DUF3306 - PFAM28P - GREMLIN Contacts

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DUF3306 - Protein of unknown function (DUF3306)

PFAM:	PF11748	Sequences: GFLSRWSRRKREARAEAEAPEPAAPPEAAAPPAAAAPAAAAAAAAAPAAAAAAPAEPAFDPATLPPIESLTADSDFSAFLAPGVPEELRRAALRKLWADPAFNVFDGLDDYIDDYTDPDPL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	121 (117)
Sequences:	5539 (4733)
Seq/√Len:	437.5
META:	0.891

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
109_D	112_I	5.653	1.00
11_R	14_R	3.689	1.00
95_K	98_A	3.019	1.00
108_L	112_I	2.651	1.00
66_P	69_S	2.490	1.00
70_L	74_S	2.482	1.00
105_F	112_I	2.387	1.00
60_D	63_T	2.229	1.00
59_F	63_T	2.200	1.00
7_S	11_R	2.068	1.00
16_E	19_A	2.049	1.00
9_R	13_A	2.038	1.00
86_E	89_R	2.021	1.00
86_E	90_R	2.006	1.00
106_D	112_I	2.004	1.00
65_P	69_S	1.980	1.00
76_F	96_L	1.936	1.00
117_D	120_P	1.771	1.00
105_F	109_D	1.763	1.00
20_P	23_A	1.757	1.00
107_G	112_I	1.697	1.00
18_E	21_E	1.666	1.00
70_L	76_F	1.665	1.00
110_D	113_D	1.659	1.00
16_E	21_E	1.596	1.00
78_A	82_P	1.591	1.00
113_D	117_D	1.526	1.00
77_S	81_A	1.504	1.00
91_A	95_K	1.488	1.00
65_P	68_E	1.457	1.00
67_I	91_A	1.450	1.00
106_D	109_D	1.420	1.00
111_Y	115_Y	1.340	1.00
8_R	12_E	1.318	1.00
17_A	20_P	1.311	1.00
71_T	74_S	1.246	1.00
113_D	118_P	1.241	1.00
59_F	62_A	1.182	1.00
85_P	97_W	1.162	1.00
19_A	22_P	1.160	1.00
94_R	98_A	1.155	1.00
76_F	95_K	1.153	1.00
71_T	76_F	1.152	1.00
87_E	91_A	1.127	1.00
1_G	4_S	1.115	1.00
105_F	108_L	1.111	1.00
113_D	116_T	1.069	1.00
112_I	115_Y	1.061	1.00
64_L	67_I	1.021	1.00
36_A	39_A	1.020	1.00
27_E	30_A	1.011	1.00
72_A	99_D	0.996	1.00
28_A	31_P	0.971	1.00
55_A	58_A	0.969	1.00
65_P	80_L	0.959	1.00
32_P	35_A	0.952	1.00
41_A	48_A	0.946	1.00
104_V	109_D	0.946	1.00
7_S	10_K	0.945	1.00
109_D	113_D	0.933	1.00
42_A	47_P	0.929	1.00
35_A	38_A	0.925	1.00
108_L	115_Y	0.924	1.00
62_A	84_V	0.923	1.00
71_T	75_D	0.921	1.00
61_P	64_L	0.914	1.00
85_P	90_R	0.896	1.00
9_R	12_E	0.894	1.00
18_E	23_A	0.882	1.00
106_D	111_Y	0.873	1.00
102_F	105_F	0.866	1.00
41_A	47_P	0.862	1.00
57_P	60_D	0.859	1.00
96_L	102_F	0.849	1.00
34_A	37_P	0.849	1.00
75_D	78_A	0.845	1.00
42_A	46_A	0.839	1.00
105_F	110_D	0.839	1.00
39_A	42_A	0.838	1.00
34_A	40_A	0.823	1.00
99_D	105_F	0.814	1.00
66_P	91_A	0.808	1.00
40_A	43_A	0.795	1.00
36_A	43_A	0.791	1.00
80_L	89_R	0.788	1.00
105_F	113_D	0.787	1.00
102_F	106_D	0.786	1.00
45_A	48_A	0.785	1.00
29_A	32_P	0.784	1.00
