DUF4212 - PFAM28P - GREMLIN Contacts

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DUF4212 - Domain of unknown function (DUF4212)

PFAM:	PF13937	Sequences: HKAYWRANLRLTAILLAIWFVVSFGFGILFADELNQIRTFGGFPLGFWFAQQGSIYVFVVLIFVYARRMNRLDREYGVH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	79 (76)
Sequences:	9630 (4157)
Seq/√Len:	476.8
META:	0.906

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
7_A	75_E	2.621	1.00
11_L	68_R	2.609	1.00
68_R	71_R	2.574	1.00
22_V	57_V	2.351	1.00
21_V	26_F	2.165	1.00
64_V	68_R	2.079	1.00
10_R	14_I	2.029	1.00
67_R	71_R	2.008	1.00
33_E	36_Q	1.967	1.00
13_A	17_A	1.931	1.00
30_F	33_E	1.904	1.00
63_F	67_R	1.901	1.00
26_F	49_F	1.830	1.00
38_R	41_G	1.807	1.00
9_L	13_A	1.764	1.00
35_N	46_G	1.735	1.00
33_E	37_I	1.652	1.00
31_A	35_N	1.617	1.00
15_L	64_V	1.556	1.00
25_G	29_L	1.552	1.00
7_A	76_Y	1.542	1.00
45_L	49_F	1.468	1.00
26_F	30_F	1.398	1.00
3_A	7_A	1.391	1.00
23_S	58_F	1.381	1.00
60_V	64_V	1.297	1.00
21_V	25_G	1.252	1.00
14_I	18_I	1.221	1.00
3_A	76_Y	1.165	1.00
14_I	17_A	1.163	1.00
25_G	30_F	1.143	1.00
64_V	67_R	1.126	1.00
17_A	21_V	1.122	1.00
68_R	72_L	1.120	1.00
7_A	11_L	1.097	1.00
3_A	6_R	1.094	1.00
8_N	12_T	1.076	1.00
7_A	10_R	1.075	1.00
38_R	44_P	1.041	1.00
15_L	61_L	1.021	1.00
47_F	51_Q	1.018	1.00
71_R	75_E	1.009	1.00
69_M	73_D	0.982	1.00
37_I	45_L	0.964	1.00
28_I	50_A	0.950	1.00
59_V	63_F	0.929	1.00
14_I	64_V	0.909	1.00
48_W	52_Q	0.893	1.00
69_M	72_L	0.843	1.00
8_N	69_M	0.830	1.00
70_N	74_R	0.828	1.00
40_F	43_F	0.828	1.00
10_R	13_A	0.819	1.00
7_A	72_L	0.816	1.00
62_I	65_Y	0.797	1.00
6_R	10_R	0.796	1.00
18_I	61_L	0.790	1.00
18_I	57_V	0.787	1.00
35_N	44_P	0.770	1.00
24_F	28_I	0.761	1.00
51_Q	55_I	0.760	1.00
11_L	72_L	0.746	1.00
24_F	29_L	0.739	1.00
67_R	70_N	0.733	1.00
2_K	6_R	0.728	1.00
19_W	58_F	0.721	1.00
52_Q	56_Y	0.717	1.00
16_L	19_W	0.705	1.00
40_F	45_L	0.696	1.00
63_F	66_A	0.693	1.00
48_W	51_Q	0.687	1.00
66_A	70_N	0.685	1.00
22_V	26_F	0.684	1.00
4_Y	73_D	0.671	1.00
65_Y	69_M	0.671	1.00
6_R	9_L	0.664	1.00
18_I	64_V	0.663	1.00
71_R	74_R	0.659	1.00
43_F	46_G	0.649	1.00
32_D	35_N	0.638	1.00
38_R	43_F	0.631	1.00
20_F	25_G	0.630	1.00
60_V	63_F	0.623	0.99
27_G	50_A	0.622	0.99
5_W	8_N	0.608	0.99
27_G	49_F	0.601	0.99
31_A	43_F	0.592	0.99
11_L	14_I	0.589	0.99
3_A	77_G	0.587	0.99
4_Y	8_N	0.587	0.99
54_S	58_F	0.582	0.99
15_L	18_I	0.571	0.99
49_F	57_V	0.571	0.99
56_Y	60_V	0.568	0.99
32_D	36_Q	0.563	0.99
31_A	44_P	0.562	0.99
70_N	73_D	0.562	0.99
45_L	48_W	0.561	0.99
14_I	68_R	0.555	0.99
27_G	46_G	0.554	0.99
8_N	15_L	0.537	0.98
40_F	44_P	0.536	0.98
9_L	12_T	0.534	0.98
31_A	78_V	0.523	0.98
57_V	61_L	0.521	0.98
3_A	78_V	0.518	0.98
26_F	34_L	0.510	0.98
55_I	59_V	0.509	0.98
29_L	33_E	0.506	0.98
72_L	75_E	0.505	0.98
50_A	53_G	0.504	0.98
3_A	10_R	0.502	0.98
56_Y	62_I	0.501	0.98
18_I	22_V	0.500	0.98

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
4i0uA	4	0.7975	30.2	0.862	Contact Map
4ev6A	3	0.8228	26.2	0.866	Contact Map
2lonA	1	0.962	9.4	0.89	Contact Map
2kogA	1	0.4051	9.3	0.891	Contact Map
3nd0A	2	0.9241	6.2	0.899	Contact Map
2zxeA	1	0.9114	6	0.9	Contact Map
2wswA	3	0.9494	5.9	0.9	Contact Map
3hd7A	1	0.4051	5.5	0.902	Contact Map
2lomA	1	0.9367	5.1	0.903	Contact Map
4wgvA	2	0.9494	4.6	0.905	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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