49_Q	0.560	0.80
13_A	79_A	0.544	0.78
65_E	72_V	0.542	0.77
11_A	37_R	0.533	0.76
28_R	33_G	0.532	0.76
62_A	68_L	0.525	0.75
20_A	56_E	0.525	0.75
26_A	66_A	0.523	0.75
28_R	74_A	0.517	0.74
34_R	89_R	0.514	0.74
21_L	77_L	0.510	0.73
63_A	68_L	0.506	0.72
61_A	66_A	0.503	0.72
16_A	20_A	0.502	0.72
63_A	75_A	0.500	0.72

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
2gffA	2	0.956	90.4	0.815	Contact Map
3fgvA	2	0.9231	90	0.817	Contact Map
2omoA	2	0.956	88.2	0.823	Contact Map
1y0hA	2	0.956	87.7	0.824	Contact Map
3bm7A	2	0.956	87.3	0.826	Contact Map
4dpoA	2	0.956	86.1	0.828	Contact Map
4zosA	2	0.956	85.4	0.83	Contact Map
3e8oA	2	0.956	84.8	0.832	Contact Map
4hl9A	2	0.956	84.8	0.832	Contact Map
2pd1A	5	0.9451	84	0.833	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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