DUF1851 - PFAM28P - GREMLIN Contacts

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DUF1851 - Domain of unknown function (DUF1851)

PFAM:	PF08906	Sequences: AESREEFFALLDDDEFLDDWLMPPLVDEARAKGGPLGPGECYGFKPPPVLGGEYEVENLEKVDLREHLSLLGQLH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	75 (71)
Sequences:	3450 (2759)
Seq/√Len:	327.5
META:	0.878

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
45_K	60_E	3.599	1.00
40_E	61_K	3.189	1.00
63_D	66_E	2.845	1.00
43_G	62_V	2.438	1.00
37_G	40_E	2.347	1.00
43_G	67_H	2.318	1.00
29_A	59_L	2.023	1.00
40_E	63_D	1.835	1.00
47_P	71_L	1.753	1.00
6_E	10_L	1.713	1.00
54_Y	58_N	1.664	1.00
39_G	63_D	1.524	1.00
44_F	48_P	1.494	1.00
48_P	54_Y	1.416	1.00
65_R	69_S	1.407	1.00
34_G	61_K	1.378	1.00
33_G	42_Y	1.339	1.00
17_L	21_L	1.337	1.00
17_L	23_P	1.334	1.00
36_L	42_Y	1.323	1.00
25_L	44_F	1.307	1.00
29_A	34_G	1.295	1.00
30_R	35_P	1.254	1.00
32_K	56_V	1.227	1.00
44_F	59_L	1.208	1.00
18_D	24_P	1.202	1.00
55_E	58_N	1.186	1.00
67_H	71_L	1.173	1.00
29_A	42_Y	1.166	1.00
16_F	20_W	1.149	1.00
36_L	61_K	1.144	1.00
62_V	66_E	1.130	1.00
4_R	8_F	1.124	1.00
28_E	56_V	1.107	1.00
30_R	42_Y	1.101	1.00
69_S	73_Q	1.082	1.00
30_R	36_L	1.075	1.00
56_V	59_L	1.073	1.00
11_L	21_L	1.043	1.00
26_V	30_R	0.977	1.00
8_F	12_D	0.974	1.00
25_L	59_L	0.956	1.00
68_L	72_G	0.934	1.00
44_F	54_Y	0.922	1.00
18_D	23_P	0.902	1.00
24_P	28_E	0.883	1.00
53_E	58_N	0.859	1.00
70_L	74_L	0.849	1.00
66_E	70_L	0.841	1.00
5_E	8_F	0.824	1.00
9_A	12_D	0.819	1.00
24_P	27_D	0.814	1.00
34_G	45_K	0.804	1.00
12_D	15_E	0.802	1.00
23_P	27_D	0.798	1.00
27_D	30_R	0.793	1.00
60_E	66_E	0.788	1.00
66_E	73_Q	0.786	1.00
47_P	74_L	0.772	1.00
33_G	61_K	0.772	1.00
6_E	9_A	0.766	1.00
66_E	69_S	0.755	0.99
13_D	16_F	0.750	0.99
62_V	67_H	0.747	0.99
68_L	71_L	0.743	0.99
22_M	54_Y	0.730	0.99
16_F	19_D	0.724	0.99
37_G	61_K	0.703	0.99
41_C	64_L	0.686	0.99
59_L	67_H	0.666	0.99
70_L	73_Q	0.659	0.99
10_L	14_D	0.656	0.99
26_V	29_A	0.655	0.99
25_L	28_E	0.653	0.99
25_L	56_V	0.643	0.98
17_L	20_W	0.639	0.98
6_E	15_E	0.627	0.98
64_L	72_G	0.616	0.98
41_C	67_H	0.603	0.98
11_L	17_L	0.600	0.97
8_F	11_L	0.594	0.97
10_L	15_E	0.594	0.97
8_F	13_D	0.587	0.97
25_L	54_Y	0.587	0.97
4_R	7_F	0.580	0.97
44_F	67_H	0.575	0.97
11_L	14_D	0.571	0.97
4_R	12_D	0.571	0.97
13_D	17_L	0.566	0.96
14_D	18_D	0.562	0.96
5_E	9_A	0.558	0.96
9_A	13_D	0.554	0.96
4_R	11_L	0.550	0.96
65_R	68_L	0.546	0.96
7_F	11_L	0.534	0.95
43_G	60_E	0.528	0.95
9_A	14_D	0.524	0.94
63_D	73_Q	0.521	0.94
20_W	64_L	0.520	0.94
39_G	65_R	0.519	0.94
18_D	35_P	0.518	0.94
27_D	31_A	0.511	0.94
20_W	54_Y	0.509	0.94
64_L	67_H	0.508	0.94
19_D	22_M	0.506	0.93
5_E	15_E	0.500	0.93

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
7ceiB	1	0.92	24.7	0.85	Contact Map
4uhqA	1	0.9867	13.1	0.867	Contact Map
1fr2B	1	0.92	11.5	0.871	Contact Map
1mgpA	1	0.92	7.8	0.88	Contact Map
4qkoB	2	0.9733	6.1	0.886	Contact Map
3v53A	1	0.4533	4.9	0.891	Contact Map
1q55A	2	0	4.5	0.893	Contact Map
3zfkA	1	0.9067	4.2	0.894	Contact Map
2prvA	2	0.36	3.9	0.896	Contact Map
4rh7A	1	1	3.6	0.898	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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