DUF3263 - PFAM28P - GREMLIN Contacts

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DUF3263 - Protein of unknown function (DUF3263)

PFAM:	PF11662	Sequences: ELSERDRAILDFERQWWRYAGAKEQAIRERFGLSPTRYYQLLNALIDRPEALAYDPLLVRRLRRLRDARRRARS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	74 (72)
Sequences:	3492 (1865)
Seq/√Len:	219.8
META:	0.841

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
14_R	55_D	3.794	1.00
13_E	23_K	2.887	1.00
3_S	6_D	2.865	1.00
11_D	54_Y	2.748	1.00
52_L	60_R	2.573	1.00
47_D	66_R	2.012	1.00
6_D	48_R	2.009	1.00
23_K	39_Y	1.926	1.00
4_E	8_A	1.923	1.00
37_R	40_Q	1.906	1.00
12_F	31_F	1.887	1.00
5_R	41_L	1.832	1.00
37_R	41_L	1.793	1.00
27_I	35_P	1.744	1.00
6_D	41_L	1.711	1.00
33_L	41_L	1.633	1.00
7_R	54_Y	1.580	1.00
15_Q	30_R	1.548	1.00
25_Q	29_E	1.534	1.00
8_A	30_R	1.421	1.00
46_I	62_L	1.269	1.00
9_I	45_L	1.183	1.00
11_D	55_D	1.146	1.00
67_D	70_R	1.139	1.00
12_F	26_A	1.126	1.00
4_E	7_R	1.117	1.00
55_D	58_L	1.116	1.00
44_A	48_R	1.114	1.00
24_E	35_P	1.110	1.00
38_Y	42_L	1.077	1.00
9_I	41_L	1.041	1.00
60_R	69_R	1.032	1.00
9_I	31_F	1.028	1.00
43_N	46_I	1.020	1.00
47_D	63_R	1.010	1.00
41_L	44_A	1.001	1.00
43_N	66_R	0.995	1.00
28_R	34_S	0.983	1.00
68_A	72_A	0.939	1.00
5_R	8_A	0.914	0.99
13_E	38_Y	0.888	0.99
7_R	11_D	0.887	0.99
45_L	51_A	0.880	0.99
60_R	70_R	0.871	0.99
17_W	20_A	0.871	0.99
26_A	29_E	0.850	0.99
67_D	71_R	0.842	0.99
51_A	59_V	0.831	0.99
57_L	64_R	0.831	0.99
60_R	63_R	0.830	0.99
45_L	48_R	0.828	0.99
9_I	12_F	0.794	0.98
6_D	45_L	0.789	0.98
19_Y	30_R	0.777	0.98
28_R	32_G	0.773	0.98
68_A	71_R	0.768	0.98
51_A	54_Y	0.752	0.98
58_L	62_L	0.745	0.98
57_L	60_R	0.744	0.98
24_E	43_N	0.742	0.98
28_R	35_P	0.741	0.98
9_I	33_L	0.739	0.97
59_V	62_L	0.731	0.97
16_W	19_Y	0.716	0.97
10_L	59_V	0.709	0.97
40_Q	44_A	0.692	0.96
15_Q	18_R	0.688	0.96
40_Q	43_N	0.683	0.96
19_Y	22_A	0.670	0.96
30_R	70_R	0.668	0.95
22_A	25_Q	0.661	0.95
33_L	37_R	0.656	0.95
5_R	9_I	0.651	0.95
10_L	58_L	0.646	0.95
49_P	53_A	0.646	0.95
26_A	30_R	0.641	0.94
65_L	69_R	0.637	0.94
33_L	38_Y	0.634	0.94
43_N	47_D	0.634	0.94
46_I	65_L	0.627	0.94
13_E	39_Y	0.623	0.93
39_Y	43_N	0.603	0.92
23_K	38_Y	0.603	0.92
20_A	68_A	0.600	0.92
48_R	51_A	0.590	0.92
65_L	70_R	0.586	0.91
8_A	12_F	0.578	0.91
40_Q	62_L	0.576	0.91
18_R	36_T	0.576	0.91
65_L	68_A	0.575	0.90
32_G	37_R	0.575	0.90
16_W	20_A	0.575	0.90
48_R	54_Y	0.572	0.90
24_E	28_R	0.560	0.89
63_R	67_D	0.558	0.89
59_V	66_R	0.553	0.89
56_P	60_R	0.539	0.87
18_R	57_L	0.535	0.87
16_W	47_D	0.527	0.86
69_R	72_A	0.524	0.86
21_G	27_I	0.523	0.86
46_I	66_R	0.523	0.86
52_L	59_V	0.520	0.86
27_I	39_Y	0.519	0.85
19_Y	36_T	0.518	0.85
46_I	58_L	0.514	0.85
32_G	53_A	0.508	0.84
16_W	57_L	0.500	0.83

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
3k2zA	2	0.8108	29.3	0.854	Contact Map
4un1B	1	1	26.8	0.857	Contact Map
1ku3A	1	0.7297	24.1	0.86	Contact Map
3eyiA	1	0.6892	23.8	0.86	Contact Map
4nqwA	1	0.6757	20.9	0.864	Contact Map
4un1A	1	1	20.8	0.864	Contact Map
1u5tA	1	0.7973	19.6	0.866	Contact Map
4ou0A	1	0.8514	19.6	0.866	Contact Map
4g6dA	1	0.7027	18.9	0.867	Contact Map
1l9zH	1	0.8649	18.4	0.868	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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