DEDD_Tnp_IS110 - PFAM28P - GREMLIN Contacts

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DEDD_Tnp_IS110 - Transposase

PFAM:	PF01548	Sequences: VGIDVHKDTLDVAFDNTAVRAGFRRLLAWLAKLRGGPVLVAMEATGGYWRPLARALAGFEVVVVNPRQVKAFAGATGRRAKTDRIDAEWLARLLRRPVFVPSEEQRELRALVRRRRQLVRERTRLKN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	127 (123)
Sequences:	81675 (47415)
Seq/√Len:	4275.2
META:	0.924

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_A	94_L	3.880	1.00
71_A	74_G	2.863	1.00
121_E	124_R	2.514	1.00
39_L	62_V	2.277	1.00
13_A	87_A	2.202	1.00
102_S	105_Q	2.181	1.00
40_V	59_F	2.170	1.00
81_K	86_D	2.160	1.00
92_R	96_R	2.085	1.00
39_L	60_E	2.055	1.00
13_A	88_E	2.031	1.00
115_R	119_V	1.991	1.00
69_V	90_L	1.953	1.00
122_R	126_K	1.942	1.00
3_I	10_L	1.898	1.00
67_R	71_A	1.877	1.00
114_R	125_L	1.855	1.00
41_A	90_L	1.803	1.00
54_R	106_R	1.738	1.00
119_V	122_R	1.695	1.00
73_A	89_W	1.669	1.00
62_V	97_P	1.638	1.00
121_E	125_L	1.577	1.00
29_W	33_L	1.538	1.00
6_H	11_D	1.497	1.00
29_W	32_K	1.434	1.00
17_T	22_G	1.375	1.00
41_A	64_V	1.367	1.00
49_W	53_A	1.362	1.00
53_A	61_V	1.358	1.00
114_R	118_L	1.346	1.00
64_V	69_V	1.337	1.00
80_A	85_I	1.321	1.00
42_M	61_V	1.316	1.00
119_V	123_T	1.304	1.00
70_K	74_G	1.293	1.00
123_T	126_K	1.282	1.00
15_D	22_G	1.266	1.00
53_A	63_V	1.266	1.00
60_E	97_P	1.260	1.00
114_R	117_Q	1.254	1.00
27_L	57_A	1.239	1.00
3_I	12_V	1.236	1.00
117_Q	121_E	1.222	1.00
88_E	92_R	1.199	1.00
39_L	94_L	1.185	1.00
92_R	95_R	1.182	1.00
50_R	106_R	1.162	1.00
116_R	120_R	1.160	1.00
6_H	9_T	1.158	1.00
45_T	48_Y	1.148	1.00
101_P	109_R	1.134	1.00
11_D	84_R	1.132	1.00
62_V	94_L	1.131	1.00
23_F	55_A	1.127	1.00
103_E	107_E	1.125	1.00
27_L	55_A	1.103	1.00
70_K	73_A	1.081	1.00
1_V	40_V	1.077	1.00
30_L	40_V	1.030	1.00
69_V	93_L	1.030	1.00
5_V	42_M	1.027	1.00
42_M	53_A	1.027	1.00
27_L	31_A	1.021	1.00
104_E	107_E	1.014	1.00
13_A	91_A	1.011	1.00
2_G	87_A	0.993	1.00
22_G	25_R	0.991	1.00
65_N	68_Q	0.990	1.00
37_P	60_E	0.988	1.00
40_V	61_V	0.974	1.00
23_F	51_P	0.971	1.00
44_A	63_V	0.970	1.00
21_A	25_R	0.963	1.00
51_P	55_A	0.959	1.00
120_R	124_R	0.953	1.00
16_N	23_F	0.928	1.00
5_V	10_L	0.911	1.00
38_V	59_F	0.909	1.00
50_R	53_A	0.892	1.00
50_R	54_R	0.889	1.00
18_A	21_A	0.887	1.00
49_W	52_L	0.884	1.00
110_A	114_R	0.876	1.00
2_G	91_A	0.872	1.00
30_L	34_R	0.872	1.00
47_G	50_R	0.872	1.00
85_I	88_E	0.871	1.00
45_T	49_W	0.871	1.00
6_H	10_L	0.857	1.00
21_A	24_R	0.855	1.00
109_R	113_R	0.842	1.00
18_A	24_R	0.837	1.00
3_I	52_L	0.832	1.00
