DUF5049 - PFAM28P - GREMLIN Contacts

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DUF5049 - Domain of unknown function (DUF5049)

PFAM:	PF16468	Sequences: MTEKIKEQILAIRDTGLTNMFDVNAVQRIANEMGFYELVDFIEEHRKEYAHFILTGE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	57 (56)
Sequences:	1020 (680)
Seq/√Len:	90.9
META:	0.941

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_H	48_E	2.611	1.00
22_D	25_A	2.546	1.00
18_T	25_A	2.389	1.00
12_I	29_I	2.375	1.00
10_L	14_D	2.182	1.00
17_L	32_E	2.041	1.00
11_A	35_F	1.920	1.00
8_Q	38_L	1.825	1.00
6_K	10_L	1.813	1.00
31_N	40_D	1.761	1.00
27_Q	43_E	1.740	1.00
17_L	33_M	1.705	1.00
28_R	32_E	1.700	1.00
18_T	29_I	1.560	1.00
17_L	29_I	1.470	1.00
40_D	44_E	1.410	0.99
10_L	13_R	1.359	0.99
15_T	18_T	1.303	0.99
51_H	57_E	1.301	0.99
9_I	52_F	1.273	0.99
31_N	39_V	1.233	0.98
29_I	33_M	1.188	0.98
25_A	29_I	1.180	0.98
28_R	31_N	1.172	0.98
23_V	46_R	1.158	0.97
30_A	38_L	1.157	0.97
21_F	54_L	1.024	0.95
23_V	50_A	1.012	0.94
27_Q	36_Y	0.976	0.93
15_T	33_M	0.967	0.93
10_L	52_F	0.939	0.92
23_V	42_I	0.936	0.92
28_R	36_Y	0.912	0.91
29_I	32_E	0.906	0.90
27_Q	40_D	0.879	0.89
38_L	41_F	0.870	0.89
27_Q	31_N	0.853	0.88
31_N	36_Y	0.827	0.86
27_Q	39_V	0.807	0.84
43_E	46_R	0.790	0.83
12_I	15_T	0.766	0.81
8_Q	12_I	0.765	0.81
39_V	43_E	0.737	0.79
31_N	34_G	0.736	0.79
53_I	56_G	0.734	0.78
12_I	35_F	0.734	0.78
25_A	28_R	0.726	0.78
38_L	52_F	0.726	0.78
8_Q	52_F	0.724	0.77
18_T	22_D	0.721	0.77
15_T	29_I	0.720	0.77
12_I	16_G	0.713	0.76
40_D	43_E	0.709	0.76
12_I	33_M	0.708	0.76
4_K	34_G	0.702	0.75
3_E	7_E	0.690	0.74
40_D	48_E	0.666	0.71
11_A	33_M	0.647	0.69
39_V	44_E	0.640	0.68
4_K	8_Q	0.640	0.68
41_F	45_H	0.637	0.68
50_A	54_L	0.629	0.67
36_Y	39_V	0.628	0.67
9_I	13_R	0.628	0.67
15_T	21_F	0.624	0.66
24_N	45_H	0.618	0.66
5_I	41_F	0.615	0.65
41_F	48_E	0.610	0.65
24_N	28_R	0.604	0.64
8_Q	37_E	0.596	0.63
36_Y	40_D	0.584	0.61
4_K	7_E	0.563	0.59
7_E	11_A	0.562	0.58
3_E	6_K	0.559	0.58
3_E	51_H	0.556	0.58
36_Y	44_E	0.542	0.56
28_R	43_E	0.542	0.56
10_L	21_F	0.542	0.56
8_Q	35_F	0.528	0.54
52_F	55_T	0.522	0.53
24_N	46_R	0.517	0.52
14_D	26_V	0.514	0.52
28_R	40_D	0.505	0.51
22_D	42_I	0.500	0.50

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
2miiA	1	0.9474	14.9	0.876	Contact Map
2qsfX	1	0.7193	12.9	0.879	Contact Map
4ddgA	3	0.9123	10.9	0.883	Contact Map
4fjvA	2	1	10.1	0.885	Contact Map
4q6vA	1	0.9474	9.4	0.887	Contact Map
2hjpA	4	0.7719	7.2	0.893	Contact Map
2zfyA	1	0.9123	6.5	0.894	Contact Map
4dhiB	1	0.9123	5.8	0.897	Contact Map
4lrvA	5	0.9298	5.6	0.897	Contact Map
3m03A	1	0.6491	5.2	0.899	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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