DUF2484 - PFAM28P - GREMLIN Contacts

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DUF2484 - Protein of unknown function (DUF2484)

PFAM:	PF10658	Sequences: MSLSLILACLWVLAANVVAMLPSRNHWRPAYVLIALGPPLLGWVTYQNGPWWGLLALAAGASMLRWPLIYLWRWLR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	76 (76)
Sequences:	1010 (718)
Seq/√Len:	82.3
META:	0.781

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
4_S	47_Q	3.535	1.00
45_T	53_G	3.367	1.00
7_L	43_W	3.067	1.00
18_V	29_P	2.700	1.00
8_A	44_V	2.607	1.00
2_S	48_N	2.224	1.00
21_L	29_P	2.091	1.00
43_W	47_Q	1.996	1.00
42_G	45_T	1.914	1.00
69_I	73_R	1.830	1.00
44_V	56_A	1.826	1.00
45_T	50_P	1.687	1.00
3_L	7_L	1.606	1.00
12_V	16_N	1.605	1.00
4_S	7_L	1.574	1.00
38_P	45_T	1.492	0.99
9_C	12_V	1.460	0.99
25_N	29_P	1.432	0.99
66_W	69_I	1.427	0.99
18_V	21_L	1.402	0.99
41_L	53_G	1.380	0.99
59_A	62_S	1.354	0.99
29_P	33_L	1.336	0.99
38_P	42_G	1.316	0.98
42_G	46_Y	1.310	0.98
37_G	60_G	1.290	0.98
16_N	20_M	1.260	0.98
34_I	38_P	1.180	0.97
50_P	54_L	1.167	0.97
38_P	50_P	1.143	0.96
41_L	56_A	1.134	0.96
15_A	66_W	1.134	0.96
23_S	30_A	1.123	0.96
19_A	59_A	1.094	0.95
4_S	43_W	1.091	0.95
27_W	31_Y	1.082	0.95
12_V	19_A	1.060	0.94
55_L	58_A	1.059	0.94
70_Y	73_R	1.011	0.93
72_W	76_R	0.980	0.92
32_V	36_L	0.979	0.92
9_C	13_L	0.979	0.92
58_A	61_A	0.978	0.91
71_L	75_L	0.964	0.91
46_Y	53_G	0.926	0.89
18_V	33_L	0.916	0.89
25_N	28_R	0.910	0.88
26_H	63_M	0.900	0.88
28_R	31_Y	0.886	0.87
61_A	68_L	0.879	0.86
33_L	62_S	0.848	0.84
3_L	6_I	0.843	0.84
12_V	56_A	0.839	0.84
5_L	44_V	0.812	0.82
8_A	40_L	0.807	0.81
29_P	32_V	0.787	0.80
54_L	58_A	0.744	0.76
25_N	31_Y	0.742	0.76
42_G	53_G	0.741	0.76
22_P	62_S	0.734	0.75
4_S	46_Y	0.730	0.74
15_A	36_L	0.725	0.74
19_A	63_M	0.724	0.74
18_V	26_H	0.724	0.74
42_G	50_P	0.721	0.74
53_G	56_A	0.706	0.72
27_W	34_I	0.705	0.72
57_L	61_A	0.697	0.71
30_A	63_M	0.690	0.70
14_A	21_L	0.690	0.70
4_S	48_N	0.684	0.70
51_W	54_L	0.669	0.68
8_A	59_A	0.665	0.67
45_T	60_G	0.658	0.67
51_W	55_L	0.650	0.66
72_W	75_L	0.646	0.65
8_A	56_A	0.644	0.65
27_W	71_L	0.644	0.65
52_W	55_L	0.644	0.65
34_I	66_W	0.628	0.63
21_L	28_R	0.628	0.63
19_A	62_S	0.615	0.61
7_L	40_L	0.614	0.61
28_R	32_V	0.612	0.61
69_I	72_W	0.612	0.61
60_G	66_W	0.610	0.61
16_N	23_S	0.609	0.61
46_Y	50_P	0.606	0.60
3_L	43_W	0.601	0.60
48_N	52_W	0.589	0.58
22_P	40_L	0.580	0.57
49_G	52_W	0.576	0.56
24_R	28_R	0.572	0.56
21_L	24_R	0.566	0.55
35_A	74_W	0.565	0.55
49_G	55_L	0.559	0.54
41_L	60_G	0.548	0.53
13_L	17_V	0.545	0.52
70_Y	74_W	0.533	0.51
1_M	6_I	0.533	0.51
61_A	72_W	0.519	0.49
62_S	65_R	0.519	0.49
61_A	76_R	0.516	0.49
30_A	67_P	0.511	0.48
6_I	10_L	0.511	0.48
68_L	71_L	0.510	0.48
31_Y	37_G	0.509	0.48
16_N	63_M	0.508	0.47
40_L	48_N	0.508	0.47
6_I	13_L	0.506	0.47
27_W	32_V	0.504	0.47
31_Y	66_W	0.503	0.47
22_P	65_R	0.503	0.47
56_A	60_G	0.500	0.46

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
1zcdA	1	0.9868	2.5	0.921	Contact Map
4czbA	2	0.9605	1.1	0.936	Contact Map
2qi9A	2	0.8553	1	0.937	Contact Map
4p02B	1	0.3158	0.9	0.939	Contact Map
2nq2A	2	0.6316	0.9	0.939	Contact Map
4ev6A	3	0.7763	0.9	0.94	Contact Map
4hygA	3	0.9868	0.8	0.942	Contact Map
4p02A	1	1	0.7	0.944	Contact Map
2mv6A	1	0.4211	0.7	0.945	Contact Map
4q65A	1	0.9868	0.6	0.945	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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