DDE_Tnp_1_6 - PFAM28P - GREMLIN Contacts

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DDE_Tnp_1_6 - Transposase DDE domain

PFAM:	PF13751	Sequences: TCPAGKTLTYRGTNREKGRGYKRYRARYRASDCRACPLRAQCTKSKKGRTIRRSPELEELLEAARARLDTEEGKELYRRRKATVEHVFGTLKRNHGLRRFRLRGLEKVRTEFLLAALAYNLKRLI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	125 (123)
Sequences:	50299 (30726)
Seq/√Len:	2770.4
META:	0.962

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
4_A	38_L	3.854	1.00
6_K	32_D	3.663	1.00
70_T	73_G	3.004	1.00
38_L	41_Q	2.456	1.00
95_H	122_K	2.332	1.00
84_V	87_V	2.273	1.00
29_R	32_D	2.150	1.00
92_K	98_R	2.130	1.00
58_E	62_E	2.095	1.00
102_L	107_K	2.047	1.00
10_Y	13_T	1.998	1.00
100_F	108_V	1.962	1.00
64_A	67_R	1.940	1.00
109_R	113_L	1.931	1.00
39_R	43_T	1.899	1.00
93_R	98_R	1.896	1.00
1_T	7_T	1.818	1.00
90_T	94_N	1.701	1.00
90_T	95_H	1.699	1.00
104_G	107_K	1.698	1.00
64_A	68_L	1.680	1.00
10_Y	26_A	1.655	1.00
90_T	119_Y	1.647	1.00
91_L	115_A	1.638	1.00
30_A	34_R	1.601	1.00
97_L	115_A	1.586	1.00
79_R	82_A	1.523	1.00
59_E	63_A	1.495	1.00
100_F	111_E	1.494	1.00
101_R	111_E	1.482	1.00
88_F	92_K	1.466	1.00
91_L	119_Y	1.449	1.00
68_L	73_G	1.368	1.00
77_Y	81_K	1.360	1.00
51_I	55_P	1.351	1.00
112_F	116_A	1.349	1.00
105_L	109_R	1.348	1.00
78_R	81_K	1.340	1.00
60_L	63_A	1.322	1.00
79_R	83_T	1.302	1.00
90_T	122_K	1.285	1.00
63_A	67_R	1.249	1.00
21_Y	24_Y	1.244	1.00
4_A	37_P	1.231	1.00
62_E	66_A	1.183	1.00
82_A	86_H	1.176	1.00
86_H	89_G	1.171	1.00
83_T	86_H	1.152	1.00
65_R	69_D	1.149	1.00
73_G	77_Y	1.149	1.00
53_R	56_E	1.149	1.00
75_E	79_R	1.145	1.00
87_V	119_Y	1.137	1.00
56_E	60_L	1.080	1.00
89_G	94_N	1.066	1.00
86_H	90_T	1.065	1.00
113_L	116_A	1.063	1.00
111_E	115_A	1.036	1.00
71_E	75_E	1.013	1.00
93_R	99_R	1.003	1.00
51_I	54_S	1.000	1.00
89_G	93_R	0.996	1.00
102_L	111_E	0.977	1.00
33_C	36_C	0.976	1.00
21_Y	25_R	0.968	1.00
11_R	29_R	0.964	1.00
107_K	110_T	0.961	1.00
49_R	52_R	0.953	1.00
22_K	25_R	0.952	1.00
49_R	53_R	0.948	1.00
63_A	66_A	0.941	1.00
34_R	39_R	0.939	1.00
91_L	97_L	0.928	1.00
102_L	108_V	0.921	1.00
100_F	112_F	0.917	1.00
74_K	77_Y	0.910	1.00
27_R	50_T	0.910	1.00
58_E	61_L	0.906	1.00
110_T	114_L	0.902	1.00
95_H	119_Y	0.898	1.00
66_A	70_T	0.890	1.00
76_L	79_R	0.877	1.00
72_E	75_E	0.869	1.00
20_G	23_R	0.869	1.00
43_T	48_G	0.851	1.00
32_D	35_A	0.845	1.00
115_A	118_A	0.841	1.00
61_L	65_R	0.839	1.00
66_A	69_D	0.837	1.00
91_L	112_F	0.834	1.00
94_N	122_K	0.831	1.00
36_C	42_C	0.831	1.00
71_E	74_K	0.817	1.00
