DUF2838 - PFAM28P - GREMLIN Contacts

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DUF2838 - Protein of unknown function (DUF2838)

PFAM:	PF10998	Sequences: DKVSFTLGVLNIFISGYLLGAYPEYFHYWYTVQLLYLLPIRFYTYRKKGWHYFLLDFCYFVNLLLLLYIWVFPKSKRLFIACFALANGPLAWAIIAWRNSLVFHSLDKVTS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	111 (111)
Sequences:	648 (465)
Seq/√Len:	44.1
META:	0.585

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_T	70_W	3.874	1.00
83_F	87_N	3.451	1.00
16_G	20_G	3.187	1.00
57_F	85_L	3.181	1.00
37_L	110_T	3.032	1.00
9_V	103_F	2.934	1.00
11_N	33_Q	2.799	1.00
41_R	59_Y	2.402	1.00
93_A	97_W	2.321	1.00
67_L	72_F	2.272	1.00
46_R	51_H	2.228	1.00
106_L	110_T	2.002	0.99
53_F	97_W	1.974	0.99
17_Y	20_G	1.847	0.99
105_S	108_K	1.735	0.98
41_R	45_Y	1.724	0.98
67_L	71_V	1.671	0.97
8_G	103_F	1.653	0.97
8_G	23_P	1.609	0.97
94_I	99_N	1.587	0.96
4_S	9_V	1.585	0.96
97_W	108_K	1.578	0.96
17_Y	21_A	1.519	0.95
43_Y	47_K	1.517	0.95
45_Y	59_Y	1.510	0.95
1_D	8_G	1.483	0.95
57_F	61_V	1.463	0.94
66_L	70_W	1.426	0.93
4_S	8_G	1.420	0.93
13_F	16_G	1.404	0.93
25_Y	28_Y	1.394	0.93
89_P	94_I	1.394	0.93
57_F	70_W	1.378	0.92
99_N	107_D	1.369	0.92
61_V	85_L	1.348	0.91
35_L	39_P	1.317	0.90
34_L	38_L	1.300	0.90
98_R	108_K	1.289	0.89
14_I	29_W	1.263	0.88
40_I	105_S	1.228	0.87
73_P	78_L	1.202	0.86
102_V	108_K	1.188	0.85
24_E	28_Y	1.132	0.82
45_Y	56_D	1.132	0.82
76_K	80_I	1.121	0.82
52_Y	55_L	1.107	0.81
107_D	111_S	1.089	0.80
26_F	30_Y	1.088	0.80
6_T	51_H	1.030	0.76
20_G	53_F	1.017	0.75
7_L	74_K	1.010	0.74
15_S	29_W	0.999	0.74
64_L	78_L	0.997	0.73
45_Y	51_H	0.997	0.73
61_V	84_A	0.970	0.71
44_T	48_K	0.970	0.71
3_V	103_F	0.963	0.71
25_Y	49_G	0.959	0.70
30_Y	53_F	0.959	0.70
83_F	98_R	0.953	0.70
12_I	19_L	0.944	0.69
46_R	55_L	0.915	0.67
81_A	85_L	0.908	0.66
61_V	90_L	0.852	0.61
5_F	8_G	0.851	0.61
1_D	86_A	0.847	0.61
46_R	52_Y	0.831	0.59
59_Y	97_W	0.828	0.59
30_Y	56_D	0.819	0.58
3_V	7_L	0.819	0.58
26_F	65_L	0.818	0.58
33_Q	109_V	0.814	0.58
48_K	81_A	0.811	0.57
36_Y	39_P	0.811	0.57
62_N	78_L	0.811	0.57
56_D	98_R	0.809	0.57
1_D	57_F	0.802	0.57
45_Y	106_L	0.793	0.56
7_L	26_F	0.790	0.55
67_L	76_K	0.787	0.55
18_L	91_A	0.776	0.54
57_F	88_G	0.775	0.54
18_L	29_W	0.770	0.53
103_F	109_V	0.754	0.52
69_I	75_S	0.747	0.51
