DDE_Tnp_1_5 - PFAM28P - GREMLIN Contacts

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DDE_Tnp_1_5 - Transposase DDE domain

PFAM:	PF13737	Sequences: VQRGSLTVWFDEEAIAAWDRAEPRGKRGRPFRYSDLAIETALTLRAVFHLPLRQTEGFVRSLLKLLGLDLPVPDYSTLSRRAKTLEVPLPRRKSDGPLHLVVDSTGLKVYGE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	112 (109)
Sequences:	7209 (4105)
Seq/√Len:	393.2
META:	0.923

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	59_V	4.873	1.00
51_P	54_Q	4.229	1.00
74_D	77_T	3.797	1.00
41_A	78_L	2.762	1.00
42_L	82_A	2.705	1.00
56_E	60_R	2.481	1.00
2_Q	5_S	2.459	1.00
63_L	72_V	2.379	1.00
77_T	80_R	2.223	1.00
45_R	82_A	2.128	1.00
5_S	64_K	1.959	1.00
75_Y	79_S	1.933	1.00
32_R	71_P	1.820	1.00
36_L	39_E	1.799	1.00
56_E	75_Y	1.765	1.00
39_E	88_P	1.729	1.00
52_L	79_S	1.723	1.00
79_S	83_K	1.643	1.00
45_R	52_L	1.587	1.00
52_L	75_Y	1.559	1.00
50_L	58_F	1.553	1.00
52_L	82_A	1.512	1.00
101_V	110_Y	1.456	1.00
41_A	55_T	1.427	1.00
63_L	68_L	1.413	1.00
94_S	97_P	1.386	1.00
4_G	54_Q	1.356	1.00
29_R	32_R	1.355	1.00
17_A	36_L	1.354	1.00
27_R	30_P	1.342	1.00
36_L	40_T	1.341	1.00
56_E	74_D	1.313	1.00
5_S	60_R	1.303	1.00
20_R	31_F	1.272	1.00
60_R	72_V	1.262	1.00
63_L	70_L	1.261	1.00
5_S	61_S	1.245	1.00
25_G	30_P	1.184	1.00
21_A	31_F	1.167	1.00
34_S	37_A	1.157	1.00
59_V	63_L	1.138	1.00
93_K	96_G	1.131	1.00
26_K	31_F	1.131	1.00
12_E	16_A	1.087	1.00
79_S	82_A	1.082	1.00
61_S	64_K	1.075	1.00
43_T	47_V	1.041	1.00
23_P	31_F	1.034	1.00
73_P	77_T	1.031	1.00
10_F	63_L	1.030	1.00
75_Y	80_R	1.027	1.00
55_T	78_L	1.011	1.00
43_T	48_F	1.008	1.00
102_V	109_V	1.008	1.00
38_I	78_L	1.001	1.00
21_A	24_R	0.977	1.00
58_F	61_S	0.972	1.00
18_W	37_A	0.956	1.00
45_R	51_P	0.945	1.00
20_R	23_P	0.944	1.00
37_A	40_T	0.933	1.00
42_L	45_R	0.914	1.00
35_D	39_E	0.905	1.00
22_E	26_K	0.903	1.00
20_R	71_P	0.898	1.00
24_R	31_F	0.897	1.00
5_S	8_V	0.890	1.00
37_A	77_T	0.888	1.00
76_S	80_R	0.880	1.00
21_A	26_K	0.877	1.00
24_R	30_P	0.875	1.00
7_T	99_H	0.867	1.00
14_A	18_W	0.862	1.00
23_P	26_K	0.861	1.00
5_S	9_W	0.848	1.00
76_S	79_S	0.828	1.00
76_S	81_R	0.827	1.00
11_D	14_A	0.824	1.00
92_R	95_D	0.822	1.00
90_P	93_K	0.818	1.00
50_L	54_Q	0.815	1.00
14_A	17_A	0.814	1.00
33_Y	80_R	0.803	1.00
45_R	55_T	0.779	1.00
