DDE_Tnp_4 - PFAM28P - GREMLIN Contacts

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DDE_Tnp_4 - DDE superfamily endonuclease

PFAM:	PF13359	Sequences: IDGTEIPIQRPKDKERQKEYYSGKKKRHTIKVQVVVDPDGRIIHVSVGTPGSVHDSTVLRESGLLDLLEEALPPGLYVLGDSGYPGAEKLLTPYKKPRGGPLTEEQKAFNRRLSSVRIVVEHAFGRLKRRFRILKDRYRNRKLKKADKIVLACCGLHN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	158 (153)
Sequences:	21420 (14050)
Seq/√Len:	1135.8
META:	0.766

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
33_Q	84_Y	4.328	1.00
34_V	124_F	4.007	1.00
7_P	27_R	3.442	1.00
56_S	60_R	3.130	1.00
36_V	120_V	2.589	1.00
97_P	100_G	2.564	1.00
37_D	43_I	2.425	1.00
94_Y	109_F	2.395	1.00
94_Y	106_Q	2.387	1.00
42_I	123_A	2.371	1.00
132_R	136_D	2.333	1.00
119_V	122_H	2.252	1.00
103_T	106_Q	2.250	1.00
49_T	58_V	2.185	1.00
118_I	122_H	2.092	1.00
5_E	29_T	2.086	1.00
4_T	128_K	2.082	1.00
34_V	42_I	2.042	1.00
36_V	123_A	1.925	1.00
45_V	154_C	1.920	1.00
138_Y	146_A	1.862	1.00
127_L	154_C	1.844	1.00
33_Q	44_H	1.801	1.00
125_G	130_R	1.792	1.00
37_D	41_R	1.787	1.00
53_V	57_T	1.764	1.00
40_G	126_R	1.733	1.00
23_G	29_T	1.686	1.00
109_F	113_L	1.675	1.00
80_G	92_T	1.658	1.00
32_V	48_G	1.621	1.00
134_L	153_C	1.620	1.00
82_S	85_P	1.604	1.00
40_G	122_H	1.519	1.00
79_L	113_L	1.519	1.00
23_G	27_R	1.498	1.00
23_G	26_K	1.491	1.00
59_L	65_L	1.420	1.00
29_T	51_G	1.388	1.00
111_R	115_S	1.331	1.00
57_T	61_E	1.314	1.00
50_P	53_V	1.304	1.00
136_D	139_R	1.303	1.00
1_I	80_G	1.295	1.00
97_P	101_P	1.273	1.00
53_V	61_E	1.247	1.00
132_R	135_K	1.222	1.00
152_A	155_G	1.200	1.00
93_P	96_K	1.197	1.00
110_N	114_S	1.189	1.00
17_Q	28_H	1.173	1.00
35_V	64_L	1.163	1.00
133_I	149_I	1.157	1.00
17_Q	20_Y	1.148	1.00
117_R	121_E	1.135	1.00
8_I	11_P	1.128	1.00
92_T	95_K	1.125	1.00
49_T	53_V	1.122	1.00
40_G	119_V	1.110	1.00
148_K	151_L	1.100	1.00
6_I	32_V	1.088	1.00
127_L	153_C	1.075	1.00
5_E	31_K	1.074	1.00
104_E	108_A	1.064	1.00
126_R	130_R	1.057	1.00
120_V	124_F	1.055	1.00
143_L	146_A	1.029	1.00
54_H	57_T	1.022	1.00
149_I	153_C	1.021	1.00
79_L	116_V	1.016	1.00
25_K	29_T	1.014	1.00
35_V	78_V	1.011	1.00
133_I	153_C	1.006	1.00
127_L	134_L	1.005	1.00
22_S	28_H	1.004	1.00
140_N	149_I	0.995	1.00
46_S	49_T	0.993	1.00
129_R	132_R	0.980	1.00
3_G	31_K	0.980	1.00
145_K	149_I	0.975	1.00
31_K	58_V	0.974	1.00
49_T	62_S	0.970	1.00
108_A	112_R	0.970	1.00
17_Q	21_Y	0.968	1.00
63_G	66_D	0.964	1.00
90_L	93_P	0.958	1.00
9_Q	139_R	0.954	1.00
20_Y	28_H	0.950	1.00
114_S	118_I	0.947	1.00
72_L	75_G	0.942	1.00
49_T	61_E	0.934	1.00
91_L	109_F	0.914	1.00
73_P	76_L	0.913	1.00
146_A	149_I	0.907	1.00
5_E	25_K	0.901	1.00
3_G	33_Q	0.888	1.00
56_S	85_P	0.879	1.00
13_D	16_R	0.869	1.00
3_G	58_V	0.858	1.00
140_N	145_K	0.854	1.00
21_Y	26_K	0.851	1.00
78_V	81_D	0.846	1.00
146_A	150_V	0.842	1.00
51_G	55_D	0.835	1.00
30_I	48_G	0.829	1.00
20_Y	30_I	0.823	1.00
33_Q	58_V	0.820	1.00
147_D	151_L	0.819	1.00
8_I	20_Y	0.815	1.00
36_V	119_V	0.810	1.00
98_R	101_P	0.800	1.00
35_V	43_I	0.799	1.00
116_V	119_V	0.796	1.00
21_Y	28_H	0.794	1.00
6_I	146_A	0.792	1.00
148_K	152_A	0.788	1.00
