DUF4980 - PFAM28P - GREMLIN Contacts

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DUF4980 - Domain of unknown function (DUF4980)

PFAM:	PF16352	Sequences: GDNHTMVRVTVTKKYLLLPVQEGAPEARVRVLVDGKVVREFNVRLAVDKVDYWVPLDLSAFKGKKVTLDIDFLGDRRSTGLKDFVCWKEIKLSDTFDTTNREKYRPQY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	108 (104)
Sequences:	872 (658)
Seq/√Len:	64.6
META:	0.922

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
20_V	43_V	3.874	1.00
21_Q	48_D	2.920	1.00
102_E	105_R	2.669	1.00
11_V	58_L	2.638	1.00
20_V	54_V	2.590	1.00
31_V	56_L	2.494	1.00
30_R	69_D	2.493	1.00
97_D	100_N	2.390	1.00
76_R	80_G	2.234	1.00
28_R	40_E	2.095	1.00
33_V	66_V	2.062	1.00
26_E	44_R	2.057	1.00
102_E	106_P	2.030	1.00
75_D	80_G	2.005	1.00
22_E	52_Y	1.979	1.00
29_V	43_V	1.846	1.00
81_L	84_F	1.843	1.00
17_L	53_W	1.792	1.00
34_D	64_K	1.704	0.99
33_V	64_K	1.622	0.99
30_R	40_E	1.611	0.99
18_L	68_L	1.562	0.99
17_L	96_F	1.535	0.99
16_L	58_L	1.506	0.99
56_L	68_L	1.487	0.98
23_G	44_R	1.447	0.98
50_V	53_W	1.395	0.98
7_V	11_V	1.375	0.97
50_V	89_E	1.363	0.97
76_R	79_T	1.346	0.97
18_L	45_L	1.344	0.97
104_Y	108_Y	1.303	0.96
29_V	44_R	1.289	0.96
69_D	87_W	1.289	0.96
13_K	94_D	1.270	0.96
38_V	41_F	1.257	0.96
98_T	101_R	1.252	0.95
46_A	94_D	1.250	0.95
57_D	60_A	1.203	0.94
39_R	56_L	1.173	0.94
14_K	58_L	1.170	0.93
21_Q	44_R	1.108	0.91
50_V	85_V	1.098	0.91
11_V	66_V	1.091	0.91
37_V	40_E	1.065	0.90
29_V	41_F	1.054	0.89
40_E	43_V	1.052	0.89
75_D	79_T	1.021	0.88
17_L	55_P	1.007	0.87
51_D	102_E	0.996	0.86
75_D	78_S	0.985	0.86
17_L	91_K	0.967	0.85
12_T	62_K	0.964	0.85
33_V	38_V	0.946	0.83
98_T	102_E	0.930	0.82
20_V	45_L	0.926	0.82
103_K	106_P	0.925	0.82
77_R	80_G	0.912	0.81
22_E	26_E	0.909	0.81
28_R	42_N	0.902	0.80
48_D	88_K	0.896	0.80
16_L	68_L	0.891	0.80
57_D	66_V	0.886	0.79
20_V	39_R	0.866	0.78
44_R	52_Y	0.865	0.77
87_W	92_L	0.865	0.77
39_R	60_A	0.862	0.77
96_F	104_Y	0.842	0.76
21_Q	49_K	0.841	0.75
38_V	61_F	0.830	0.75
28_R	58_L	0.830	0.75
31_V	85_V	0.830	0.75
4_H	107_Q	0.825	0.74
53_W	91_K	0.810	0.73
14_K	57_D	0.800	0.72
80_G	84_F	0.797	0.71
22_E	44_R	0.797	0.71
34_D	37_V	0.796	0.71
18_L	90_I	0.796	0.71
29_V	55_P	0.794	0.71
22_E	51_D	0.776	0.69
32_L	69_D	0.772	0.69
20_V	41_F	0.764	0.68
31_V	73_L	0.751	0.67
84_F	92_L	0.748	0.67
21_Q	43_V	0.738	0.66
10_T	90_I	0.737	0.65
18_L	70_I	0.731	0.65
101_R	104_Y	0.730	0.65
42_N	52_Y	0.729	0.65
14_K	99_T	0.719	0.64
33_V	94_D	0.715	0.63
30_R	43_V	0.715	0.63
84_F	87_W	0.703	0.62
32_L	35_G	0.701	0.62
30_R	37_V	0.697	0.61
7_V	78_S	0.696	0.61
88_K	93_S	0.695	0.61
53_W	89_E	0.695	0.61
40_E	61_F	0.685	0.60
10_T	66_V	0.681	0.59
21_Q	50_V	0.672	0.58
10_T	65_K	0.662	0.57
41_F	56_L	0.662	0.57
11_V	31_V	0.659	0.57
14_K	73_L	0.658	0.57
86_C	92_L	0.655	0.56
8_R	12_T	0.648	0.56
29_V	64_K	0.642	0.55
26_E	79_T	0.640	0.55
55_P	61_F	0.631	0.54
70_I	73_L	0.631	0.54
4_H	35_G	0.631	0.54
92_L	97_D	0.619	0.52
68_L	90_I	0.607	0.51
15_Y	55_P	0.606	0.51
83_D	87_W	0.600	0.50
99_T	107_Q	0.598	0.50
15_Y	57_D	0.593	0.49
100_N	105_R	0.587	0.49
27_A	47_V	0.583	0.48
24_A	44_R	0.581	0.48
25_P	82_K	0.576	0.47
71_D	78_S	0.575	0.47
103_K	107_Q	0.575	0.47
17_L	50_V	0.572	0.47
44_R	54_V	0.569	0.46
52_Y	55_P	0.568	0.46
105_R	108_Y	0.568	0.46
99_T	103_K	0.563	0.46
76_R	104_Y	0.563	0.46
18_L	27_A	0.563	0.46
49_K	68_L	0.562	0.46
26_E	52_Y	0.561	0.46
16_L	88_K	0.556	0.45
72_F	79_T	0.548	0.44
81_L	92_L	0.543	0.43
34_D	98_T	0.542	0.43
78_S	81_L	0.542	0.43
87_W	96_F	0.532	0.42
48_D	77_R	0.532	0.42
11_V	64_K	0.531	0.42
8_R	34_D	0.531	0.42
85_V	104_Y	0.530	0.42
34_D	82_K	0.526	0.41
37_V	65_K	0.515	0.40
27_A	70_I	0.512	0.40
58_L	108_Y	0.512	0.40
46_A	50_V	0.509	0.40
9_V	98_T	0.509	0.40
100_N	108_Y	0.509	0.40
81_L	85_V	0.507	0.39
47_V	82_K	0.506	0.39
7_V	43_V	0.504	0.39
59_S	62_K	0.502	0.39
13_K	88_K	0.500	0.39

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	0.7685	14.7	0.921	Contact Map
4p02B	1	0.9352	13.2	0.923	Contact Map
3h2tA	2	0.8241	12	0.924	Contact Map
1o7dD	1	0.8704	9.5	0.927	Contact Map
3lr0A	2	0.5	8.5	0.929	Contact Map
3a3jA	1	0.4722	6.8	0.932	Contact Map
3te8A	2	0.5833	6.4	0.933	Contact Map
4dixA	1	0.7037	5.6	0.935	Contact Map
3mzfA	1	0.4815	5.4	0.935	Contact Map
1x1iA	1	0.6759	4.4	0.938	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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