Transpos_assoc - PFAM28P - GREMLIN Contacts

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Transpos_assoc - Transposase-associated domain

PFAM:	PF13963	Sequences: RSWMYNADRLSPEYINGVEEFLEFAFAHAENKNGGKIRCPCRKCKNRKYLTRDTVRDHLIRNGFMPNYTRWTHHGE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	76 (76)
Sequences:	2360 (1714)
Seq/√Len:	196.6
META:	0.681

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
26_F	52_R	3.657	1.00
38_R	49_Y	3.033	1.00
43_K	62_N	2.810	1.00
19_E	56_R	2.725	1.00
22_L	52_R	2.334	1.00
4_M	64_F	2.301	1.00
14_Y	18_V	2.095	1.00
50_L	58_H	2.094	1.00
23_E	52_R	2.029	1.00
41_C	44_C	1.873	1.00
40_P	44_C	1.787	1.00
18_V	59_L	1.744	1.00
12_P	16_N	1.664	1.00
51_T	54_T	1.664	1.00
39_C	44_C	1.606	1.00
16_N	20_E	1.594	1.00
5_Y	64_F	1.591	1.00
57_D	61_R	1.547	1.00
14_Y	64_F	1.545	1.00
50_L	54_T	1.538	1.00
28_H	31_N	1.469	1.00
14_Y	59_L	1.421	1.00
1_R	5_Y	1.327	1.00
22_L	26_F	1.254	1.00
70_R	73_H	1.244	1.00
68_Y	74_H	1.177	1.00
19_E	23_E	1.166	1.00
50_L	55_V	1.160	1.00
23_E	27_A	1.103	1.00
41_C	46_N	1.056	1.00
44_C	58_H	1.054	1.00
32_K	35_G	1.037	1.00
2_S	13_E	1.029	1.00
30_E	42_R	1.025	1.00
21_F	25_A	1.015	1.00
26_F	37_I	1.004	1.00
37_I	55_V	0.997	1.00
54_T	57_D	0.987	1.00
14_Y	60_I	0.968	0.99
25_A	68_Y	0.953	0.99
41_C	63_G	0.945	0.99
24_F	43_K	0.939	0.99
45_K	65_M	0.938	0.99
52_R	56_R	0.930	0.99
57_D	60_I	0.897	0.99
9_R	60_I	0.862	0.99
21_F	68_Y	0.851	0.99
21_F	46_N	0.849	0.99
18_V	22_L	0.830	0.98
9_R	12_P	0.828	0.98
21_F	71_W	0.820	0.98
7_A	10_L	0.811	0.98
68_Y	71_W	0.802	0.98
22_L	56_R	0.796	0.98
1_R	7_A	0.794	0.98
27_A	66_P	0.793	0.98
64_F	67_N	0.789	0.98
40_P	58_H	0.783	0.98
27_A	57_D	0.780	0.97
65_M	73_H	0.775	0.97
18_V	56_R	0.775	0.97
31_N	34_G	0.774	0.97
54_T	58_H	0.766	0.97
33_N	36_K	0.754	0.97
4_M	59_L	0.751	0.97
46_N	74_H	0.731	0.96
34_G	65_M	0.712	0.96
7_A	11_S	0.706	0.95
53_D	57_D	0.698	0.95
7_A	33_N	0.697	0.95
39_C	63_G	0.687	0.95
4_M	7_A	0.676	0.94
34_G	37_I	0.676	0.94
12_P	15_I	0.670	0.94
17_G	63_G	0.668	0.94
14_Y	47_R	0.667	0.94
38_R	67_N	0.666	0.94
13_E	16_N	0.659	0.93
23_E	30_E	0.648	0.93
53_D	66_P	0.639	0.92
69_T	72_T	0.635	0.92
42_R	62_N	0.626	0.92
8_D	11_S	0.625	0.92
23_E	26_F	0.619	0.91
39_C	75_G	0.619	0.91
10_L	67_N	0.616	0.91
28_H	32_K	0.615	0.91
25_A	46_N	0.613	0.91
30_E	53_D	0.606	0.90
26_F	55_V	0.606	0.90
57_D	62_N	0.605	0.90
39_C	58_H	0.601	0.90
4_M	65_M	0.597	0.90
47_R	61_R	0.595	0.89
20_E	23_E	0.592	0.89
6_N	11_S	0.583	0.88
31_N	56_R	0.576	0.88
30_E	66_P	0.567	0.87
45_K	64_F	0.566	0.87
31_N	37_I	0.563	0.87
2_S	6_N	0.562	0.87
20_E	66_P	0.559	0.86
36_K	54_T	0.554	0.86
10_L	69_T	0.553	0.86
69_T	73_H	0.544	0.85
26_F	32_K	0.543	0.85
36_K	72_T	0.541	0.85
2_S	42_R	0.537	0.84
56_R	60_I	0.528	0.83
16_N	66_P	0.520	0.82
42_R	45_K	0.512	0.81
10_L	15_I	0.508	0.81
40_P	46_N	0.508	0.81
5_Y	69_T	0.500	0.80

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
3bbnC	1	0.5658	10.1	0.896	Contact Map
1dvkA	2	0.3947	4.2	0.913	Contact Map
1ubdC	1	0.5132	3	0.919	Contact Map
2a7kA	3	0.1842	2.7	0.921	Contact Map
2w45A	1	0.8421	2.6	0.922	Contact Map
3l3sA	3	0.1711	2.6	0.922	Contact Map
1sz9A	1	0.3947	2.5	0.922	Contact Map
3qmjA	3	0.0395	2.4	0.923	Contact Map
1zx4A	2	0.4079	2.4	0.923	Contact Map
4kiyC	1	0.5658	2.3	0.924	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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