YBFQ - ECOLI - GREMLIN Contacts

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YBFQ - Putative defective transposase YbfQ

UniProt:	Q2EEQ8	Sequences: MELKKLMEHISITPDYRQAWKVVHKLSDILLLTICAVISGAEGWEDIEDFGETHLDFLKQYGDFENGIPVHDTIARVVSQGKIT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG14419
Length:	84 (75)
Sequences:	302 (247)
Seq/√Len:	28.6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
18_Q	21_K	3.450	1.00
73_T	76_R	3.337	1.00
33_T	74_I	2.665	1.00
18_Q	22_V	2.601	0.99
26_L	77_V	2.573	0.99
48_E	52_E	2.321	0.99
55_L	59_K	2.255	0.98
29_I	77_V	2.230	0.98
25_K	28_D	1.710	0.92
32_L	51_G	1.654	0.91
28_D	63_D	1.589	0.89
36_A	51_G	1.586	0.89
32_L	64_F	1.569	0.88
34_I	38_I	1.568	0.88
32_L	58_L	1.557	0.88
45_E	75_A	1.539	0.87
51_G	64_F	1.513	0.86
36_A	47_I	1.509	0.86
6_L	10_I	1.451	0.84
42_E	46_D	1.364	0.80
19_A	22_V	1.346	0.79
39_S	54_H	1.327	0.78
74_I	78_V	1.319	0.77
31_L	57_F	1.303	0.76
43_G	53_T	1.287	0.76
32_L	74_I	1.284	0.75
32_L	55_L	1.188	0.69
31_L	64_F	1.153	0.67
46_D	75_A	1.143	0.66
7_M	10_I	1.142	0.66
28_D	59_K	1.102	0.63
16_Y	57_F	1.049	0.60
70_V	78_V	1.046	0.59
36_A	41_A	1.033	0.58
28_D	65_E	1.016	0.57
7_M	11_S	0.994	0.55
25_K	63_D	0.993	0.55
28_D	64_F	0.986	0.55
44_W	78_V	0.982	0.54
43_G	78_V	0.956	0.52
23_V	34_I	0.945	0.52
38_I	54_H	0.944	0.52
47_I	58_L	0.942	0.51
45_E	79_S	0.925	0.50
13_T	30_L	0.920	0.50
48_E	71_H	0.908	0.49
64_F	67_G	0.898	0.48
41_A	53_T	0.882	0.47
22_V	39_S	0.875	0.46
41_A	47_I	0.843	0.44
52_E	56_D	0.830	0.43
13_T	79_S	0.822	0.42
55_L	64_F	0.812	0.41
46_D	73_T	0.811	0.41
44_W	75_A	0.806	0.41
62_G	70_V	0.805	0.41
29_I	32_L	0.805	0.41
44_W	50_F	0.795	0.40
10_I	13_T	0.780	0.39
31_L	61_Y	0.775	0.39
24_H	64_F	0.764	0.38
37_V	40_G	0.757	0.37
24_H	27_S	0.746	0.37
24_H	33_T	0.740	0.36
62_G	78_V	0.739	0.36
9_H	34_I	0.735	0.36
12_I	34_I	0.730	0.35
7_M	61_Y	0.727	0.35
22_V	35_C	0.719	0.35
35_C	61_Y	0.714	0.34
8_E	36_A	0.713	0.34
10_I	79_S	0.709	0.34
50_F	54_H	0.702	0.33
40_G	45_E	0.681	0.32
47_I	75_A	0.671	0.31
75_A	79_S	0.667	0.31
57_F	60_Q	0.653	0.30
26_L	34_I	0.649	0.30
24_H	65_E	0.645	0.30
48_E	68_I	0.640	0.29
25_K	35_C	0.637	0.29
6_L	31_L	0.633	0.29
15_D	70_V	0.633	0.29
33_T	49_D	0.630	0.29
33_T	47_I	0.624	0.28
31_L	35_C	0.622	0.28
21_K	79_S	0.618	0.28
33_T	37_V	0.617	0.28
11_S	38_I	0.610	0.27
28_D	32_L	0.585	0.26
24_H	28_D	0.584	0.26
59_K	62_G	0.583	0.26
24_H	50_F	0.581	0.26
49_D	52_E	0.576	0.25
45_E	59_K	0.570	0.25
5_K	42_E	0.568	0.25
71_H	79_S	0.566	0.25
27_S	76_R	0.564	0.25
25_K	59_K	0.556	0.24
14_P	40_G	0.553	0.24
12_I	39_S	0.540	0.23
6_L	27_S	0.534	0.23
50_F	69_P	0.526	0.23
28_D	74_I	0.524	0.22
24_H	30_L	0.516	0.22
46_D	76_R	0.509	0.22
34_I	57_F	0.509	0.22
8_E	13_T	0.507	0.22
45_E	53_T	0.507	0.22
15_D	69_P	0.505	0.21
10_I	72_D	0.503	0.21
37_V	49_D	0.500	0.21

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
2jqtA	1	0.3452	18.2	0.923	Contact Map
2yicA	2	0.8571	13.5	0.928	Contact Map
2xt6A	2	0.9524	11.5	0.93	Contact Map
4nyzA	1	0.631	11	0.93	Contact Map
4wfzA	1	0.8095	11	0.93	Contact Map
3n6mA	1	0.6548	9.4	0.933	Contact Map
4icgC	1	0.3452	9.1	0.933	Contact Map
4qnlA	3	0.7143	7.9	0.935	Contact Map
2kvcA	1	0.4643	7.4	0.936	Contact Map
4wznA	6	0.0595	7	0.936	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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