DUF4404 - PFAM28P - GREMLIN Contacts

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DUF4404 - Domain of unknown function (DUF4404)

PFAM:	PF14357	Sequences: LRELLEELHAELAQAESLDEETRELLAELAADIERLLEREEAAPEADESLLERLEEAVERFEASHPRLAAALRRIIDTLSNMGI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	84 (84)
Sequences:	6264 (4733)
Seq/√Len:	516.4
META:	0.961

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
77_D	81_N	3.736	1.00
19_D	22_T	3.008	1.00
62_E	69_A	2.572	1.00
3_E	7_E	2.461	1.00
78_T	82_M	2.296	1.00
73_R	77_D	2.252	1.00
67_R	70_A	2.111	1.00
70_A	74_R	1.874	1.00
6_E	10_A	1.800	1.00
68_L	71_A	1.767	1.00
30_A	34_E	1.762	1.00
54_L	72_L	1.710	1.00
69_A	73_R	1.675	1.00
74_R	81_N	1.650	1.00
9_H	34_E	1.587	1.00
59_E	73_R	1.570	1.00
78_T	81_N	1.523	1.00
9_H	13_A	1.511	1.00
4_L	7_E	1.508	1.00
55_E	59_E	1.497	1.00
22_T	60_R	1.395	1.00
51_L	55_E	1.387	1.00
7_E	10_A	1.327	1.00
58_V	62_E	1.324	1.00
15_A	18_L	1.294	1.00
59_E	69_A	1.283	1.00
21_E	24_E	1.265	1.00
32_D	53_R	1.235	1.00
21_E	25_L	1.227	1.00
24_E	28_E	1.209	1.00
74_R	78_T	1.206	1.00
73_R	76_I	1.202	1.00
74_R	77_D	1.185	1.00
7_E	11_E	1.148	1.00
67_R	74_R	1.133	1.00
70_A	73_R	1.127	1.00
25_L	28_E	1.124	1.00
75_I	78_T	1.112	1.00
58_V	76_I	1.096	1.00
67_R	71_A	1.078	1.00
42_A	45_E	1.074	1.00
77_D	80_S	1.049	1.00
44_P	47_D	1.033	1.00
25_L	32_D	1.018	1.00
57_A	60_R	1.011	1.00
42_A	46_A	0.986	1.00
61_F	65_H	0.974	1.00
34_E	38_E	0.942	1.00
57_A	64_S	0.932	1.00
22_T	25_L	0.922	1.00
56_E	59_E	0.914	1.00
11_E	15_A	0.913	1.00
35_R	39_R	0.890	1.00
30_A	36_L	0.889	1.00
55_E	76_I	0.888	1.00
71_A	74_R	0.864	1.00
60_R	64_S	0.846	1.00
42_A	47_D	0.836	1.00
45_E	48_E	0.834	1.00
53_R	56_E	0.830	1.00
11_E	14_Q	0.820	1.00
28_E	32_D	0.817	1.00
20_E	24_E	0.798	1.00
28_E	31_A	0.797	1.00
34_E	37_L	0.795	1.00
58_V	72_L	0.795	1.00
23_R	27_A	0.793	1.00
4_L	12_L	0.792	1.00
3_E	6_E	0.780	1.00
29_L	36_L	0.768	1.00
50_L	75_I	0.765	1.00
48_E	52_E	0.763	1.00
7_E	74_R	0.751	1.00
24_E	27_A	0.747	1.00
80_S	84_I	0.742	1.00
75_I	81_N	0.741	1.00
43_A	47_D	0.741	1.00
27_A	34_E	0.737	1.00
27_A	30_A	0.736	1.00
59_E	63_A	0.734	1.00
58_V	69_A	0.733	1.00
29_L	32_D	0.731	1.00
52_E	59_E	0.714	1.00
55_E	73_R	0.710	1.00
71_A	75_I	0.706	1.00
76_I	82_M	0.687	1.00
36_L	53_R	0.682	1.00
41_E	45_E	0.670	1.00
58_V	73_R	0.669	1.00
44_P	49_S	0.666	1.00
22_T	28_E	0.665	1.00
54_L	76_I	0.658	1.00
31_A	34_E	0.657	1.00
38_E	41_E	0.649	1.00
20_E	23_R	0.645	1.00
35_R	38_E	0.627	1.00
39_R	43_A	0.610	1.00
41_E	44_P	0.608	1.00
43_A	48_E	0.608	1.00
76_I	80_S	0.604	1.00
23_R	26_L	0.601	1.00
32_D	36_L	0.600	0.99
49_S	52_E	0.597	0.99
10_A	14_Q	0.596	0.99
25_L	29_L	0.592	0.99
51_L	59_E	0.589	0.99
24_E	31_A	0.581	0.99
50_L	53_R	0.581	0.99
6_E	9_H	0.580	0.99
8_L	11_E	0.580	0.99
27_A	31_A	0.570	0.99
11_E	67_R	0.568	0.99
77_D	82_M	0.563	0.99
29_L	53_R	0.549	0.99
60_R	67_R	0.544	0.99
12_L	18_L	0.539	0.99
2_R	12_L	0.535	0.99
61_F	68_L	0.533	0.99
62_E	73_R	0.532	0.99
39_R	42_A	0.532	0.99
72_L	75_I	0.523	0.99
25_L	30_A	0.511	0.98
54_L	57_A	0.510	0.98
73_R	80_S	0.503	0.98
58_V	81_N	0.501	0.98
10_A	13_A	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
3qwpA	1	1	75.5	0.734	Contact Map
4wuyA	1	1	47.1	0.778	Contact Map
3n71A	1	1	40.1	0.788	Contact Map
4wmuA	1	0.9881	37.7	0.791	Contact Map
3a6mA	2	1	29.1	0.803	Contact Map
4l6yA	2	1	27.4	0.805	Contact Map
4aniA	2	0.9167	25.8	0.808	Contact Map
4cr2Z	1	0.8929	21.9	0.814	Contact Map
3ojaB	1	1	19.3	0.819	Contact Map
4uxvA	1	0.9881	18.4	0.821	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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