DUF4091 - PFAM28P - GREMLIN Contacts

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DUF4091 - Domain of unknown function (DUF4091)

PFAM:	PF13320	Sequences: GIDGFLYWGYNYWTSDPWTDPDAGGGWPNGDGFLVYPGPDGGPVPSIRLEALRDGIEDYEYLRLLE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	66 (64)
Sequences:	11116 (6861)
Seq/√Len:	857.6
META:	0.966

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
59_Y	63_R	2.939	1.00
45_P	49_L	2.813	1.00
45_P	50_E	2.720	1.00
16_D	19_T	2.448	1.00
18_W	44_V	2.418	1.00
51_A	54_D	2.183	1.00
60_E	63_R	2.073	1.00
36_Y	46_S	2.050	1.00
53_R	57_E	1.968	1.00
10_Y	35_V	1.951	1.00
54_D	57_E	1.929	1.00
35_V	49_L	1.790	1.00
61_Y	64_L	1.606	1.00
60_E	64_L	1.543	1.00
38_G	41_G	1.538	1.00
9_G	12_Y	1.536	1.00
57_E	60_E	1.406	1.00
34_L	52_L	1.401	1.00
47_I	51_A	1.381	1.00
50_E	57_E	1.320	1.00
52_L	56_I	1.238	1.00
7_Y	10_Y	1.128	1.00
21_P	24_G	1.072	1.00
12_Y	15_S	1.065	1.00
17_P	21_P	1.052	1.00
22_D	25_G	1.050	1.00
54_D	58_D	1.042	1.00
7_Y	52_L	1.041	1.00
61_Y	65_L	1.023	1.00
38_G	44_V	1.020	1.00
21_P	25_G	1.007	1.00
39_P	44_V	1.006	1.00
51_A	55_G	0.970	1.00
20_D	24_G	0.963	1.00
50_E	54_D	0.959	1.00
28_P	31_D	0.929	1.00
38_G	43_P	0.926	1.00
58_D	61_Y	0.920	1.00
10_Y	49_L	0.910	1.00
7_Y	31_D	0.881	1.00
34_L	49_L	0.858	1.00
7_Y	32_G	0.850	1.00
38_G	42_G	0.849	1.00
5_F	52_L	0.833	1.00
16_D	20_D	0.826	1.00
6_L	9_G	0.817	1.00
20_D	23_A	0.810	1.00
49_L	53_R	0.800	1.00
8_W	12_Y	0.790	1.00
51_A	56_I	0.783	1.00
18_W	23_A	0.781	1.00
20_D	25_G	0.774	1.00
28_P	33_F	0.773	1.00
17_P	22_D	0.768	1.00
8_W	11_N	0.763	1.00
17_P	20_D	0.732	1.00
15_S	27_W	0.726	1.00
23_A	32_G	0.723	1.00
56_I	60_E	0.712	1.00
11_N	14_T	0.711	1.00
19_T	39_P	0.709	1.00
19_T	22_D	0.700	1.00
18_W	21_P	0.699	1.00
7_Y	34_L	0.692	1.00
30_G	48_R	0.686	1.00
15_S	24_G	0.672	1.00
50_E	53_R	0.671	1.00
18_W	22_D	0.659	1.00
50_E	65_L	0.659	1.00
17_P	37_P	0.636	1.00
16_D	22_D	0.633	1.00
17_P	23_A	0.632	1.00
46_S	51_A	0.609	1.00
14_T	23_A	0.608	1.00
6_L	10_Y	0.601	1.00
23_A	33_F	0.579	1.00
39_P	42_G	0.577	1.00
45_P	51_A	0.576	1.00
54_D	60_E	0.576	1.00
15_S	26_G	0.572	1.00
33_F	36_Y	0.550	1.00
4_G	7_Y	0.550	1.00
34_L	48_R	0.542	1.00
14_T	22_D	0.537	1.00
18_W	24_G	0.532	1.00
22_D	29_N	0.532	1.00
29_N	32_G	0.531	1.00
9_G	14_T	0.523	1.00
37_P	47_I	0.521	1.00
53_R	60_E	0.512	1.00
48_R	60_E	0.509	1.00
35_V	45_P	0.509	1.00
15_S	25_G	0.507	1.00
35_V	43_P	0.504	1.00
26_G	63_R	0.501	1.00
19_T	24_G	0.500	1.00

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
3g4nA	1	0.8788	15.3	0.855	Contact Map
3sf4D	1	0.3636	9.1	0.869	Contact Map
1ll7A	1	0.8333	8	0.873	Contact Map
3g6mA	1	0.7424	5.8	0.88	Contact Map
1w9pA	1	0.8333	5.8	0.881	Contact Map
1nq6A	1	0.6364	4.8	0.885	Contact Map
4qp0A	1	0.6515	4.5	0.886	Contact Map
1i1wA	1	0.6667	3.5	0.892	Contact Map
2axoA	2	0	3.1	0.895	Contact Map
4d1iA	4	0.7879	2.8	0.897	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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