1_D	47_K	0.744	0.51
63_L	74_K	0.739	0.50
54_L	59_Y	0.733	0.50
72_F	75_S	0.730	0.50
90_L	94_I	0.730	0.50
72_F	86_A	0.727	0.49
65_L	95_I	0.720	0.49
65_L	82_C	0.720	0.49
14_I	25_Y	0.710	0.48
43_Y	65_L	0.710	0.48
40_I	90_L	0.693	0.46
54_L	80_I	0.692	0.46
98_R	107_D	0.691	0.46
101_L	104_H	0.691	0.46
96_A	101_L	0.682	0.45
71_V	75_S	0.677	0.45
32_V	66_L	0.674	0.44
67_L	73_P	0.673	0.44
1_D	16_G	0.668	0.44
99_N	102_V	0.668	0.44
43_Y	46_R	0.667	0.44
50_W	77_R	0.664	0.43
6_T	10_L	0.659	0.43
45_Y	108_K	0.644	0.41
82_C	89_P	0.641	0.41
20_G	85_L	0.628	0.40
102_V	105_S	0.625	0.40
1_D	21_A	0.622	0.39
53_F	99_N	0.617	0.39
86_A	91_A	0.617	0.39
46_R	82_C	0.615	0.39
45_Y	65_L	0.614	0.39
4_S	65_L	0.611	0.38
100_S	108_K	0.610	0.38
67_L	78_L	0.604	0.38
17_Y	71_V	0.604	0.38
56_D	97_W	0.601	0.37
51_H	59_Y	0.600	0.37
45_Y	107_D	0.600	0.37
5_F	23_P	0.600	0.37
6_T	68_Y	0.599	0.37
2_K	52_Y	0.599	0.37
26_F	54_L	0.591	0.37
45_Y	98_R	0.591	0.37
24_E	35_L	0.590	0.36
11_N	22_Y	0.587	0.36
20_G	68_Y	0.582	0.36
36_Y	82_C	0.582	0.36
6_T	77_R	0.580	0.36
98_R	102_V	0.573	0.35
1_D	39_P	0.569	0.35
13_F	64_L	0.560	0.34
15_S	74_K	0.560	0.34
5_F	104_H	0.560	0.34
15_S	33_Q	0.558	0.34
10_L	46_R	0.554	0.33
101_L	108_K	0.552	0.33
15_S	18_L	0.552	0.33
39_P	84_A	0.550	0.33
41_R	107_D	0.549	0.33
3_V	95_I	0.546	0.33
16_G	34_L	0.543	0.32
16_G	97_W	0.538	0.32
31_T	68_Y	0.538	0.32
28_Y	81_A	0.533	0.32
28_Y	66_L	0.532	0.31
12_I	15_S	0.531	0.31
5_F	46_R	0.531	0.31
35_L	63_L	0.530	0.31
12_I	34_L	0.529	0.31
72_F	80_I	0.528	0.31
41_R	110_T	0.527	0.31
46_R	92_W	0.522	0.31
31_T	66_L	0.521	0.31
19_L	76_K	0.520	0.30
30_Y	69_I	0.517	0.30
42_F	52_Y	0.514	0.30
20_G	36_Y	0.514	0.30
30_Y	94_I	0.503	0.29
59_Y	75_S	0.501	0.29
39_P	87_N	0.500	0.29

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
4i0uA	4	0.4324	5.9	0.934	Contact Map
4ev6A	3	0.4505	5.4	0.935	Contact Map
3fqmA	2	0.1892	2.5	0.945	Contact Map
4p02B	1	0.4054	1.2	0.954	Contact Map
3zd0A	1	0.4144	1.1	0.955	Contact Map
1hksA	1	0.3604	0.8	0.958	Contact Map
2mtsA	1	0.3964	0.8	0.958	Contact Map
2jm6A	1	0.1081	0.8	0.959	Contact Map
2lzlA	2	0.2252	0.7	0.96	Contact Map
4w8pB	1	0.0811	0.7	0.96	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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