DUF4913 - PFAM28P - GREMLIN Contacts

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DUF4913 - Domain of unknown function (DUF4913)

PFAM:	PF16259	Sequences: YPSVEEWVEEYLLPVYRRRVGGGARTRWCPQWWEHPEAVARLEALWRAWEALRLDPGTGMSVWWRDHLDPHMAVLLDPDGPFAGCSPDRHRPPHRLEPLPVEPPP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	105 (97)
Sequences:	917 (662)
Seq/√Len:	67.3
META:	0.569

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
31_Q	34_E	4.085	1.00
41_R	69_D	3.625	1.00
61_S	67_H	3.312	1.00
40_A	64_W	3.014	1.00
29_C	35_H	2.869	1.00
29_C	85_C	2.665	1.00
35_H	85_C	2.635	1.00
8_V	42_L	2.516	1.00
61_S	71_H	2.498	1.00
38_A	75_L	2.464	1.00
2_P	6_E	2.381	1.00
43_E	47_R	2.319	1.00
46_W	50_E	2.202	1.00
38_A	82_F	2.147	1.00
18_R	37_E	2.036	1.00
3_S	6_E	1.926	1.00
16_Y	72_M	1.738	1.00
4_V	42_L	1.727	1.00
70_P	73_A	1.727	1.00
52_L	59_G	1.544	0.99
5_E	9_E	1.481	0.99
67_H	71_H	1.474	0.99
50_E	53_R	1.425	0.98
11_Y	15_V	1.410	0.98
7_W	49_W	1.398	0.98
4_V	8_V	1.394	0.98
49_W	63_W	1.372	0.98
62_V	66_D	1.339	0.97
52_L	58_T	1.338	0.97
52_L	62_V	1.336	0.97
7_W	11_Y	1.270	0.96
46_W	53_R	1.253	0.96
75_L	82_F	1.251	0.96
11_Y	40_A	1.192	0.95
65_R	70_P	1.112	0.92
8_V	13_L	1.097	0.92
54_L	59_G	1.083	0.91
87_P	90_H	1.067	0.91
6_E	10_E	1.066	0.91
48_A	52_L	1.046	0.90
7_W	72_M	1.044	0.90
86_S	90_H	1.025	0.89
42_L	75_L	1.015	0.88
64_W	68_L	0.998	0.88
12_L	72_M	0.992	0.87
47_R	60_M	0.990	0.87
22_G	25_R	0.966	0.86
9_E	13_L	0.945	0.85
74_V	81_P	0.896	0.81
36_P	39_V	0.892	0.81
51_A	57_G	0.890	0.81
85_C	90_H	0.888	0.81
52_L	56_P	0.882	0.80
68_L	76_L	0.877	0.80
68_L	72_M	0.865	0.79
62_V	65_R	0.860	0.79
64_W	71_H	0.853	0.78
90_H	93_P	0.851	0.78
43_E	46_W	0.850	0.78
16_Y	76_L	0.840	0.77
70_P	74_V	0.839	0.77
37_E	82_F	0.825	0.76
7_W	12_L	0.808	0.74
45_L	71_H	0.786	0.72
52_L	67_H	0.784	0.72
12_L	42_L	0.775	0.71
1_Y	10_E	0.774	0.71
11_Y	50_E	0.768	0.70
44_A	60_M	0.749	0.68
39_V	42_L	0.744	0.68
30_P	91_R	0.733	0.67
82_F	85_C	0.731	0.67
41_R	71_H	0.723	0.66
37_E	69_D	0.720	0.65
74_V	77_D	0.713	0.65
3_S	60_M	0.712	0.64
87_P	95_R	0.704	0.64
19_R	78_P	0.698	0.63
55_D	62_V	0.697	0.63
12_L	16_Y	0.697	0.63
42_L	63_W	0.696	0.63
16_Y	64_W	0.687	0.62
72_M	79_D	0.663	0.59
16_Y	46_W	0.653	0.58
7_W	53_R	0.644	0.57
11_Y	46_W	0.644	0.57
48_A	57_G	0.639	0.56
24_A	79_D	0.635	0.56
18_R	72_M	0.630	0.55
7_W	50_E	0.626	0.55
92_P	95_R	0.620	0.54
21_G	25_R	0.616	0.53
56_P	59_G	0.616	0.53
21_G	24_A	0.614	0.53
76_L	83_A	0.614	0.53
57_G	71_H	0.610	0.53
48_A	67_H	0.605	0.52
15_V	39_V	0.600	0.52
35_H	90_H	0.599	0.51
58_T	62_V	0.598	0.51
11_Y	49_W	0.594	0.51
47_R	62_V	0.593	0.51
47_R	55_D	0.593	0.51
45_L	67_H	0.589	0.50
5_E	10_E	0.588	0.50
21_G	89_R	0.586	0.50
77_D	81_P	0.585	0.50
86_S	91_R	0.584	0.50
18_R	49_W	0.582	0.49
1_Y	49_W	0.580	0.49
7_W	45_L	0.580	0.49
1_Y	21_G	0.568	0.48
87_P	91_R	0.568	0.48
84_G	87_P	0.567	0.48
45_L	68_L	0.565	0.47
56_P	95_R	0.563	0.47
62_V	67_H	0.563	0.47
47_R	53_R	0.562	0.47
79_D	83_A	0.560	0.47
86_S	89_R	0.556	0.46
29_C	90_H	0.553	0.46
14_P	57_G	0.553	0.46
41_R	61_S	0.548	0.45
72_M	76_L	0.547	0.45
36_P	58_T	0.546	0.45
43_E	54_L	0.542	0.45
48_A	61_S	0.536	0.44
68_L	77_D	0.535	0.44
40_A	83_A	0.534	0.44
23_G	84_G	0.533	0.44
69_D	74_V	0.527	0.43
41_R	67_H	0.524	0.43
34_E	92_P	0.522	0.42
51_A	84_G	0.519	0.42
12_L	25_R	0.518	0.42
22_G	88_D	0.517	0.42
60_M	64_W	0.517	0.42
20_V	87_P	0.516	0.42
94_H	98_P	0.515	0.42
49_W	53_R	0.511	0.41
89_R	93_P	0.508	0.41
1_Y	51_A	0.506	0.41
20_V	89_R	0.503	0.40
16_Y	61_S	0.503	0.40
25_R	84_G	0.501	0.40
15_V	36_P	0.500	0.40

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
3pgwS	1	0.0857	32.7	0.904	Contact Map
3sdoA	2	0.8857	5.3	0.934	Contact Map
1e9gA	2	0.8952	4.6	0.935	Contact Map
1tvlA	2	0.8857	3	0.941	Contact Map
3f7fA	2	0.3333	2.7	0.942	Contact Map
1kqpA	2	0.419	2.5	0.943	Contact Map
3ec3A	1	0.1905	2.3	0.945	Contact Map
3f6dA	2	0.3143	2.3	0.945	Contact Map
3nivA	2	0.2571	2.1	0.946	Contact Map
1nhyA	1	0.3333	2.1	0.946	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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