60_R	63_L	0.778	1.00
13_E	17_A	0.770	1.00
8_V	43_T	0.762	1.00
107_L	111_G	0.761	1.00
56_E	78_L	0.760	1.00
15_I	20_R	0.753	1.00
42_L	78_L	0.742	1.00
101_V	109_V	0.742	1.00
42_L	52_L	0.735	1.00
26_K	30_P	0.735	1.00
44_L	58_F	0.733	1.00
90_P	94_S	0.726	1.00
10_F	14_A	0.722	1.00
9_W	99_H	0.716	1.00
21_A	30_P	0.689	0.99
46_A	49_H	0.679	0.99
91_R	94_S	0.679	0.99
31_F	34_S	0.665	0.99
64_K	67_G	0.664	0.99
35_D	85_L	0.657	0.99
105_T	108_K	0.657	0.99
64_K	69_D	0.653	0.99
46_A	52_L	0.648	0.99
89_L	92_R	0.647	0.99
12_E	15_I	0.643	0.99
14_A	20_R	0.635	0.99
36_L	102_V	0.628	0.99
24_R	27_R	0.626	0.99
20_R	25_G	0.624	0.99
83_K	86_E	0.621	0.99
25_G	31_F	0.621	0.99
38_I	73_P	0.617	0.99
6_L	98_L	0.614	0.99
93_K	97_P	0.606	0.99
17_A	20_R	0.603	0.99
2_Q	7_T	0.603	0.99
15_I	36_L	0.599	0.99
51_P	55_T	0.597	0.99
25_G	29_R	0.595	0.99
98_L	102_V	0.593	0.98
92_R	97_P	0.587	0.98
99_H	109_V	0.586	0.98
13_E	18_W	0.586	0.98
59_V	72_V	0.583	0.98
26_K	29_R	0.574	0.98
46_A	82_A	0.572	0.98
40_T	75_Y	0.570	0.98
21_A	25_G	0.566	0.98
69_D	94_S	0.565	0.98
9_W	12_E	0.564	0.98
43_T	46_A	0.563	0.98
46_A	51_P	0.560	0.98
56_E	72_V	0.555	0.98
96_G	99_H	0.555	0.98
8_V	100_L	0.551	0.98
65_L	68_L	0.545	0.97
62_L	65_L	0.545	0.97
10_F	44_L	0.545	0.97
60_R	71_P	0.542	0.97
35_D	81_R	0.540	0.97
16_A	20_R	0.538	0.97
100_L	110_Y	0.537	0.97
55_T	58_F	0.535	0.97
33_Y	71_P	0.533	0.97
20_R	24_R	0.531	0.97
9_W	44_L	0.528	0.97
91_R	95_D	0.527	0.97
99_H	102_V	0.525	0.97
61_S	65_L	0.523	0.97
33_Y	72_V	0.521	0.97
39_E	85_L	0.514	0.96
47_V	50_L	0.510	0.96
11_D	104_S	0.509	0.96
53_R	56_E	0.509	0.96
39_E	46_A	0.509	0.96
9_W	47_V	0.507	0.96
84_T	89_L	0.507	0.96
22_E	31_F	0.506	0.96
2_Q	22_E	0.505	0.96
103_D	106_G	0.500	0.96

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
2cobA	1	0.6161	18.5	0.914	Contact Map
4u7bA	2	0.875	13	0.92	Contact Map
4fcyA	4	0.9196	10.1	0.924	Contact Map
4n78F	1	0	8.6	0.926	Contact Map
1pdnC	1	0.6964	6.4	0.93	Contact Map
4ftbD	1	0.1875	5.8	0.932	Contact Map
2rqrA	1	0.375	5.7	0.932	Contact Map
1novD	1	0.1786	5.4	0.933	Contact Map
1f8vD	3	0.2321	4.9	0.934	Contact Map
2jmlA	1	0.5893	4.8	0.934	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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