TRAUB - PFAM28P - GREMLIN Contacts

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TRAUB - Apoptosis-antagonizing transcription factor, C-terminal

PFAM:	PF08164	Sequences: YQQLLKELIESRSSDSSAAGSGQWLALQKLRKKKKKKKKVDTKASKGRKLRYTVHEKLQNFMAPEDRGTWSEEAIDELFASLF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	83 (82)
Sequences:	608 (448)
Seq/√Len:	49.5
META:	0.365

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
41_D	49_K	3.412	1.00
40_V	45_S	3.059	1.00
40_V	44_A	2.932	1.00
41_D	44_A	2.876	1.00
75_I	78_L	2.386	1.00
3_Q	6_K	2.091	1.00
56_E	59_Q	2.084	1.00
77_E	81_S	2.069	1.00
70_W	74_A	2.039	1.00
44_A	51_R	1.938	0.99
47_G	51_R	1.784	0.99
44_A	47_G	1.760	0.99
32_K	35_K	1.657	0.98
63_A	74_A	1.567	0.97
61_F	71_S	1.554	0.97
16_S	19_A	1.525	0.97
2_Q	7_E	1.502	0.96
44_A	49_K	1.445	0.96
24_W	27_L	1.421	0.95
42_T	49_K	1.413	0.95
2_Q	62_M	1.388	0.95
31_R	38_K	1.297	0.92
2_Q	9_I	1.282	0.92
28_Q	31_R	1.271	0.91
9_I	28_Q	1.270	0.91
40_V	49_K	1.244	0.91
50_L	53_T	1.243	0.91
24_W	29_K	1.222	0.90
12_R	70_W	1.204	0.89
27_L	32_K	1.186	0.88
2_Q	57_K	1.166	0.87
10_E	77_E	1.105	0.84
80_A	83_F	1.076	0.83
9_I	13_S	1.074	0.83
31_R	34_K	1.067	0.82
45_S	48_R	1.043	0.81
26_A	33_K	1.038	0.81
23_Q	28_Q	1.034	0.80
42_T	51_R	1.028	0.80
55_H	62_M	1.011	0.79
8_L	42_T	1.007	0.78
72_E	75_I	0.997	0.78
55_H	65_E	0.980	0.77
44_A	48_R	0.971	0.76
9_I	39_K	0.968	0.76
15_D	19_A	0.965	0.75
10_E	31_R	0.948	0.74
47_G	58_L	0.945	0.74
29_K	32_K	0.924	0.72
71_S	81_S	0.921	0.72
1_Y	4_L	0.920	0.72
7_E	10_E	0.890	0.69
51_R	54_V	0.888	0.69
41_D	51_R	0.876	0.68
71_S	74_A	0.873	0.68
50_L	75_I	0.873	0.68
62_M	78_L	0.865	0.67
72_E	77_E	0.865	0.67
1_Y	5_L	0.835	0.64
8_L	63_A	0.821	0.63
15_D	22_G	0.821	0.63
68_G	76_D	0.800	0.61
3_Q	35_K	0.795	0.61
24_W	28_Q	0.783	0.59
45_S	51_R	0.780	0.59
50_L	55_H	0.775	0.59
7_E	83_F	0.775	0.59
41_D	47_G	0.768	0.58
45_S	56_E	0.762	0.57
17_S	20_G	0.760	0.57
46_K	60_N	0.752	0.56
7_E	52_Y	0.752	0.56
7_E	45_S	0.749	0.56
4_L	75_I	0.743	0.55
70_W	73_E	0.740	0.55
42_T	53_T	0.733	0.54
49_K	60_N	0.728	0.54
14_S	28_Q	0.725	0.54
74_A	78_L	0.708	0.52
74_A	77_E	0.707	0.52
13_S	69_T	0.702	0.51
57_K	61_F	0.699	0.51
53_T	65_E	0.689	0.50
40_V	51_R	0.682	0.49
71_S	75_I	0.678	0.49
16_S	21_S	0.672	0.48
56_E	70_W	0.667	0.48
18_A	50_L	0.661	0.47
51_R	81_S	0.659	0.47
77_E	80_A	0.656	0.47
11_S	70_W	0.649	0.46
25_L	30_L	0.645	0.45
27_L	31_R	0.645	0.45
6_K	9_I	0.635	0.44
9_I	30_L	0.628	0.44
42_T	48_R	0.615	0.42
9_I	72_E	0.613	0.42
27_L	35_K	0.612	0.42
40_V	43_K	0.610	0.42
27_L	30_L	0.609	0.42
23_Q	26_A	0.597	0.41
19_A	22_G	0.592	0.40
11_S	23_Q	0.587	0.40
13_S	83_F	0.585	0.39
71_S	80_A	0.580	0.39
43_K	49_K	0.580	0.39
23_Q	30_L	0.578	0.39
26_A	30_L	0.568	0.38
15_D	18_A	0.565	0.37
40_V	48_R	0.562	0.37
66_D	76_D	0.559	0.37
63_A	81_S	0.549	0.36
23_Q	83_F	0.549	0.36
35_K	39_K	0.548	0.36
45_S	49_K	0.546	0.36
3_Q	22_G	0.546	0.36
51_R	61_F	0.538	0.35
70_W	77_E	0.523	0.34
48_R	51_R	0.522	0.33
9_I	42_T	0.521	0.33
4_L	82_L	0.519	0.33
55_H	63_A	0.507	0.32
16_S	32_K	0.500	0.32

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
4xrpB	1	0.506	8.7	0.907	Contact Map
3ww3A	3	0.6506	5.7	0.915	Contact Map
4ywtA	1	0.9759	5.4	0.916	Contact Map
3vlcE	1	0.6988	4.1	0.921	Contact Map
3odnA	1	0.7831	3.7	0.922	Contact Map
4gyvA	4	0.6627	3.3	0.924	Contact Map
3b2eE	1	0.6988	3	0.925	Contact Map
4uf5B	1	0.1325	2.8	0.927	Contact Map
3ziuA	1	0.5181	2.7	0.928	Contact Map
2cjqA	1	0.8795	2.6	0.928	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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