DUF2852 - PFAM28P - GREMLIN Contacts

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DUF2852 - Protein of unknown function (DUF2852)

PFAM:	PF11014	Sequences: LDERGKPAWIALMVLGFIVFWPLGLALLAYIIWSGRMGCWGGGRGRWQRKMERMFSKMRRMRGRGGGGGGGPRSSGNRAFDEYRAETLRRLEEEQREFREFLERLRRAKDKAEFDQFMAERR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	122 (120)
Sequences:	3802 (2477)
Seq/√Len:	226.1
META:	0.918

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
112_A	116_Q	3.793	1.00
89_R	93_E	2.571	1.00
111_K	115_D	2.396	1.00
13_M	31_I	2.377	1.00
78_R	107_R	2.334	1.00
96_R	100_E	2.283	1.00
104_R	120_E	2.089	1.00
13_M	27_L	2.004	1.00
55_F	58_M	1.949	1.00
84_R	108_A	1.934	1.00
107_R	111_K	1.858	1.00
55_F	59_R	1.845	1.00
34_S	37_M	1.802	1.00
47_W	51_M	1.798	1.00
103_E	107_R	1.778	1.00
86_E	89_R	1.708	1.00
59_R	62_R	1.708	1.00
75_S	95_Q	1.705	1.00
2_D	5_G	1.641	1.00
26_A	29_A	1.630	1.00
16_G	23_L	1.628	1.00
48_Q	52_E	1.624	1.00
92_E	102_L	1.561	1.00
48_Q	51_M	1.523	1.00
93_E	97_E	1.497	1.00
99_R	103_E	1.468	1.00
54_M	58_M	1.456	1.00
107_R	112_A	1.414	1.00
10_I	14_V	1.411	1.00
50_K	54_M	1.382	1.00
5_G	8_A	1.365	1.00
45_G	49_R	1.358	1.00
54_M	57_K	1.348	1.00
78_R	82_E	1.344	1.00
7_P	11_A	1.340	1.00
51_M	55_F	1.282	1.00
116_Q	120_E	1.278	1.00
16_G	20_F	1.265	1.00
66_G	69_G	1.253	1.00
53_R	59_R	1.245	1.00
30_Y	34_S	1.242	1.00
69_G	72_P	1.233	1.00
44_R	48_Q	1.230	1.00
90_R	94_E	1.230	1.00
29_A	33_W	1.227	1.00
13_M	16_G	1.217	1.00
57_K	61_M	1.190	1.00
33_W	37_M	1.190	1.00
44_R	49_R	1.188	1.00
67_G	70_G	1.186	1.00
46_R	50_K	1.173	1.00
57_K	62_R	1.165	1.00
43_G	47_W	1.150	1.00
101_F	109_K	1.133	1.00
5_G	9_W	1.119	1.00
58_M	61_M	1.110	1.00
2_D	6_K	1.103	1.00
114_F	118_M	1.079	1.00
84_R	105_L	1.079	1.00
60_R	63_G	1.077	1.00
26_A	30_Y	1.070	1.00
21_W	25_L	1.042	1.00
99_R	107_R	1.024	1.00
55_F	61_M	1.023	1.00
68_G	71_G	1.017	1.00
85_A	89_R	1.016	1.00
29_A	32_I	1.000	1.00
42_G	49_R	0.984	1.00
89_R	92_E	0.980	1.00
45_G	48_Q	0.976	1.00
47_W	50_K	0.966	1.00
76_G	81_D	0.959	1.00
15_L	19_V	0.957	1.00
49_R	53_R	0.956	1.00
57_K	60_R	0.945	1.00
46_R	49_R	0.942	1.00
23_L	27_L	0.937	1.00
13_M	17_F	0.935	1.00
52_E	55_F	0.925	1.00
43_G	46_R	0.922	1.00
82_E	107_R	0.913	0.99
51_M	54_M	0.911	0.99
49_R	54_M	0.910	0.99
50_K	53_R	0.899	0.99
28_L	32_I	0.886	0.99
46_R	51_M	0.879	0.99
83_Y	87_T	0.877	0.99
19_V	23_L	0.876	0.99
55_F	62_R	0.875	0.99
98_F	101_F	0.859	0.99
64_R	67_G	0.843	0.99
