DUF2523 - PFAM28P - GREMLIN Contacts

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DUF2523 - Protein of unknown function (DUF2523)

PFAM:	PF10734	Sequences: LAGFLASLLGSLVGRVLVALGLGFVTYTGVDALLDQLKSQIQSAFGGLPADVLQLLGLLGVDVALSIILSAIVARLALKG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	80 (77)
Sequences:	1723 (1510)
Seq/√Len:	172.1
META:	0.762

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
60_G	63_V	3.453	1.00
57_G	62_D	3.179	1.00
56_L	61_V	2.834	1.00
71_A	75_R	2.536	1.00
38_K	42_Q	2.429	1.00
33_L	36_Q	2.384	1.00
31_D	35_D	2.097	1.00
38_K	69_L	2.075	1.00
66_S	70_S	1.894	1.00
35_D	39_S	1.878	1.00
41_I	69_L	1.798	1.00
29_G	32_A	1.784	1.00
63_V	67_I	1.664	1.00
13_V	16_V	1.650	1.00
45_F	62_D	1.593	1.00
51_D	54_Q	1.577	1.00
36_Q	40_Q	1.489	1.00
11_S	14_G	1.477	1.00
2_A	8_L	1.441	1.00
14_G	17_L	1.411	1.00
64_A	67_I	1.402	1.00
6_A	9_L	1.369	1.00
72_I	75_R	1.343	1.00
28_T	31_D	1.339	1.00
74_A	77_A	1.298	1.00
9_L	16_V	1.253	1.00
64_A	68_I	1.217	1.00
70_S	74_A	1.205	1.00
10_G	13_V	1.187	1.00
15_R	18_V	1.186	1.00
44_A	47_G	1.183	1.00
67_I	71_A	1.164	1.00
40_Q	44_A	1.158	1.00
69_L	73_V	1.130	1.00
3_G	7_S	1.129	1.00
41_I	65_L	1.120	1.00
12_L	16_V	1.096	1.00
14_G	18_V	1.070	1.00
8_L	12_L	1.030	0.99
60_G	64_A	0.999	0.99
39_S	43_S	0.974	0.99
63_V	66_S	0.944	0.99
55_L	59_L	0.939	0.99
73_V	77_A	0.927	0.99
16_V	19_A	0.910	0.99
23_G	27_Y	0.890	0.98
39_S	42_Q	0.887	0.98
45_F	57_G	0.876	0.98
48_L	53_L	0.869	0.98
54_Q	57_G	0.827	0.97
24_F	28_T	0.823	0.97
28_T	32_A	0.811	0.97
30_V	34_L	0.805	0.97
68_I	71_A	0.795	0.97
5_L	9_L	0.793	0.97
31_D	66_S	0.767	0.96
42_Q	46_G	0.765	0.96
72_I	76_L	0.760	0.96
9_L	12_L	0.760	0.96
40_Q	67_I	0.753	0.95
14_G	19_A	0.749	0.95
62_D	66_S	0.743	0.95
41_I	45_F	0.734	0.95
53_L	57_G	0.731	0.95
6_A	11_S	0.727	0.94
42_Q	47_G	0.722	0.94
13_V	20_L	0.717	0.94
17_L	22_L	0.698	0.93
48_L	51_D	0.697	0.93
21_G	24_F	0.689	0.93
65_L	69_L	0.686	0.92
74_A	78_L	0.683	0.92
5_L	8_L	0.682	0.92
7_S	10_G	0.679	0.92
26_T	29_G	0.668	0.91
55_L	58_L	0.667	0.91
37_L	71_A	0.667	0.91
2_A	9_L	0.663	0.91
6_A	10_G	0.656	0.91
68_I	75_R	0.655	0.91
15_R	21_G	0.652	0.90
59_L	70_S	0.651	0.90
53_L	76_L	0.651	0.90
47_G	50_A	0.648	0.90
49_P	52_V	0.647	0.90
30_V	72_I	0.646	0.90
43_S	47_G	0.635	0.89
46_G	50_A	0.633	0.89
56_L	69_L	0.602	0.87
59_L	74_A	0.598	0.86
24_F	78_L	0.591	0.86
16_V	21_G	0.588	0.85
27_Y	70_S	0.585	0.85
73_V	76_L	0.582	0.85
56_L	63_V	0.577	0.84
43_S	50_A	0.577	0.84
10_G	16_V	0.572	0.84
29_G	33_L	0.566	0.83
25_V	29_G	0.566	0.83
15_R	22_L	0.564	0.83
30_V	74_A	0.561	0.83
20_L	27_Y	0.560	0.82
45_F	48_L	0.559	0.82
11_S	18_V	0.548	0.81
40_Q	43_S	0.547	0.81
45_F	65_L	0.546	0.81
69_L	72_I	0.546	0.81
40_Q	47_G	0.541	0.80
3_G	6_A	0.537	0.80
60_G	67_I	0.535	0.80
51_D	55_L	0.533	0.79
71_A	78_L	0.523	0.78
23_G	59_L	0.513	0.77
44_A	68_I	0.506	0.76
5_L	11_S	0.503	0.75
56_L	59_L	0.500	0.75

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
4c9yA	1	0.6	2.2	0.884	Contact Map
1ciiA	1	0.5625	2	0.887	Contact Map
4aq5C	1	0.95	1.9	0.888	Contact Map
4aq5E	1	0.9375	1.9	0.888	Contact Map
4aq5B	1	0.9375	1.6	0.894	Contact Map
2bg9B	1	0.9875	1.5	0.895	Contact Map
3wo6A	1	0.6	1.5	0.896	Contact Map
4aq5A	1	0.95	1.4	0.898	Contact Map
1oedB	1	0.9875	1.3	0.898	Contact Map
1oedC	1	0.9875	1.3	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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