31_P	34_A	0.778	1.00
58_A	61_P	0.778	1.00
87_E	90_R	0.767	1.00
30_A	33_A	0.753	1.00
37_P	40_A	0.751	1.00
81_A	85_P	0.751	1.00
16_E	20_P	0.748	1.00
44_A	50_A	0.746	1.00
107_G	113_D	0.740	1.00
39_A	44_A	0.738	1.00
4_S	8_R	0.737	1.00
43_A	47_P	0.733	1.00
70_L	75_D	0.729	1.00
104_V	107_G	0.717	1.00
65_P	78_A	0.713	1.00
116_T	119_D	0.710	1.00
81_A	89_R	0.707	1.00
110_D	116_T	0.706	1.00
47_P	50_A	0.705	1.00
98_A	103_N	0.703	1.00
2_F	5_R	0.694	1.00
33_A	44_A	0.688	1.00
89_R	93_L	0.679	1.00
29_A	34_A	0.676	1.00
39_A	48_A	0.675	1.00
76_F	80_L	0.674	1.00
42_A	49_A	0.666	1.00
23_A	28_A	0.661	1.00
78_A	81_A	0.657	1.00
33_A	36_A	0.655	1.00
8_R	11_R	0.653	0.99
110_D	115_Y	0.652	0.99
58_A	62_A	0.648	0.99
101_A	104_V	0.639	0.99
38_A	41_A	0.636	0.99
47_P	51_A	0.635	0.99
98_A	102_F	0.631	0.99
94_R	119_D	0.626	0.99
104_V	113_D	0.622	0.99
103_N	109_D	0.617	0.99
27_E	31_P	0.615	0.99
67_I	88_L	0.615	0.99
61_P	85_P	0.611	0.99
46_A	50_A	0.609	0.99
38_A	51_A	0.606	0.99
41_A	50_A	0.606	0.99
80_L	110_D	0.604	0.99
2_F	13_A	0.602	0.99
71_T	86_E	0.599	0.99
60_D	64_L	0.598	0.99
105_F	111_Y	0.593	0.99
37_P	42_A	0.588	0.99
106_D	113_D	0.585	0.99
1_G	73_D	0.579	0.99
28_A	32_P	0.576	0.99
30_A	34_A	0.572	0.99
24_A	29_A	0.569	0.99
79_F	88_L	0.567	0.99
21_E	24_A	0.567	0.99
90_R	105_F	0.565	0.99
72_A	101_A	0.560	0.98
97_W	118_P	0.556	0.98
72_A	102_F	0.552	0.98
53_A	56_E	0.552	0.98
107_G	115_Y	0.548	0.98
17_A	45_A	0.548	0.98
97_W	104_V	0.545	0.98
98_A	101_A	0.545	0.98
86_E	91_A	0.536	0.98
44_A	48_A	0.536	0.98
108_L	111_Y	0.534	0.98
97_W	101_A	0.530	0.98
63_T	85_P	0.527	0.98
74_S	77_S	0.522	0.98
72_A	80_L	0.522	0.98
85_P	93_L	0.518	0.97
73_D	78_A	0.515	0.97
35_A	42_A	0.514	0.97
35_A	48_A	0.514	0.97
88_L	91_A	0.513	0.97
101_A	110_D	0.511	0.97
29_A	33_A	0.506	0.97
34_A	42_A	0.506	0.97
54_P	58_A	0.503	0.97
33_A	39_A	0.501	0.97
35_A	43_A	0.500	0.97
17_A	21_E	0.500	0.97

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
1pzqA	2	0.1818	8	0.929	Contact Map
2pifA	2	0.3306	3.2	0.941	Contact Map
3n5mA	4	0.3719	3.2	0.942	Contact Map
3echC	1	0.1983	2.6	0.944	Contact Map
4zgjA	2	0.3388	2.5	0.945	Contact Map
1k8rB	1	0.438	2.4	0.945	Contact Map
4i6yA	2	0.3884	2.4	0.945	Contact Map
3winD	1	0.124	2.3	0.946	Contact Map
4ayoA	1	0.2727	2.3	0.946	Contact Map
3ismC	1	0.4959	2.3	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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