11_D	87_A	0.824	1.00
69_V	89_W	0.824	1.00
27_L	30_L	0.819	1.00
91_A	95_R	0.815	1.00
117_Q	120_R	0.808	1.00
30_L	33_L	0.804	1.00
49_W	63_V	0.799	1.00
12_V	26_L	0.796	1.00
29_W	34_R	0.795	1.00
26_L	29_W	0.790	1.00
1_V	38_V	0.782	1.00
28_A	32_K	0.778	1.00
51_P	54_R	0.775	1.00
18_A	23_F	0.770	1.00
120_R	123_T	0.769	1.00
28_A	31_A	0.767	1.00
37_P	59_F	0.763	1.00
85_I	89_W	0.758	1.00
40_V	56_L	0.758	1.00
99_F	102_S	0.756	1.00
123_T	127_N	0.734	1.00
1_V	12_V	0.728	1.00
118_L	122_R	0.721	1.00
42_M	63_V	0.719	1.00
67_R	74_G	0.711	1.00
82_T	85_I	0.711	1.00
99_F	105_Q	0.709	1.00
28_A	33_L	0.702	1.00
26_L	30_L	0.700	1.00
42_M	52_L	0.698	1.00
44_A	66_P	0.692	1.00
14_F	22_G	0.691	1.00
68_Q	72_F	0.689	1.00
72_F	93_L	0.686	1.00
72_F	96_R	0.682	1.00
78_R	85_I	0.673	1.00
27_L	33_L	0.671	1.00
31_A	34_R	0.669	1.00
68_Q	79_R	0.665	1.00
46_G	49_W	0.663	1.00
68_Q	77_G	0.656	1.00
15_D	21_A	0.652	1.00
27_L	32_K	0.652	1.00
15_D	25_R	0.644	1.00
15_D	18_A	0.636	1.00
67_R	77_G	0.636	1.00
68_Q	74_G	0.630	1.00
35_G	38_V	0.628	1.00
31_A	57_A	0.625	1.00
106_R	110_A	0.622	1.00
17_T	21_A	0.622	1.00
16_N	22_G	0.621	1.00
101_P	105_Q	0.611	1.00
10_L	52_L	0.606	1.00
14_F	18_A	0.602	1.00
113_R	117_Q	0.599	1.00
122_R	125_L	0.591	1.00
25_R	29_W	0.589	1.00
113_R	116_R	0.584	1.00
27_L	34_R	0.583	1.00
118_L	121_E	0.582	1.00
48_Y	51_P	0.579	1.00
103_E	106_R	0.577	1.00
111_L	114_R	0.575	1.00
111_L	115_R	0.574	1.00
106_R	109_R	0.574	1.00
43_E	86_D	0.571	1.00
72_F	78_R	0.569	1.00
41_A	62_V	0.568	1.00
3_I	40_V	0.561	1.00
24_R	28_A	0.558	1.00
114_R	121_E	0.556	1.00
78_R	89_W	0.547	1.00
14_F	17_T	0.546	1.00
91_A	94_L	0.543	1.00
1_V	37_P	0.541	1.00
14_F	29_W	0.539	1.00
27_L	59_F	0.534	1.00
72_F	89_W	0.529	1.00
54_R	103_E	0.528	1.00
117_Q	124_R	0.527	1.00
63_V	66_P	0.524	1.00
68_Q	71_A	0.515	1.00
16_N	21_A	0.513	1.00
3_I	26_L	0.507	1.00
18_A	22_G	0.503	1.00
112_V	115_R	0.502	1.00
38_V	60_E	0.501	1.00
104_E	108_L	0.500	1.00
105_Q	108_L	0.500	1.00

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
1hjrA	2	0.7874	66.4	0.85	Contact Map
1nu0A	1	0.7087	31.7	0.879	Contact Map
4ep4A	2	0.9449	25.5	0.885	Contact Map
1iv0A	1	0.5354	14.8	0.896	Contact Map
1vhxA	2	0.7717	12.8	0.899	Contact Map
3menA	3	0.4961	10.1	0.904	Contact Map
4zurA	2	0.4409	9.5	0.905	Contact Map
1zz1A	4	0.7874	8.5	0.907	Contact Map
1c3pA	1	0.8031	8.1	0.908	Contact Map
4bkxB	1	0.7323	7.2	0.91	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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