Tox-GHH - PFAM28P - GREMLIN Contacts

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Tox-GHH - GHH signature containing HNH/Endo VII superfamily nuclease toxin

PFAM:	PF15636	Sequences: EERARLLEHARQRAVRRAWKQERELVREGGKGTRDWTEEEKQEILSTGKVPGYEGHHINSVEQYPELAGDPNNIQFVK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	78 (72)
Sequences:	741 (579)
Seq/√Len:	68.2
META:	0.741

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
44_I	50_V	3.321	1.00
60_S	63_Q	3.073	1.00
40_E	53_Y	2.936	1.00
15_V	55_G	2.766	1.00
26_V	44_I	2.621	1.00
23_R	27_R	2.539	1.00
7_L	61_V	2.332	1.00
42_Q	46_S	2.276	1.00
13_R	17_R	2.246	1.00
14_A	69_G	2.231	1.00
25_L	30_G	1.979	1.00
41_K	45_L	1.931	1.00
18_A	76_F	1.903	1.00
13_R	69_G	1.850	1.00
17_R	20_K	1.786	1.00
27_R	45_L	1.723	1.00
43_E	51_P	1.572	0.99
56_H	59_N	1.565	0.99
24_E	28_E	1.443	0.98
47_T	50_V	1.438	0.98
14_A	17_R	1.405	0.98
25_L	33_T	1.377	0.98
29_G	41_K	1.284	0.97
25_L	29_G	1.211	0.95
10_A	13_R	1.119	0.93
20_K	62_E	1.104	0.92
10_A	69_G	1.010	0.89
24_E	37_T	1.008	0.88
19_W	53_Y	0.982	0.87
47_T	51_P	0.957	0.86
23_R	28_E	0.941	0.85
11_R	15_V	0.928	0.84
11_R	61_V	0.926	0.84
67_L	70_D	0.912	0.83
19_W	50_V	0.904	0.82
54_E	57_H	0.897	0.82
21_Q	72_N	0.867	0.80
11_R	33_T	0.862	0.79
21_Q	24_E	0.823	0.76
73_N	76_F	0.821	0.76
26_V	29_G	0.817	0.75
58_I	73_N	0.806	0.74
24_E	71_P	0.796	0.74
55_G	74_I	0.796	0.74
26_V	32_G	0.794	0.73
11_R	57_H	0.793	0.73
21_Q	42_Q	0.792	0.73
39_E	46_S	0.786	0.73
59_N	64_Y	0.776	0.72
6_L	10_A	0.772	0.71
23_R	45_L	0.763	0.70
60_S	64_Y	0.762	0.70
43_E	52_G	0.754	0.69
23_R	40_E	0.754	0.69
43_E	50_V	0.748	0.69
44_I	53_Y	0.732	0.67
32_G	36_W	0.728	0.67
39_E	43_E	0.707	0.64
22_E	36_W	0.700	0.64
13_R	16_R	0.699	0.64
9_H	13_R	0.696	0.63
37_T	40_E	0.690	0.63
57_H	60_S	0.689	0.62
8_E	12_Q	0.688	0.62
50_V	57_H	0.683	0.62
59_N	67_L	0.676	0.61
10_A	14_A	0.675	0.61
43_E	47_T	0.673	0.61
19_W	76_F	0.672	0.61
38_E	46_S	0.670	0.60
67_L	72_N	0.667	0.60
26_V	36_W	0.662	0.59
39_E	47_T	0.659	0.59
17_R	71_P	0.657	0.59
15_V	18_A	0.650	0.58
7_L	68_A	0.637	0.56
61_V	68_A	0.635	0.56
17_R	47_T	0.635	0.56
14_A	18_A	0.623	0.55
34_R	75_Q	0.622	0.55
43_E	49_K	0.621	0.55
36_W	50_V	0.620	0.54
46_S	49_K	0.620	0.54
18_A	74_I	0.613	0.54
21_Q	71_P	0.606	0.53
43_E	48_G	0.603	0.52
34_R	53_Y	0.602	0.52
16_R	46_S	0.599	0.52
38_E	41_K	0.588	0.51
11_R	14_A	0.583	0.50
8_E	17_R	0.582	0.50
65_P	68_A	0.572	0.49
8_E	66_E	0.563	0.48
40_E	50_V	0.550	0.46
29_G	32_G	0.549	0.46
51_P	75_Q	0.545	0.46
65_P	69_G	0.540	0.45
43_E	65_P	0.530	0.44
7_L	10_A	0.530	0.44
49_K	76_F	0.523	0.43
32_G	73_N	0.518	0.42
44_I	52_G	0.510	0.41
27_R	38_E	0.509	0.41
14_A	55_G	0.509	0.41
6_L	76_F	0.505	0.41
33_T	58_I	0.503	0.41
25_L	60_S	0.500	0.40
12_Q	39_E	0.500	0.40

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
3mabA	2	0.6923	7.5	0.909	Contact Map
2xsaA	2	0.7051	6.2	0.913	Contact Map
4pysA	1	1	4.7	0.918	Contact Map
3dmyA	2	0.2821	4.3	0.919	Contact Map
7ceiB	1	0.8846	4.2	0.919	Contact Map
4jg2A	1	0.1282	4.2	0.919	Contact Map
4ogeA	1	0.8974	4.1	0.92	Contact Map
3hwkA	5	0.641	4.1	0.92	Contact Map
1usuB	1	0.0256	4.1	0.92	Contact Map
3zfkA	1	0.8846	3.8	0.921	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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