DUF3493 - PFAM28P - GREMLIN Contacts

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DUF3493 - Protein of unknown function (DUF3493)

PFAM:	PF11998	Sequences: PELKARLLAEAQAPFRGLRRFLYIAFGASAFIGLLIMLSRLAAGRSGGDGAPDLEEALPNLAIQLGAVALFVFLLRLDR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	79 (71)
Sequences:	767 (397)
Seq/√Len:	47.1
META:	0.7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
30_A	68_V	2.706	1.00
26_F	71_F	2.616	1.00
40_R	57_A	2.555	1.00
37_M	64_Q	2.115	1.00
58_L	62_A	2.098	1.00
65_L	69_A	2.081	1.00
36_I	39_S	1.931	0.99
32_I	59_P	1.869	0.99
38_L	42_A	1.832	0.99
22_L	26_F	1.831	0.99
74_L	78_D	1.768	0.99
20_R	78_D	1.764	0.99
18_L	22_L	1.726	0.98
66_G	70_L	1.692	0.98
33_G	36_I	1.617	0.97
63_I	67_A	1.551	0.97
32_I	35_L	1.473	0.95
19_R	78_D	1.456	0.95
33_G	40_R	1.446	0.95
67_A	71_F	1.373	0.93
21_F	25_A	1.364	0.93
39_S	42_A	1.326	0.92
41_L	54_L	1.300	0.91
16_R	78_D	1.284	0.91
4_K	8_L	1.273	0.90
73_F	77_L	1.255	0.90
65_L	68_V	1.228	0.89
34_L	67_A	1.155	0.86
60_N	67_A	1.142	0.85
7_L	11_A	1.139	0.85
10_E	14_P	1.114	0.83
20_R	24_I	1.104	0.83
7_L	10_E	1.100	0.83
27_G	75_L	1.095	0.82
31_F	34_L	1.087	0.82
41_L	57_A	1.079	0.81
29_S	34_L	1.059	0.80
9_A	13_A	1.056	0.80
29_S	44_G	1.016	0.77
5_A	8_L	1.009	0.77
22_L	55_E	0.992	0.76
35_L	39_S	0.974	0.74
31_F	35_L	0.951	0.72
20_R	79_R	0.947	0.72
40_R	56_E	0.943	0.72
8_L	36_I	0.922	0.70
28_A	31_F	0.914	0.69
41_L	58_L	0.912	0.69
13_A	19_R	0.895	0.68
29_S	64_Q	0.895	0.68
28_A	68_V	0.870	0.66
23_Y	74_L	0.844	0.63
54_L	57_A	0.817	0.61
28_A	32_I	0.787	0.58
31_F	42_A	0.781	0.57
6_R	63_I	0.767	0.56
39_S	43_A	0.767	0.56
40_R	54_L	0.759	0.55
34_L	65_L	0.749	0.54
29_S	37_M	0.742	0.53
60_N	72_V	0.733	0.52
29_S	33_G	0.726	0.52
53_D	56_E	0.703	0.49
5_A	9_A	0.699	0.49
76_R	79_R	0.692	0.48
8_L	11_A	0.691	0.48
8_L	12_Q	0.683	0.47
15_F	18_L	0.679	0.47
17_G	37_M	0.676	0.47
44_G	64_Q	0.675	0.47
15_F	76_R	0.670	0.46
33_G	61_L	0.663	0.45
32_I	45_R	0.662	0.45
70_L	74_L	0.659	0.45
25_A	75_L	0.658	0.45
34_L	68_V	0.645	0.44
2_E	9_A	0.643	0.43
31_F	63_I	0.639	0.43
41_L	61_L	0.637	0.43
62_A	66_G	0.629	0.42
35_L	53_D	0.626	0.42
24_I	31_F	0.623	0.42
3_L	11_A	0.613	0.41
22_L	39_S	0.607	0.40
34_L	38_L	0.603	0.40
26_F	67_A	0.602	0.40
13_A	76_R	0.582	0.38
75_L	78_D	0.578	0.37
6_R	12_Q	0.569	0.36
27_G	76_R	0.568	0.36
55_E	59_P	0.565	0.36
12_Q	75_L	0.564	0.36
28_A	76_R	0.563	0.36
55_E	68_V	0.560	0.36
17_G	27_G	0.559	0.36
11_A	56_E	0.556	0.35
53_D	61_L	0.555	0.35
19_R	23_Y	0.552	0.35
69_A	73_F	0.548	0.35
6_R	11_A	0.542	0.34
25_A	28_A	0.538	0.34
3_L	12_Q	0.519	0.32
39_S	61_L	0.515	0.32
2_E	8_L	0.514	0.32
28_A	70_L	0.504	0.31
5_A	77_L	0.500	0.30

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
2ki0A	1	0.2911	16.8	0.887	Contact Map
4efhB	1	0.2532	8.9	0.9	Contact Map
1m56C	2	0.7722	3.4	0.917	Contact Map
1sk7A	1	0.3418	3.2	0.919	Contact Map
3l1lA	2	0.9747	3.2	0.919	Contact Map
1mhsA	2	0.8861	3.2	0.919	Contact Map
3ar4A	1	0.9367	3	0.92	Contact Map
2oasA	3	0.2405	3	0.92	Contact Map
4k7cA	5	0.3418	3	0.92	Contact Map
1abzA	1	0.1646	2.8	0.921	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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