17_F	28_L	0.833	0.99
26_A	33_W	0.825	0.99
100_E	103_E	0.818	0.99
45_G	51_M	0.809	0.99
70_G	73_R	0.807	0.99
46_R	52_E	0.798	0.99
87_T	95_Q	0.789	0.99
50_K	55_F	0.787	0.98
56_S	61_M	0.782	0.98
95_Q	99_R	0.777	0.98
2_D	9_W	0.775	0.98
20_F	27_L	0.773	0.98
105_L	108_A	0.757	0.98
52_E	56_S	0.754	0.98
19_V	27_L	0.751	0.98
53_R	58_M	0.750	0.98
4_R	7_P	0.745	0.98
92_E	96_R	0.744	0.98
13_M	18_I	0.737	0.98
54_M	59_R	0.733	0.98
95_Q	104_R	0.732	0.98
116_Q	119_A	0.731	0.98
105_L	109_K	0.730	0.98
93_E	96_R	0.724	0.97
54_M	61_M	0.723	0.97
102_L	105_L	0.716	0.97
9_W	31_I	0.716	0.97
65_G	69_G	0.710	0.97
75_S	81_D	0.709	0.97
66_G	70_G	0.708	0.97
4_R	12_L	0.706	0.97
56_S	59_R	0.706	0.97
83_Y	101_F	0.706	0.97
42_G	46_R	0.696	0.97
17_F	24_G	0.696	0.97
20_F	23_L	0.694	0.97
34_S	39_C	0.685	0.96
49_R	55_F	0.677	0.96
12_L	27_L	0.672	0.96
59_R	63_G	0.666	0.96
104_R	107_R	0.664	0.96
39_C	42_G	0.658	0.95
14_V	17_F	0.657	0.95
42_G	45_G	0.653	0.95
111_K	119_A	0.652	0.95
9_W	12_L	0.651	0.95
56_S	60_R	0.647	0.95
68_G	73_R	0.646	0.95
32_I	37_M	0.642	0.95
74_S	81_D	0.640	0.95
16_G	31_I	0.638	0.95
50_K	58_M	0.628	0.94
5_G	36_R	0.628	0.94
65_G	68_G	0.625	0.94
53_R	61_M	0.624	0.94
9_W	13_M	0.616	0.94
57_K	63_G	0.615	0.94
108_A	117_F	0.610	0.93
20_F	24_G	0.605	0.93
93_E	117_F	0.602	0.93
53_R	57_K	0.600	0.93
88_L	92_E	0.600	0.93
27_L	35_G	0.580	0.91
20_F	31_I	0.580	0.91
51_M	57_K	0.572	0.91
43_G	51_M	0.571	0.91
62_R	65_G	0.571	0.91
16_G	27_L	0.571	0.91
27_L	31_I	0.565	0.90
45_G	50_K	0.562	0.90
3_E	9_W	0.560	0.90
92_E	105_L	0.559	0.90
11_A	19_V	0.556	0.90
44_R	52_E	0.555	0.90
43_G	49_R	0.547	0.89
3_E	7_P	0.537	0.88
82_E	86_E	0.536	0.88
53_R	56_S	0.532	0.88
88_L	91_L	0.527	0.87
8_A	11_A	0.525	0.87
107_R	118_M	0.525	0.87
12_L	68_G	0.524	0.87
58_M	62_R	0.509	0.85
47_W	52_E	0.508	0.85
51_M	58_M	0.506	0.85
4_R	9_W	0.502	0.84
30_Y	33_W	0.501	0.84
97_E	100_E	0.500	0.84
5_G	30_Y	0.500	0.84

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
1cd1A	1	0.041	11.5	0.936	Contact Map
1o5hA	2	0.5984	9.9	0.937	Contact Map
1s7qA	1	0.0574	9.4	0.938	Contact Map
2l9uA	2	0.3279	6.2	0.943	Contact Map
1m8oB	1	0.1639	5.5	0.944	Contact Map
1ciiA	1	0.418	5	0.946	Contact Map
2k1kA	2	0.2869	5	0.946	Contact Map
3mk7A	1	0.3689	4.8	0.946	Contact Map
4um9B	2	0	4.8	0.946	Contact Map
2kncB	1	0.6148	4.7	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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