DUF4920 - PFAM28P - GREMLIN Contacts

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DUF4920 - Domain of unknown function (DUF4920)

PFAM:	PF16267	Sequences: KYKKLKKGDTLTVKVEGKVTEVCQKKGCWMKLALGDGETVRVKFKDYGFFVPKDAAGKTVVVEGKAFVKETSVEELKHYAEDAGKSK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	87 (79)
Sequences:	5230 (3391)
Seq/√Len:	381.6
META:	0.937

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
14_K	63_E	2.450	1.00
24_Q	56_A	2.285	1.00
16_E	59_T	2.273	1.00
32_L	62_V	2.199	1.00
14_K	61_V	2.183	1.00
72_S	75_E	2.174	1.00
73_V	76_L	2.022	1.00
19_V	55_A	1.966	1.00
73_V	77_K	1.944	1.00
31_K	41_R	1.928	1.00
26_K	47_Y	1.867	1.00
18_K	33_A	1.778	1.00
31_K	39_T	1.727	1.00
20_T	33_A	1.653	1.00
30_M	51_V	1.633	1.00
12_T	65_K	1.616	1.00
45_K	48_G	1.612	1.00
16_E	61_V	1.546	1.00
18_K	59_T	1.531	1.00
21_E	31_K	1.527	1.00
78_H	81_E	1.458	1.00
22_V	55_A	1.456	1.00
47_Y	50_F	1.417	1.00
78_H	82_D	1.413	1.00
76_L	80_A	1.406	1.00
17_G	32_L	1.383	1.00
75_E	79_Y	1.364	1.00
12_T	63_E	1.344	1.00
30_M	60_V	1.313	1.00
10_T	65_K	1.264	1.00
71_T	76_L	1.246	1.00
24_Q	53_K	1.221	1.00
15_V	40_V	1.200	1.00
21_E	56_A	1.180	1.00
19_V	60_V	1.155	1.00
44_F	50_F	1.127	1.00
44_F	47_Y	1.089	1.00
20_T	39_T	1.057	1.00
44_F	51_V	1.053	1.00
51_V	55_A	1.050	1.00
26_K	50_F	1.017	1.00
8_G	11_L	1.016	1.00
34_L	39_T	0.982	1.00
80_A	85_K	0.981	1.00
34_L	37_G	0.964	1.00
77_K	81_E	0.959	1.00
55_A	58_K	0.941	1.00
55_A	60_V	0.928	1.00
41_R	79_Y	0.917	1.00
71_T	79_Y	0.915	1.00
22_V	54_D	0.912	1.00
21_E	83_A	0.911	1.00
23_C	28_C	0.903	1.00
72_S	76_L	0.883	1.00
35_G	38_E	0.863	1.00
34_L	38_E	0.861	1.00
19_V	30_M	0.860	1.00
30_M	42_V	0.857	1.00
22_V	56_A	0.855	1.00
44_F	48_G	0.794	1.00
30_M	44_F	0.764	1.00
73_V	80_A	0.760	1.00
74_E	77_K	0.757	1.00
8_G	13_V	0.755	1.00
32_L	60_V	0.754	1.00
77_K	80_A	0.753	1.00
47_Y	51_V	0.752	1.00
9_D	67_F	0.751	1.00
20_T	31_K	0.747	1.00
13_V	17_G	0.741	1.00
42_V	62_V	0.739	1.00
71_T	75_E	0.722	1.00
81_E	84_G	0.715	1.00
43_K	79_Y	0.713	1.00
33_A	36_D	0.711	1.00
53_K	56_A	0.709	1.00
12_T	16_E	0.706	1.00
15_V	62_V	0.701	0.99
19_V	22_V	0.691	0.99
69_K	75_E	0.685	0.99
10_T	67_F	0.679	0.99
9_D	65_K	0.679	0.99
48_G	51_V	0.676	0.99
70_E	73_V	0.664	0.99
77_K	84_G	0.660	0.99
43_K	47_Y	0.657	0.99
22_V	53_K	0.647	0.99
46_D	50_F	0.641	0.99
9_D	68_V	0.624	0.99
73_V	79_Y	0.621	0.99
22_V	51_V	0.615	0.99
34_L	40_V	0.615	0.99
9_D	12_T	0.608	0.99
11_L	66_A	0.603	0.98
29_W	53_K	0.602	0.98
42_V	49_F	0.591	0.98
33_A	37_G	0.586	0.98
8_G	65_K	0.584	0.98
21_E	24_Q	0.582	0.98
13_V	16_E	0.563	0.98
19_V	56_A	0.562	0.98
65_K	69_K	0.561	0.98
54_D	58_K	0.543	0.97
45_K	49_F	0.543	0.97
81_E	85_K	0.539	0.97
9_D	13_V	0.535	0.97
8_G	12_T	0.533	0.97
17_G	57_G	0.530	0.97
17_G	40_V	0.524	0.96
45_K	65_K	0.516	0.96
26_K	30_M	0.515	0.96
27_G	46_D	0.515	0.96
66_A	80_A	0.510	0.96
43_K	75_E	0.509	0.96
79_Y	82_D	0.509	0.96
43_K	46_D	0.505	0.96
79_Y	83_A	0.503	0.95
29_W	83_A	0.500	0.95

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
2xgtA	2	0.9885	46	0.868	Contact Map
1n9wA	2	0.8851	45.6	0.869	Contact Map
1nnxA	1	0.8621	37.1	0.875	Contact Map
2vovA	1	0.4138	29.6	0.882	Contact Map
1e1oA	2	0.9425	27	0.884	Contact Map
4pg3A	2	0.977	23.2	0.887	Contact Map
4ycuA	3	0.9885	18.9	0.892	Contact Map
3m4pA	2	0.9885	15.8	0.896	Contact Map
1eovA	2	0.977	15.2	0.896	Contact Map
4up7A	2	0.977	14.6	0.897	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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