138_Y	149_I	0.786	1.00
57_T	60_R	0.778	1.00
45_V	151_L	0.777	1.00
33_Q	62_S	0.776	1.00
65_L	69_E	0.774	1.00
32_V	150_V	0.773	1.00
21_Y	24_K	0.760	1.00
77_Y	91_L	0.756	1.00
47_V	147_D	0.753	1.00
54_H	82_S	0.749	1.00
40_G	123_A	0.747	1.00
22_S	26_K	0.742	1.00
34_V	123_A	0.741	1.00
30_I	146_A	0.739	1.00
92_T	96_K	0.735	1.00
4_T	34_V	0.732	1.00
107_K	111_R	0.720	1.00
7_P	137_R	0.720	1.00
126_R	157_H	0.717	1.00
53_V	58_V	0.703	1.00
144_K	147_D	0.701	1.00
115_S	118_I	0.700	1.00
80_G	87_A	0.697	1.00
38_P	116_V	0.696	1.00
1_I	35_V	0.695	1.00
42_I	127_L	0.692	1.00
127_L	157_H	0.690	1.00
150_V	154_C	0.689	1.00
145_K	148_K	0.686	1.00
46_S	62_S	0.684	1.00
122_H	125_G	0.684	1.00
80_G	90_L	0.682	1.00
103_T	107_K	0.680	1.00
20_Y	24_K	0.672	1.00
55_D	121_E	0.670	1.00
17_Q	22_S	0.668	1.00
123_A	126_R	0.667	1.00
45_V	150_V	0.667	1.00
18_K	22_S	0.666	1.00
102_L	106_Q	0.660	1.00
87_A	90_L	0.658	1.00
5_E	23_G	0.658	1.00
82_S	92_T	0.657	1.00
80_G	83_G	0.654	1.00
81_D	84_Y	0.651	1.00
32_V	47_V	0.651	1.00
64_L	67_L	0.643	1.00
10_R	13_D	0.640	1.00
140_N	146_A	0.634	1.00
144_K	148_K	0.630	1.00
16_R	20_Y	0.629	1.00
63_G	67_L	0.626	1.00
20_Y	23_G	0.624	1.00
86_G	92_T	0.620	1.00
112_R	116_V	0.617	1.00
100_G	103_T	0.615	1.00
79_L	91_L	0.614	1.00
10_R	28_H	0.612	1.00
149_I	152_A	0.611	1.00
133_I	139_R	0.611	1.00
40_G	44_H	0.605	1.00
23_G	28_H	0.603	1.00
98_R	102_L	0.603	1.00
25_K	28_H	0.602	1.00
91_L	94_Y	0.600	1.00
54_H	83_G	0.594	1.00
17_Q	23_G	0.592	1.00
81_D	121_E	0.587	1.00
56_S	83_G	0.586	1.00
94_Y	110_N	0.583	1.00
141_R	145_K	0.582	1.00
9_Q	137_R	0.579	1.00
42_I	154_C	0.578	1.00
135_K	139_R	0.572	1.00
143_L	147_D	0.563	1.00
131_F	157_H	0.560	1.00
12_K	16_R	0.558	1.00
18_K	21_Y	0.557	1.00
129_R	135_K	0.556	1.00
141_R	146_A	0.552	1.00
125_G	129_R	0.548	1.00
6_I	150_V	0.542	1.00
112_R	115_S	0.537	1.00
97_P	102_L	0.537	1.00
132_R	139_R	0.536	1.00
22_S	25_K	0.535	1.00
121_E	125_G	0.535	1.00
129_R	134_L	0.533	1.00
22_S	27_R	0.532	1.00
133_I	138_Y	0.530	1.00
90_L	94_Y	0.528	1.00
104_E	107_K	0.527	1.00
128_K	135_K	0.527	1.00
16_R	19_E	0.526	1.00
80_G	88_E	0.525	1.00
33_Q	59_L	0.525	1.00
48_G	147_D	0.524	1.00
137_R	140_N	0.524	1.00
81_D	86_G	0.523	1.00
90_L	95_K	0.521	1.00
105_E	109_F	0.521	1.00
107_K	110_N	0.519	1.00
140_N	143_L	0.517	1.00
24_K	28_H	0.515	1.00
55_D	117_R	0.513	1.00
147_D	150_V	0.513	1.00
127_L	150_V	0.513	1.00
59_L	87_A	0.510	1.00
69_E	89_K	0.507	1.00
153_C	156_L	0.504	1.00
11_P	16_R	0.503	1.00
123_A	131_F	0.502	1.00
72_L	76_L	0.501	1.00
59_L	62_S	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
4u7bA	2	0.9367	20.6	0.901	Contact Map
1musA	2	0.9747	14.3	0.908	Contact Map
4fw1A	2	0.8354	14.3	0.908	Contact Map
4cf8A	2	0.8101	11.6	0.911	Contact Map
3kksA	2	0.7722	10.4	0.913	Contact Map
4mq3A	1	0.7722	10	0.914	Contact Map
3l3uA	2	0.8101	10	0.914	Contact Map
1ex4A	5	0.8038	9.4	0.915	Contact Map
1cxqA	2	0.8101	9.1	0.916	Contact Map
4fw2A	2	0.7848	8.8	0.916	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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