Transposase_24 - PFAM28P - GREMLIN Contacts

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Transposase_24 - Plant transposase (Ptta/En/Spm family)

PFAM:	PF03004	Sequences: DPDQWEELVAYWNSPKFKKKSEKNKANRDGKGKHKHTSGSKSFARVREEMEKELGRPPSRLELFKKTHTKKDGTFVDEKAEEIIEKLEELVEERESQLSSDSSSESDGSSVLTEEENDIFLEVLGPEKKGRVRGLGSGVTP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	141 (129)
Sequences:	735 (583)
Seq/√Len:	51.3
META:	0.004

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_K	49_E	6.231	1.00
24_N	27_N	3.614	1.00
81_E	85_E	3.273	1.00
14_S	17_F	3.199	1.00
56_R	62_E	2.932	1.00
8_L	12_W	2.716	1.00
50_M	53_E	2.481	1.00
75_F	84_I	2.282	1.00
133_R	138_G	2.171	1.00
120_F	124_L	2.143	1.00
15_P	18_K	2.023	1.00
12_W	17_F	1.995	1.00
19_K	23_K	1.977	1.00
38_S	46_V	1.931	0.99
53_E	66_K	1.907	0.99
86_K	89_E	1.885	0.99
48_E	51_E	1.751	0.99
20_K	24_N	1.709	0.99
36_H	39_G	1.700	0.99
44_A	47_R	1.653	0.98
68_H	134_G	1.643	0.98
51_E	58_P	1.621	0.98
50_M	66_K	1.557	0.97
14_S	21_S	1.521	0.97
23_K	27_N	1.492	0.97
38_S	67_T	1.484	0.97
41_K	46_V	1.480	0.97
59_S	62_E	1.432	0.96
15_P	19_K	1.419	0.96
46_V	67_T	1.413	0.96
96_S	99_S	1.401	0.95
43_F	46_V	1.382	0.95
5_W	9_V	1.350	0.94
125_G	129_K	1.334	0.94
50_M	54_L	1.330	0.94
65_K	69_T	1.318	0.93
19_K	26_A	1.287	0.93
3_D	19_K	1.285	0.93
84_I	87_L	1.273	0.92
35_K	77_D	1.233	0.91
124_L	127_E	1.207	0.90
22_E	26_A	1.203	0.90
25_K	70_K	1.163	0.88
39_G	42_S	1.160	0.88
117_N	120_F	1.152	0.88
93_E	97_Q	1.149	0.88
96_S	100_S	1.146	0.88
9_V	13_N	1.144	0.87
70_K	74_T	1.142	0.87
116_E	119_I	1.128	0.87
37_T	68_H	1.125	0.87
87_L	91_V	1.124	0.86
61_L	65_K	1.082	0.84
30_G	33_K	1.076	0.84
10_A	22_E	1.062	0.83
56_R	59_S	1.049	0.82
38_S	43_F	1.042	0.82
21_S	32_G	1.029	0.81
90_L	93_E	1.027	0.81
7_E	13_N	1.019	0.81
124_L	129_K	1.016	0.80
3_D	6_E	1.015	0.80
4_Q	9_V	1.004	0.80
77_D	80_A	0.975	0.77
85_E	88_E	0.974	0.77
4_Q	17_F	0.951	0.76
2_P	6_E	0.951	0.76
96_S	104_S	0.951	0.76
94_R	97_Q	0.938	0.75
132_V	138_G	0.927	0.74
25_K	30_G	0.906	0.72
73_G	85_E	0.899	0.72
83_I	87_L	0.887	0.70
65_K	88_E	0.886	0.70
15_P	22_E	0.882	0.70
125_G	132_V	0.881	0.70
68_H	88_E	0.873	0.69
82_E	86_K	0.863	0.68
41_K	45_R	0.861	0.68
129_K	133_R	0.861	0.68
7_E	11_Y	0.855	0.68
72_D	76_V	0.841	0.66
28_R	36_H	0.837	0.66
58_P	64_F	0.833	0.66
26_A	30_G	0.828	0.65
9_V	15_P	0.827	0.65
40_S	43_F	0.827	0.65
133_R	139_V	0.825	0.65
8_L	25_K	0.820	0.64
118_D	121_L	0.808	0.63
55_G	66_K	0.807	0.63
66_K	69_T	0.805	0.63
12_W	42_S	0.803	0.63
92_E	96_S	0.799	0.62
5_W	40_S	0.798	0.62
132_V	136_G	0.797	0.62
19_K	22_E	0.795	0.62
23_K	33_K	0.792	0.62
