DUF3560 - PFAM28P - GREMLIN Contacts

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DUF3560 - Domain of unknown function (DUF3560)

PFAM:	PF12083	Sequences: DYEERAEARAERLEEYAEKAEAEAEAAYEAAREIADFIPFGQPILVGHHSERRHRRDRERIDNAMRKAVEASEKAEYYERRAAAAERNAAISSDDPEAIERLIKKLEALERKQERMKAGNKAIR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	124 (120)
Sequences:	2185 (1826)
Seq/√Len:	166.7
META:	0.886

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
54_H	58_R	3.458	1.00
62_D	66_R	3.056	1.00
51_E	55_R	3.039	1.00
23_E	71_A	2.841	1.00
34_I	57_D	2.381	1.00
47_G	51_E	2.293	1.00
42_Q	45_L	2.290	1.00
35_A	61_I	2.268	1.00
28_Y	68_A	2.199	1.00
30_A	64_A	2.177	1.00
21_E	79_E	2.060	1.00
56_R	59_E	2.042	1.00
27_A	64_A	1.970	1.00
20_A	74_K	1.950	1.00
114_E	118_A	1.759	1.00
14_E	86_E	1.740	1.00
54_H	57_D	1.738	1.00
95_D	101_R	1.731	1.00
59_E	63_N	1.719	1.00
29_E	33_E	1.672	1.00
20_A	71_A	1.593	1.00
63_N	66_R	1.566	1.00
16_Y	78_Y	1.562	1.00
16_Y	19_K	1.541	1.00
65_M	69_V	1.538	1.00
44_I	51_E	1.460	1.00
37_F	57_D	1.418	1.00
16_Y	20_A	1.412	1.00
13_L	81_R	1.406	1.00
30_A	33_E	1.398	1.00
13_L	78_Y	1.366	1.00
32_R	36_D	1.345	1.00
12_R	16_Y	1.335	1.00
57_D	61_I	1.273	1.00
20_A	23_E	1.269	1.00
6_A	10_A	1.257	1.00
73_E	76_E	1.257	1.00
52_R	56_R	1.248	1.00
77_Y	80_R	1.206	1.00
113_Q	116_M	1.195	1.00
34_I	64_A	1.182	1.00
33_E	36_D	1.156	1.00
34_I	61_I	1.155	1.00
110_E	114_E	1.149	1.00
59_E	62_D	1.142	1.00
116_M	119_G	1.140	1.00
15_E	19_K	1.119	1.00
61_I	64_A	1.110	1.00
97_E	101_R	1.103	1.00
4_E	8_A	1.102	1.00
46_V	55_R	1.101	1.00
56_R	60_R	1.096	1.00
46_V	51_E	1.093	1.00
70_E	73_E	1.062	0.99
31_A	61_I	1.055	0.99
13_L	16_Y	1.040	0.99
38_I	42_Q	1.035	0.99
52_R	59_E	1.026	0.99
31_A	65_M	1.020	0.99
53_R	57_D	1.019	0.99
66_R	69_V	1.009	0.99
98_A	101_R	1.007	0.99
68_A	72_S	0.994	0.99
115_R	119_G	0.981	0.99
10_A	86_E	0.980	0.99
20_A	78_Y	0.946	0.99
27_A	67_K	0.942	0.99
105_K	108_A	0.941	0.99
106_L	109_L	0.940	0.99
27_A	71_A	0.939	0.99
76_E	80_R	0.937	0.99
10_A	85_A	0.929	0.99
23_E	27_A	0.927	0.99
25_E	29_E	0.917	0.98
74_K	78_Y	0.916	0.98
66_R	70_E	0.913	0.98
114_E	117_K	0.901	0.98
72_S	76_E	0.893	0.98
69_V	72_S	0.882	0.98
108_A	112_K	0.881	0.98
77_Y	81_R	0.881	0.98
7_E	11_E	0.875	0.98
19_K	23_E	0.871	0.98
34_I	37_F	0.868	0.98
24_A	72_S	0.866	0.98
19_K	22_A	0.863	0.98
29_E	32_R	0.856	0.98
13_L	77_Y	0.851	0.97
105_K	109_L	0.844	0.97
9_R	85_A	0.832	0.97
28_Y	32_R	0.831	0.97