68_L	77_Y	0.816	1.00
60_L	64_A	0.813	1.00
19_R	23_R	0.800	1.00
51_I	56_E	0.794	1.00
112_F	115_A	0.791	1.00
13_T	24_Y	0.786	1.00
23_R	26_A	0.785	1.00
67_R	70_T	0.778	1.00
22_K	26_A	0.778	1.00
108_V	111_E	0.774	1.00
18_G	21_Y	0.774	1.00
46_K	49_R	0.769	1.00
74_K	78_R	0.760	1.00
53_R	58_E	0.746	1.00
62_E	65_R	0.736	1.00
19_R	22_K	0.734	1.00
87_V	90_T	0.722	1.00
56_E	59_E	0.711	1.00
106_E	109_R	0.710	1.00
90_T	123_R	0.710	1.00
72_E	76_L	0.710	1.00
33_C	42_C	0.706	1.00
28_Y	32_D	0.705	1.00
89_G	92_K	0.703	1.00
86_H	123_R	0.703	1.00
81_K	86_H	0.702	1.00
75_E	78_R	0.701	1.00
95_H	115_A	0.697	1.00
113_L	117_L	0.690	1.00
59_E	62_E	0.684	1.00
12_G	27_R	0.671	1.00
91_L	116_A	0.663	1.00
67_R	76_L	0.649	1.00
67_R	73_G	0.648	1.00
109_R	112_F	0.642	1.00
48_G	51_I	0.642	1.00
14_N	17_K	0.639	1.00
10_Y	14_N	0.636	1.00
119_Y	123_R	0.636	1.00
52_R	55_P	0.635	1.00
61_L	64_A	0.635	1.00
20_G	26_A	0.633	1.00
96_G	99_R	0.628	1.00
102_L	110_T	0.626	1.00
111_E	118_A	0.622	1.00
114_L	117_L	0.615	1.00
49_R	55_P	0.614	1.00
18_G	24_Y	0.602	1.00
110_T	113_L	0.600	1.00
97_L	112_F	0.597	1.00
12_G	15_R	0.596	1.00
15_R	22_K	0.596	1.00
3_P	38_L	0.595	1.00
35_A	39_R	0.591	1.00
14_N	52_R	0.589	1.00
84_V	88_F	0.581	1.00
25_R	52_R	0.581	1.00
30_A	47_K	0.581	1.00
94_N	99_R	0.579	1.00
84_V	89_G	0.576	1.00
77_Y	82_A	0.569	1.00
9_T	12_G	0.564	1.00
29_R	50_T	0.561	1.00
9_T	29_R	0.560	1.00
8_L	28_Y	0.559	1.00
19_R	25_R	0.557	1.00
99_R	103_R	0.557	1.00
106_E	110_T	0.557	1.00
31_S	35_A	0.552	1.00
92_K	97_L	0.550	1.00
78_R	82_A	0.547	1.00
18_G	22_K	0.544	1.00
39_R	48_G	0.542	1.00
97_L	100_F	0.538	1.00
27_R	51_I	0.537	1.00
30_A	48_G	0.536	1.00
29_R	48_G	0.536	1.00
50_T	54_S	0.534	1.00
88_F	91_L	0.533	1.00
17_K	22_K	0.529	1.00
14_N	27_R	0.528	1.00
87_V	91_L	0.517	1.00
45_S	48_G	0.516	1.00
83_T	87_V	0.514	1.00
48_G	53_R	0.512	1.00
64_A	73_G	0.509	1.00
20_G	24_Y	0.508	1.00
18_G	23_R	0.503	1.00
108_V	115_A	0.502	1.00
119_Y	122_K	0.501	1.00
27_R	52_R	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
1musA	2	0.952	51.9	0.851	Contact Map
1keaA	2	0.352	14	0.889	Contact Map
1kg2A	1	0.432	8.7	0.898	Contact Map
2abkA	1	0.368	7.4	0.901	Contact Map
4uobA	1	0.392	5	0.909	Contact Map
3d06A	1	0.36	3.6	0.915	Contact Map
1ornA	1	0.376	3.6	0.915	Contact Map
4unfA	1	0.424	3.4	0.916	Contact Map
2xwcA	2	0.44	2.8	0.92	Contact Map
2qkdA	2	0.968	2	0.925	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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