6_E	15_P	0.790	0.61
16_K	19_K	0.788	0.61
18_K	22_E	0.784	0.61
17_F	21_S	0.783	0.61
92_E	97_Q	0.781	0.61
118_D	122_E	0.767	0.59
76_V	80_A	0.764	0.59
124_L	132_V	0.764	0.59
58_P	67_T	0.760	0.58
16_K	22_E	0.756	0.58
51_E	56_R	0.755	0.58
78_E	81_E	0.754	0.58
21_S	25_K	0.733	0.56
12_W	27_N	0.730	0.55
100_S	105_E	0.722	0.55
30_G	77_D	0.722	0.55
15_P	20_K	0.721	0.55
95_E	102_S	0.719	0.54
25_K	125_G	0.714	0.54
11_Y	17_F	0.706	0.53
8_L	11_Y	0.705	0.53
132_V	139_V	0.703	0.53
26_A	79_K	0.703	0.53
24_N	39_G	0.703	0.53
32_G	138_G	0.700	0.52
20_K	139_V	0.694	0.52
44_A	56_R	0.691	0.51
89_E	94_R	0.690	0.51
47_R	131_R	0.686	0.51
4_Q	24_N	0.684	0.51
3_D	69_T	0.678	0.50
90_L	95_E	0.675	0.50
84_I	90_L	0.675	0.50
115_E	118_D	0.670	0.49
56_R	61_L	0.667	0.49
18_K	25_K	0.666	0.49
124_L	138_G	0.662	0.48
88_E	97_Q	0.660	0.48
5_W	37_T	0.659	0.48
13_N	17_F	0.658	0.48
21_S	39_G	0.654	0.48
35_K	46_V	0.648	0.47
98_L	101_D	0.647	0.47
40_S	46_V	0.638	0.46
18_K	24_N	0.637	0.46
51_E	54_L	0.632	0.45
3_D	13_N	0.630	0.45
94_R	101_D	0.630	0.45
3_D	16_K	0.630	0.45
72_D	80_A	0.628	0.45
127_E	133_R	0.622	0.44
66_K	80_A	0.617	0.44
99_S	104_S	0.616	0.44
2_P	22_E	0.614	0.43
33_K	38_S	0.614	0.43
35_K	40_S	0.613	0.43
4_Q	8_L	0.612	0.43
19_K	66_K	0.611	0.43
32_G	35_K	0.609	0.43
23_K	69_T	0.602	0.42
88_E	96_S	0.599	0.42
56_R	76_V	0.599	0.42
52_K	69_T	0.595	0.42
34_H	38_S	0.593	0.41
5_W	68_H	0.589	0.41
37_T	83_I	0.588	0.41
17_F	24_N	0.585	0.41
35_K	42_S	0.579	0.40
21_S	24_N	0.575	0.40
53_E	75_F	0.566	0.39
5_W	134_G	0.564	0.38
20_K	62_E	0.562	0.38
87_L	95_E	0.558	0.38
34_H	43_F	0.553	0.37
118_D	123_V	0.553	0.37
24_N	42_S	0.547	0.37
100_S	103_S	0.547	0.37
17_F	127_E	0.546	0.37
40_S	125_G	0.543	0.36
88_E	92_E	0.542	0.36
28_R	55_G	0.538	0.36
89_E	92_E	0.532	0.35
11_Y	67_T	0.529	0.35
125_G	128_K	0.527	0.35
25_K	33_K	0.527	0.35
129_K	135_L	0.524	0.35
39_G	43_F	0.510	0.33
91_V	98_L	0.507	0.33
92_E	103_S	0.507	0.33
10_A	58_P	0.506	0.33
85_E	92_E	0.504	0.33
98_L	103_S	0.503	0.33
70_K	80_A	0.502	0.33
10_A	13_N	0.500	0.32
14_S	25_K	0.500	0.32
40_S	45_R	0.500	0.32

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
3j7aY	1	0.6241	13.7	0.922	Contact Map
4w23T	1	0.617	7.7	0.931	Contact Map
3j60T	1	0.6099	6.2	0.934	Contact Map
4bpeT	1	0.6667	5.8	0.935	Contact Map
2wcvA	7	0.3333	4	0.939	Contact Map
1pcfA	2	0.156	3.8	0.94	Contact Map
3j38T	1	0.6879	3.8	0.94	Contact Map
4ujpU	1	0.6099	3.7	0.941	Contact Map
3e7nA	6	0.3333	3.4	0.941	Contact Map
2eixA	2	0.4539	2.3	0.947	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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