DUF4834 - PFAM28P - GREMLIN Contacts

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DUF4834 - Domain of unknown function (DUF4834)

PFAM:	PF16118	Sequences: MKFLGFLLILIILLIYYGLKILRRLFRPLFGLGRRKKASKKAQKKFQQQFQQQQQQQQQRQQTKKEGEVIIDKKPKKKKKRKKIFSKDVGEYVDFEEIK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	99 (93)
Sequences:	2704 (2379)
Seq/√Len:	246.7
META:	0.851

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
67_G	71_I	3.322	1.00
14_L	18_G	2.623	1.00
16_Y	20_K	2.432	1.00
68_E	71_I	2.425	1.00
22_L	26_F	2.176	1.00
24_R	28_P	2.004	1.00
19_L	23_R	2.003	1.00
65_K	68_E	1.827	1.00
9_I	13_L	1.825	1.00
42_A	45_K	1.816	1.00
43_Q	47_Q	1.721	1.00
11_I	15_I	1.643	1.00
67_G	70_I	1.621	1.00
28_P	31_G	1.578	1.00
23_R	27_R	1.566	1.00
24_R	27_R	1.562	1.00
86_S	89_V	1.544	1.00
45_K	49_Q	1.539	1.00
27_R	31_G	1.528	1.00
46_F	49_Q	1.526	1.00
42_A	46_F	1.522	1.00
13_L	17_Y	1.487	1.00
8_L	12_I	1.480	1.00
49_Q	52_Q	1.451	1.00
20_K	24_R	1.389	1.00
41_K	44_K	1.379	1.00
21_I	24_R	1.363	1.00
47_Q	51_Q	1.342	1.00
18_G	22_L	1.338	1.00
15_I	19_L	1.335	1.00
10_L	14_L	1.315	1.00
35_R	39_S	1.308	1.00
34_R	38_A	1.302	1.00
23_R	26_F	1.290	1.00
20_K	23_R	1.263	1.00
72_D	75_P	1.190	1.00
20_K	28_P	1.137	1.00
26_F	30_F	1.126	1.00
8_L	15_I	1.126	1.00
64_K	69_V	1.119	1.00
41_K	45_K	1.112	1.00
41_K	46_F	1.111	1.00
45_K	48_Q	1.099	1.00
73_K	76_K	1.088	1.00
48_Q	52_Q	1.085	1.00
67_G	72_D	1.044	1.00
51_Q	54_Q	1.039	1.00
46_F	50_F	1.039	1.00
62_Q	65_K	1.039	1.00
15_I	18_G	1.010	1.00
17_Y	21_I	1.008	1.00
48_Q	51_Q	1.008	1.00
25_L	28_P	1.004	1.00
81_R	86_S	0.993	1.00
59_Q	62_Q	0.970	1.00
43_Q	46_F	0.954	1.00
66_E	70_I	0.938	1.00
4_L	7_L	0.934	1.00
22_L	25_L	0.932	1.00
66_E	71_I	0.932	1.00
47_Q	50_F	0.932	1.00
19_L	24_R	0.922	1.00
51_Q	55_Q	0.918	1.00
66_E	69_V	0.913	1.00
71_I	74_K	0.909	1.00
5_G	9_I	0.894	1.00
44_K	47_Q	0.891	1.00
17_Y	20_K	0.880	1.00
89_V	92_Y	0.875	0.99
23_R	29_L	0.874	0.99
64_K	67_G	0.870	0.99
53_Q	56_Q	0.854	0.99
43_Q	49_Q	0.835	0.99
21_I	25_L	0.813	0.99
90_G	93_V	0.808	0.99
37_K	40_K	0.805	0.99
87_K	90_G	0.793	0.99
57_Q	60_R	0.791	0.99
23_R	28_P	0.783	0.99
44_K	48_Q	0.782	0.99
14_L	24_R	0.775	0.99
69_V	72_D	0.768	0.99
74_K	77_K	0.762	0.99
23_R	31_G	0.760	0.99
18_G	26_F	0.742	0.98
6_F	14_L	0.736	0.98
11_I	18_G	0.736	0.98
6_F	15_I	0.728	0.98
76_K	79_K	0.727	0.98
19_L	26_F	0.726	0.98
6_F	10_L	0.722	0.98
68_E	74_K	0.720	0.98
64_K	74_K	0.709	0.98
90_G	97_E	0.698	0.98
10_L	13_L	0.697	0.98
64_K	70_I	0.695	0.97
36_K	39_S	0.688	0.97
74_K	99_K	0.684	0.97
69_V	73_K	0.682	0.97
40_K	43_Q	0.681	0.97
89_V	99_K	0.681	0.97
65_K	71_I	0.674	0.97
53_Q	57_Q	0.672	0.97
10_L	18_G	0.667	0.97
4_L	8_L	0.666	0.97
58_Q	61_Q	0.658	0.96
86_S	95_F	0.656	0.96
63_T	66_E	0.646	0.96
67_G	75_P	0.643	0.96
52_Q	55_Q	0.642	0.96
17_Y	24_R	0.636	0.96
80_K	86_S	0.633	0.96
30_F	38_A	0.629	0.95
11_I	14_L	0.613	0.95
10_L	15_I	0.611	0.95
11_I	24_R	0.611	0.95
33_G	37_K	0.601	0.94
7_L	11_I	0.594	0.94
12_I	17_Y	0.592	0.94
40_K	44_K	0.583	0.93
70_I	73_K	0.580	0.93
57_Q	62_Q	0.577	0.93
83_K	88_D	0.576	0.93
6_F	16_Y	0.573	0.93
13_L	19_L	0.560	0.92
49_Q	53_Q	0.559	0.92
5_G	14_L	0.558	0.92
54_Q	58_Q	0.553	0.91
13_L	18_G	0.547	0.91
67_G	73_K	0.542	0.90
52_Q	56_Q	0.540	0.90
33_G	36_K	0.536	0.90
16_Y	28_P	0.529	0.89
38_A	42_A	0.527	0.89
47_Q	53_Q	0.522	0.89
64_K	68_E	0.520	0.89
20_K	26_F	0.515	0.88
37_K	42_A	0.511	0.88
11_I	17_Y	0.511	0.88
61_Q	64_K	0.500	0.87

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
4um9B	2	0	27.9	0.851	Contact Map
2w1kA	1	0	11	0.876	Contact Map
5a2fA	1	0	10.8	0.877	Contact Map
2l16A	1	0.4848	10.2	0.878	Contact Map
4cylA	1	0.0101	8.5	0.882	Contact Map
3lb6C	1	0	7.4	0.885	Contact Map
1cd1A	1	0	7.1	0.886	Contact Map
3oduA	2	0.9596	6.7	0.888	Contact Map
1pi7A	1	0.1919	6.5	0.888	Contact Map
3j0cA	4	0.3636	5.7	0.891	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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