DUF3329 - PFAM28P - GREMLIN Contacts

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DUF3329 - Domain of unknown function (DUF3329)

PFAM:	PF11808	Sequences: AWRRELLRLALLLLAALLLGLLFGAPAAALLLGLLLYLAWHLRQLYRLLRWLRGPRRAPPPEGSGLWGEVFARLYRLQRRNRKRKK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	86 (82)
Sequences:	7869 (5865)
Seq/√Len:	647.7
META:	0.902

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
25_A	28_A	2.619	1.00
63_G	71_F	2.602	1.00
27_A	31_L	2.434	1.00
46_Y	50_R	2.102	1.00
78_Q	81_N	2.065	1.00
49_L	53_R	2.018	1.00
51_W	61_P	1.993	1.00
81_N	84_R	1.883	1.00
26_P	29_A	1.758	1.00
25_A	29_A	1.703	1.00
16_A	29_A	1.695	1.00
68_G	72_A	1.676	1.00
36_L	40_W	1.670	1.00
37_Y	41_H	1.644	1.00
44_Q	47_R	1.621	1.00
48_L	74_L	1.594	1.00
34_L	38_L	1.579	1.00
31_L	34_L	1.555	1.00
23_F	29_A	1.532	1.00
40_W	44_Q	1.511	1.00
48_L	71_F	1.508	1.00
4_R	7_L	1.438	1.00
26_P	30_L	1.406	1.00
18_L	22_L	1.387	1.00
44_Q	63_G	1.366	1.00
45_L	66_L	1.359	1.00
43_R	47_R	1.334	1.00
28_A	31_L	1.317	1.00
4_R	8_R	1.317	1.00
49_L	73_R	1.314	1.00
37_Y	42_L	1.296	1.00
39_A	43_R	1.293	1.00
23_F	26_P	1.280	1.00
53_R	73_R	1.278	1.00
13_L	34_L	1.250	1.00
77_L	81_N	1.233	1.00
12_L	16_A	1.180	1.00
20_G	28_A	1.166	1.00
20_G	25_A	1.158	1.00
72_A	75_Y	1.139	1.00
7_L	11_L	1.127	1.00
38_L	42_L	1.081	1.00
12_L	33_G	1.077	1.00
18_L	21_L	1.051	1.00
27_A	30_L	1.034	1.00
77_L	80_R	1.031	1.00
5_E	8_R	1.020	1.00
8_R	12_L	1.012	1.00
17_L	26_P	1.002	1.00
49_L	69_E	0.980	1.00
40_W	43_R	0.935	1.00
72_A	76_R	0.930	1.00
16_A	33_G	0.928	1.00
7_L	10_A	0.923	1.00
19_L	23_F	0.910	1.00
11_L	15_A	0.906	1.00
32_L	36_L	0.903	1.00
17_L	21_L	0.849	1.00
5_E	37_Y	0.842	1.00
48_L	70_V	0.829	1.00
63_G	68_G	0.828	1.00
51_W	55_P	0.823	1.00
67_W	70_V	0.815	1.00
10_A	13_L	0.806	1.00
6_L	10_A	0.794	1.00
37_Y	40_W	0.794	1.00
41_H	44_Q	0.791	1.00
19_L	27_A	0.788	1.00
45_L	70_V	0.778	1.00
17_L	20_G	0.778	1.00
20_G	24_G	0.771	1.00
54_G	57_R	0.763	1.00
20_G	26_P	0.762	1.00
49_L	70_V	0.753	1.00
21_L	25_A	0.751	1.00
46_Y	49_L	0.751	1.00
21_L	24_G	0.745	1.00
82_R	85_K	0.740	1.00
20_G	23_F	0.725	1.00
45_L	49_L	0.723	1.00
43_R	64_S	0.720	1.00
28_A	32_L	0.690	1.00
47_R	69_E	0.685	1.00
21_L	29_A	0.679	1.00
37_Y	66_L	0.662	1.00
21_L	26_P	0.655	1.00
41_H	67_W	0.652	1.00
46_Y	66_L	0.646	1.00
17_L	30_L	0.631	1.00
13_L	17_L	0.628	1.00
74_L	81_N	0.614	1.00
56_R	59_P	0.613	1.00
76_R	80_R	0.610	1.00
60_P	77_L	0.595	1.00
9_L	12_L	0.593	1.00
41_H	45_L	0.588	1.00
42_L	66_L	0.583	1.00
50_R	54_G	0.579	1.00
67_W	71_F	0.578	1.00
43_R	46_Y	0.575	1.00
35_L	39_A	0.572	1.00
63_G	67_W	0.571	1.00
62_E	72_A	0.565	1.00
43_R	69_E	0.563	1.00
5_E	9_L	0.553	1.00
58_A	82_R	0.552	1.00
72_A	79_R	0.548	1.00
64_S	68_G	0.547	1.00
54_G	58_A	0.547	1.00
44_Q	71_F	0.547	1.00
73_R	77_L	0.539	1.00
71_F	75_Y	0.535	0.99
81_N	85_K	0.534	0.99
24_G	27_A	0.529	0.99
41_H	70_V	0.525	0.99
52_L	73_R	0.520	0.99
71_F	78_Q	0.515	0.99
8_R	11_L	0.513	0.99
55_P	58_A	0.509	0.99
69_E	73_R	0.508	0.99
29_A	33_G	0.507	0.99
71_F	74_L	0.505	0.99
73_R	85_K	0.500	0.99

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
2m20A	2	0.6395	30.9	0.828	Contact Map
4c7rA	3	0.9884	10.7	0.861	Contact Map
2j69A	1	0.9884	5	0.881	Contact Map
3pjsK	4	0.8721	4.8	0.881	Contact Map
1ji6A	1	0.7326	4.3	0.884	Contact Map
1wazA	1	0.5	4.2	0.885	Contact Map
4ry2A	2	0.9884	3.6	0.889	Contact Map
2mgyA	1	0.7907	3.3	0.89	Contact Map
3effK	4	0.9302	3	0.892	Contact Map
4lxjA	1	0.8837	2.9	0.894	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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