58_R	62_D	0.831	0.97
38_I	45_L	0.821	0.97
45_L	51_E	0.819	0.97
21_E	75_A	0.817	0.97
36_D	39_P	0.812	0.97
48_H	51_E	0.806	0.97
57_D	64_A	0.797	0.96
31_A	64_A	0.796	0.96
69_V	73_E	0.789	0.96
24_A	28_Y	0.782	0.96
32_R	35_A	0.781	0.96
78_Y	81_R	0.781	0.96
111_R	115_R	0.778	0.96
27_A	30_A	0.775	0.96
2_Y	92_S	0.773	0.96
35_A	40_F	0.771	0.96
24_A	68_A	0.770	0.95
44_I	55_R	0.761	0.95
2_Y	6_A	0.749	0.95
86_E	89_A	0.745	0.95
107_E	110_E	0.741	0.94
118_A	121_K	0.740	0.94
19_K	78_Y	0.734	0.94
99_I	103_I	0.733	0.94
67_K	70_E	0.727	0.94
13_L	74_K	0.703	0.93
95_D	98_A	0.687	0.92
5_R	8_A	0.686	0.92
109_L	113_Q	0.683	0.92
30_A	34_I	0.680	0.91
103_I	107_E	0.677	0.91
85_A	88_N	0.667	0.91
45_L	55_R	0.667	0.91
10_A	14_E	0.665	0.91
31_A	62_D	0.663	0.90
38_I	54_H	0.659	0.90
34_I	54_H	0.658	0.90
58_R	61_I	0.654	0.90
37_F	54_H	0.653	0.90
74_K	77_Y	0.649	0.90
23_E	26_A	0.648	0.89
17_A	75_A	0.640	0.89
6_A	89_A	0.637	0.89
107_E	111_R	0.636	0.89
116_M	120_N	0.634	0.88
57_D	60_R	0.633	0.88
44_I	48_H	0.629	0.88
45_L	48_H	0.627	0.88
44_I	54_H	0.625	0.88
99_I	106_L	0.624	0.88
6_A	85_A	0.623	0.88
10_A	89_A	0.622	0.87
110_E	113_Q	0.619	0.87
79_E	83_A	0.619	0.87
88_N	92_S	0.619	0.87
23_E	74_K	0.618	0.87
44_I	47_G	0.613	0.87
76_E	79_E	0.612	0.87
85_A	89_A	0.601	0.86
62_D	65_M	0.599	0.85
64_A	67_K	0.595	0.85
112_K	116_M	0.590	0.85
17_A	82_A	0.586	0.84
6_A	9_R	0.582	0.84
47_G	55_R	0.580	0.84
17_A	79_E	0.577	0.83
7_E	10_A	0.573	0.83
6_A	88_N	0.573	0.83
21_E	72_S	0.572	0.83
38_I	58_R	0.567	0.82
45_L	50_S	0.567	0.82
33_E	37_F	0.563	0.82
83_A	87_R	0.548	0.80
53_R	56_R	0.546	0.80
11_E	14_E	0.544	0.80
71_A	74_K	0.543	0.79
112_K	115_R	0.538	0.79
36_D	61_I	0.534	0.78
46_V	50_S	0.532	0.78
80_R	83_A	0.532	0.78
26_A	30_A	0.531	0.78
44_I	49_H	0.530	0.78
39_P	61_I	0.520	0.76
28_Y	65_M	0.519	0.76
84_A	88_N	0.518	0.76
93_S	102_L	0.516	0.76
34_I	60_R	0.513	0.75
113_Q	117_K	0.503	0.74
14_E	79_E	0.500	0.74

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
3zqeA	1	0.4274	4.1	0.934	Contact Map
3ioxA	1	0.4355	3	0.939	Contact Map
3fb2A	1	0.5323	2.7	0.94	Contact Map
2nutC	1	0.0323	2.4	0.941	Contact Map
2uw1A	2	0.371	2.4	0.941	Contact Map
5bv0C	1	0.1613	2.2	0.942	Contact Map
2q2fA	2	0.4032	2.1	0.944	Contact Map
2l2lA	1	0.25	2.1	0.944	Contact Map
1sfcA	1	0.4355	1.9	0.944	Contact Map
1urqA	1	0.3065	1.7	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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