YjhX_toxin - PFAM28P - GREMLIN Contacts

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YjhX_toxin - Putative toxin of bacterial toxin-antitoxin pair

PFAM:	PF09857	Sequences: MNISRAEQRVLHALAQGGRIEHERDDRGRIVEVECFTRDGWRLSDCTLALFRKLKRKRLIASRGGGPYRITRRGLEAVRAQLDNR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	85 (85)
Sequences:	896 (542)
Seq/√Len:	58.8
META:	0.759

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
34_E	42_R	3.724	1.00
72_R	76_E	3.181	1.00
7_E	53_K	3.098	1.00
61_A	71_T	3.022	1.00
73_R	77_A	2.823	1.00
16_Q	39_D	2.466	1.00
8_Q	12_H	2.420	1.00
36_F	42_R	2.416	1.00
52_R	55_K	2.014	1.00
16_Q	84_N	1.838	1.00
53_K	57_K	1.812	0.99
1_M	7_E	1.754	0.99
53_K	78_V	1.745	0.99
35_C	43_L	1.650	0.99
47_T	50_L	1.630	0.99
23_E	34_E	1.623	0.99
33_V	46_C	1.525	0.98
10_V	46_C	1.463	0.98
71_T	75_L	1.421	0.97
35_C	46_C	1.385	0.97
6_A	10_V	1.378	0.97
13_A	43_L	1.361	0.96
22_H	30_I	1.357	0.96
30_I	51_F	1.325	0.96
10_V	29_R	1.284	0.95
16_Q	85_R	1.274	0.95
41_W	71_T	1.231	0.94
24_R	60_I	1.218	0.93
45_D	81_Q	1.189	0.92
63_R	69_R	1.137	0.90
72_R	75_L	1.136	0.90
59_L	77_A	1.126	0.90
23_E	36_F	1.114	0.90
27_R	55_K	1.107	0.89
20_I	48_L	1.101	0.89
73_R	76_E	1.097	0.89
2_N	59_L	1.085	0.88
52_R	56_R	1.084	0.88
22_H	71_T	1.050	0.87
67_P	79_R	1.017	0.85
22_H	33_V	0.976	0.82
19_R	69_R	0.960	0.81
3_I	39_D	0.936	0.80
24_R	41_W	0.931	0.79
43_L	59_L	0.929	0.79
4_S	7_E	0.914	0.78
19_R	53_K	0.909	0.78
1_M	6_A	0.908	0.77
28_G	43_L	0.898	0.77
23_E	32_E	0.890	0.76
12_H	78_V	0.886	0.76
6_A	45_D	0.884	0.76
10_V	71_T	0.876	0.75
13_A	16_Q	0.875	0.75
2_N	77_A	0.862	0.74
37_T	44_S	0.845	0.72
2_N	5_R	0.842	0.72
38_R	65_G	0.838	0.72
43_L	46_C	0.836	0.71
61_A	75_L	0.826	0.70
49_A	64_G	0.820	0.70
38_R	51_F	0.816	0.70
5_R	59_L	0.813	0.69
35_C	56_R	0.810	0.69
13_A	41_W	0.805	0.69
22_H	29_R	0.800	0.68
36_F	60_I	0.796	0.68
12_H	15_A	0.769	0.65
10_V	50_L	0.753	0.63
2_N	81_Q	0.747	0.63
21_E	34_E	0.732	0.61
59_L	71_T	0.732	0.61
39_D	78_V	0.725	0.60
2_N	45_D	0.724	0.60
2_N	35_C	0.715	0.59
27_R	30_I	0.711	0.59
46_C	50_L	0.707	0.58
49_A	56_R	0.704	0.58
41_W	60_I	0.696	0.57
61_A	66_G	0.688	0.56
26_D	64_G	0.680	0.56
22_H	65_G	0.679	0.55
34_E	41_W	0.673	0.55
8_Q	78_V	0.670	0.54
21_E	85_R	0.664	0.54
75_L	82_L	0.663	0.54
10_V	45_D	0.662	0.54
18_G	53_K	0.661	0.53
37_T	42_R	0.657	0.53
55_K	66_G	0.655	0.53
33_V	48_L	0.649	0.52
1_M	47_T	0.643	0.51
50_L	61_A	0.640	0.51
11_L	14_L	0.634	0.50
28_G	32_E	0.627	0.50
25_D	31_V	0.621	0.49
2_N	46_C	0.619	0.49
70_I	74_G	0.619	0.49
63_R	66_G	0.612	0.48
20_I	46_C	0.612	0.48
24_R	28_G	0.603	0.47
77_A	80_A	0.600	0.47
6_A	55_K	0.599	0.47
55_K	63_R	0.591	0.46
13_A	83_D	0.586	0.45
31_V	66_G	0.585	0.45
22_H	78_V	0.583	0.45
24_R	71_T	0.580	0.44
10_V	43_L	0.580	0.44
35_C	45_D	0.566	0.43
26_D	49_A	0.560	0.42
7_E	24_R	0.557	0.42
26_D	65_G	0.556	0.42
60_I	66_G	0.553	0.42
8_Q	79_R	0.550	0.41
65_G	80_A	0.547	0.41
1_M	4_S	0.543	0.40
2_N	43_L	0.541	0.40
21_E	36_F	0.539	0.40
30_I	33_V	0.538	0.40
22_H	31_V	0.528	0.39
24_R	36_F	0.525	0.39
22_H	80_A	0.520	0.38
51_F	70_I	0.518	0.38
26_D	58_R	0.518	0.38
3_I	23_E	0.516	0.38
32_E	55_K	0.507	0.37
81_Q	84_N	0.500	0.36

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
2co5A	2	0.9176	81.2	0.893	Contact Map
2rkhA	2	0.8353	64.6	0.906	Contact Map
2x4hA	3	0.8588	57	0.91	Contact Map
3l9fA	2	0.8941	55.2	0.911	Contact Map
1s3jA	2	0.8706	52.2	0.913	Contact Map
2rdpA	2	0.8706	50.4	0.914	Contact Map
3cdhA	4	0.8706	50.2	0.914	Contact Map
3bddA	2	0.8706	50.1	0.914	Contact Map
2e1nA	2	0.9294	49.9	0.914	Contact Map
4o5vA	2	0.8588	47.7	0.915	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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