DUF4873 - PFAM28P - GREMLIN Contacts

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DUF4873 - Domain of unknown function (DUF4873)

PFAM:	PF16170	Sequences: DDGYDGPATLVVGGAEVPVRVRLRGHFDPIDGRYHWYGRVAADDELPALVGGGRRTVTLRTPHGSAPARLSEPDPWGRYRVTGVGTPPFPV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	91 (89)
Sequences:	922 (650)
Seq/√Len:	68.9
META:	0.723

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
25_G	34_Y	4.242	1.00
31_D	35_H	3.322	1.00
21_V	40_V	3.140	1.00
60_R	65_S	3.072	1.00
5_D	22_R	3.046	1.00
8_A	21_V	3.032	1.00
11_V	60_R	3.021	1.00
61_T	64_G	2.670	1.00
57_V	68_A	2.518	1.00
39_R	74_D	2.493	1.00
58_T	65_S	2.420	1.00
9_T	16_E	1.916	1.00
20_R	41_A	1.796	1.00
74_D	78_R	1.758	1.00
30_I	75_P	1.576	0.99
58_T	67_P	1.513	0.99
25_G	37_Y	1.422	0.98
23_L	81_V	1.360	0.98
8_A	19_V	1.328	0.97
46_L	51_G	1.310	0.97
59_L	81_V	1.286	0.97
47_P	77_G	1.271	0.97
42_A	47_P	1.203	0.95
44_D	58_T	1.197	0.95
79_Y	89_F	1.158	0.94
22_R	33_R	1.158	0.94
40_V	81_V	1.126	0.93
56_T	67_P	1.111	0.93
15_A	45_E	1.108	0.93
30_I	34_Y	1.108	0.93
85_G	88_P	1.101	0.92
59_L	68_A	1.077	0.92
25_G	31_D	1.065	0.91
74_D	80_R	1.054	0.91
47_P	73_P	1.054	0.91
79_Y	87_P	1.048	0.91
45_E	67_P	1.046	0.90
69_R	85_G	1.042	0.90
61_T	72_E	1.013	0.89
11_V	16_E	1.001	0.88
63_H	90_P	0.997	0.88
72_E	78_R	0.983	0.87
28_D	31_D	0.967	0.87
39_R	80_R	0.965	0.86
82_T	87_P	0.965	0.86
11_V	14_G	0.954	0.86
25_G	30_I	0.950	0.86
5_D	20_R	0.939	0.85
9_T	62_P	0.932	0.85
50_V	55_R	0.927	0.84
68_A	81_V	0.891	0.82
37_Y	72_E	0.889	0.82
35_H	82_T	0.874	0.80
31_D	69_R	0.852	0.79
72_E	87_P	0.839	0.78
4_Y	7_P	0.816	0.76
80_R	83_G	0.810	0.75
83_G	88_P	0.808	0.75
83_G	89_F	0.802	0.74
84_V	87_P	0.800	0.74
26_H	37_Y	0.791	0.73
12_V	15_A	0.783	0.73
24_R	78_R	0.776	0.72
55_R	82_T	0.772	0.72
31_D	79_Y	0.757	0.70
32_G	87_P	0.750	0.69
12_V	49_L	0.750	0.69
45_E	48_A	0.750	0.69
28_D	33_R	0.749	0.69
21_V	29_P	0.746	0.69
5_D	46_L	0.743	0.69
54_R	69_R	0.738	0.68
31_D	87_P	0.735	0.68
35_H	84_V	0.735	0.68
26_H	34_Y	0.728	0.67
13_G	16_E	0.720	0.66
50_V	53_G	0.715	0.66
35_H	71_S	0.711	0.65
12_V	46_L	0.709	0.65
20_R	23_L	0.698	0.64
65_S	70_L	0.698	0.64
37_Y	78_R	0.695	0.64
61_T	78_R	0.692	0.63
8_A	30_I	0.682	0.62
10_L	19_V	0.676	0.61
3_G	74_D	0.673	0.61
32_G	72_E	0.668	0.60
71_S	80_R	0.666	0.60
9_T	60_R	0.663	0.60
11_V	58_T	0.655	0.59
24_R	30_I	0.654	0.59
41_A	47_P	0.654	0.59
45_E	56_T	0.640	0.57
66_A	87_P	0.639	0.57
37_Y	81_V	0.638	0.57
17_V	75_P	0.635	0.57
72_E	76_W	0.632	0.56
7_P	18_P	0.629	0.56
65_S	69_R	0.628	0.56
24_R	34_Y	0.618	0.55
3_G	39_R	0.617	0.54
31_D	68_A	0.615	0.54
9_T	15_A	0.610	0.54
23_L	42_A	0.605	0.53
28_D	71_S	0.596	0.52
14_G	63_H	0.595	0.52
5_D	35_H	0.590	0.51
27_F	71_S	0.590	0.51
11_V	67_P	0.586	0.51
8_A	40_V	0.581	0.50
66_A	84_V	0.570	0.49
44_D	49_L	0.569	0.49
3_G	58_T	0.568	0.49
23_L	59_L	0.563	0.48
68_A	77_G	0.560	0.48
3_G	69_R	0.559	0.48
73_P	76_W	0.558	0.47
54_R	67_P	0.553	0.47
9_T	17_V	0.552	0.47
7_P	16_E	0.549	0.46
13_G	27_F	0.542	0.45
37_Y	74_D	0.542	0.45
35_H	75_P	0.541	0.45
69_R	90_P	0.539	0.45
24_R	72_E	0.524	0.43
15_A	28_D	0.523	0.43
48_A	81_V	0.522	0.43
10_L	75_P	0.518	0.43
43_D	76_W	0.517	0.43
17_V	48_A	0.511	0.42
35_H	70_L	0.504	0.41
33_R	84_V	0.503	0.41
73_P	77_G	0.502	0.41
3_G	17_V	0.500	0.41

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
4aw7A	1	0.8352	31	0.904	Contact Map
1jz7A	4	0.9231	20.1	0.912	Contact Map
1yq2A	4	0.9231	16.5	0.916	Contact Map
3obaA	4	0.9231	11.3	0.922	Contact Map
3bgaA	2	0.9231	7.2	0.928	Contact Map
4pj0O	1	0.3736	5.5	0.932	Contact Map
3uv1A	2	0.967	5.4	0.932	Contact Map
3wu2O	1	0.3736	5.3	0.933	Contact Map
4s3qA	1	0.967	5.2	0.933	Contact Map
3r7fA	3	0.3516	4.1	0.936	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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