DUF1413 - PFAM28P - GREMLIN Contacts

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DUF1413 - Domain of unknown function (DUF1413)

PFAM:	PF07205	Sequences: EEAIKEIENLPSGEEFLVKDLFKGYEWNRISRGDRLLLGRLFLNYVKKGKIPGIKAIEKTSSNQQRYKK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	69 (67)
Sequences:	725 (569)
Seq/√Len:	69.5
META:	0.806

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
55_K	68_K	4.222	1.00
32_R	36_L	4.060	1.00
59_K	63_N	3.524	1.00
56_A	65_Q	2.856	1.00
4_I	7_I	2.175	1.00
5_K	8_E	2.124	1.00
14_E	29_R	2.068	1.00
15_E	58_E	2.034	1.00
18_V	38_L	1.890	1.00
43_L	47_K	1.789	1.00
23_K	26_E	1.610	0.99
60_T	66_R	1.575	0.99
33_G	39_G	1.570	0.99
33_G	40_R	1.381	0.98
59_K	65_Q	1.279	0.97
17_L	64_Q	1.266	0.97
6_E	23_K	1.261	0.96
8_E	47_K	1.231	0.96
36_L	62_S	1.218	0.96
6_E	25_Y	1.206	0.95
6_E	10_L	1.176	0.95
15_E	68_K	1.173	0.95
3_A	18_V	1.161	0.94
46_V	56_A	1.130	0.94
19_K	28_N	1.127	0.93
39_G	67_Y	1.092	0.92
35_R	64_Q	1.080	0.92
46_V	49_G	1.072	0.92
16_F	42_F	1.039	0.90
4_I	53_G	1.019	0.89
11_P	14_E	1.017	0.89
22_F	26_E	0.997	0.88
30_I	34_D	0.969	0.87
20_D	23_K	0.966	0.87
46_V	53_G	0.925	0.84
14_E	17_L	0.919	0.84
12_S	69_K	0.919	0.84
37_L	41_L	0.914	0.84
28_N	35_R	0.908	0.83
16_F	21_L	0.903	0.83
19_K	36_L	0.901	0.83
43_L	65_Q	0.883	0.81
22_F	42_F	0.875	0.81
9_N	61_S	0.859	0.80
35_R	65_Q	0.852	0.79
15_E	66_R	0.843	0.78
19_K	24_G	0.839	0.78
37_L	40_R	0.835	0.78
46_V	50_K	0.799	0.75
6_E	26_E	0.758	0.71
18_V	42_F	0.758	0.71
50_K	55_K	0.740	0.69
58_E	66_R	0.728	0.67
6_E	9_N	0.722	0.67
49_G	53_G	0.720	0.67
30_I	35_R	0.719	0.67
7_I	10_L	0.699	0.64
26_E	63_N	0.695	0.64
42_F	69_K	0.685	0.63
53_G	68_K	0.685	0.63
30_I	37_L	0.672	0.61
4_I	45_Y	0.670	0.61
60_T	64_Q	0.669	0.61
19_K	44_N	0.665	0.60
26_E	33_G	0.664	0.60
42_F	54_I	0.643	0.58
5_K	47_K	0.632	0.57
4_I	47_K	0.631	0.57
49_G	52_P	0.631	0.57
40_R	44_N	0.628	0.56
38_L	64_Q	0.625	0.56
15_E	29_R	0.619	0.55
4_I	8_E	0.619	0.55
24_G	29_R	0.617	0.55
6_E	69_K	0.614	0.54
11_P	55_K	0.607	0.54
19_K	66_R	0.604	0.53
30_I	41_L	0.600	0.53
32_R	43_L	0.594	0.52
5_K	11_P	0.594	0.52
30_I	38_L	0.590	0.52
11_P	52_P	0.589	0.51
45_Y	48_K	0.588	0.51
13_G	55_K	0.587	0.51
25_Y	29_R	0.586	0.51
20_D	64_Q	0.582	0.51
21_L	24_G	0.574	0.50
10_L	21_L	0.572	0.49
33_G	58_E	0.563	0.48
12_S	50_K	0.542	0.46
57_I	68_K	0.541	0.46
8_E	53_G	0.540	0.46
5_K	52_P	0.525	0.44
15_E	57_I	0.523	0.44
17_L	34_D	0.519	0.43
31_S	58_E	0.515	0.43
16_F	22_F	0.511	0.42
10_L	29_R	0.508	0.42
3_A	7_I	0.504	0.41
19_K	33_G	0.500	0.41

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
4rxxA	1	0.4493	5.5	0.872	Contact Map
4rh7A	1	0.9565	5.2	0.874	Contact Map
1vykA	1	0.942	4.7	0.877	Contact Map
3zq4A	3	0.8551	4.7	0.877	Contact Map
1vm6A	4	0.3478	4.2	0.879	Contact Map
2irfG	1	0.5072	4	0.881	Contact Map
3v9fA	1	0.5797	3.7	0.883	Contact Map
1jg7A	1	0.6957	3.3	0.885	Contact Map
3up8A	1	0.4058	3.2	0.887	Contact Map
2dllA	1	0.5797	3.1	0.887	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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