DDE_Tnp_1_assoc - PFAM28P - GREMLIN Contacts

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DDE_Tnp_1_assoc - DDE_Tnp_1-associated

PFAM:	PF13808	Sequences: LEHFAELPDPRRARGKRHPLADILVIALCAVLCGADSWVAIAEFGRAKEEWLRRFLELPNGIPSHDTFRRVFARLDPEAFEACFLAWV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	88 (87)
Sequences:	38895 (21500)
Seq/√Len:	2305.1
META:	0.976

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
12_R	15_G	3.105	1.00
49_E	53_R	2.369	1.00
13_A	16_K	2.345	1.00
27_A	72_F	2.329	1.00
8_P	79_A	2.231	1.00
69_R	73_A	2.221	1.00
26_I	45_G	2.124	1.00
5_A	21_A	1.870	1.00
19_P	22_D	1.860	1.00
35_A	40_A	1.827	1.00
30_A	41_I	1.782	1.00
23_I	71_V	1.707	1.00
39_V	65_H	1.670	1.00
37_S	40_A	1.647	1.00
20_L	71_V	1.623	1.00
19_P	57_E	1.574	1.00
42_A	46_R	1.572	1.00
81_E	85_L	1.530	1.00
39_V	69_R	1.496	1.00
12_R	16_K	1.474	1.00
10_P	74_R	1.469	1.00
65_H	69_R	1.450	1.00
42_A	65_H	1.436	1.00
38_W	69_R	1.420	1.00
3_H	86_A	1.415	1.00
79_A	82_A	1.403	1.00
27_A	41_I	1.378	1.00
6_E	86_A	1.333	1.00
43_E	47_A	1.297	1.00
67_T	70_R	1.226	1.00
22_D	57_E	1.187	1.00
17_R	60_N	1.151	1.00
76_D	79_A	1.148	1.00
38_W	72_F	1.130	1.00
48_K	52_L	1.125	1.00
84_F	88_V	1.114	1.00
3_H	83_C	1.101	1.00
6_E	83_C	1.100	1.00
29_C	52_L	1.066	1.00
82_A	86_A	1.057	1.00
39_V	43_E	1.052	1.00
58_L	61_G	1.049	1.00
57_E	61_G	1.041	1.00
30_A	35_A	1.011	1.00
44_F	48_K	1.000	1.00
7_L	83_C	0.999	1.00
79_A	83_C	0.975	1.00
31_V	41_I	0.960	1.00
45_G	68_F	0.959	1.00
7_L	24_L	0.952	1.00
29_C	44_F	0.951	1.00
26_I	68_F	0.951	1.00
57_E	60_N	0.946	1.00
3_H	6_E	0.946	1.00
49_E	52_L	0.935	1.00
42_A	64_S	0.914	1.00
48_K	51_W	0.893	1.00
64_S	67_T	0.885	1.00
22_D	56_L	0.882	1.00
27_A	68_F	0.878	1.00
19_P	59_P	0.877	1.00
25_V	56_L	0.875	1.00
83_C	86_A	0.862	1.00
30_A	44_F	0.856	1.00
53_R	62_I	0.851	1.00
77_P	81_E	0.846	1.00
49_E	62_I	0.841	1.00
66_D	70_R	0.825	1.00
25_V	29_C	0.824	1.00
78_E	81_E	0.824	1.00
67_T	71_V	0.823	1.00
46_R	49_E	0.784	1.00
44_F	52_L	0.781	1.00
23_I	67_T	0.778	1.00
17_R	21_A	0.776	1.00
23_I	68_F	0.773	1.00
51_W	55_F	0.772	1.00
42_A	62_I	0.767	1.00
66_D	69_R	0.750	1.00
70_R	74_R	0.748	1.00
85_L	88_V	0.742	1.00
50_E	53_R	0.728	1.00
52_L	56_L	0.713	1.00
26_I	58_L	0.713	1.00
78_E	82_A	0.712	1.00
2_E	5_A	0.711	1.00
38_W	65_H	0.710	1.00
16_K	19_P	0.708	1.00
36_D	40_A	0.706	1.00
10_P	20_L	0.700	1.00
35_A	41_I	0.693	1.00
21_A	25_V	0.693	1.00
27_A	31_V	0.689	1.00
22_D	62_I	0.679	1.00
7_L	20_L	0.676	1.00
75_L	80_F	0.675	1.00
27_A	38_W	0.664	1.00
22_D	59_P	0.662	1.00
38_W	73_A	0.662	1.00
28_L	84_F	0.661	1.00
25_V	55_F	0.657	1.00
71_V	75_L	0.653	1.00
53_R	57_E	0.648	1.00
33_C	44_F	0.642	1.00
4_F	28_L	0.639	1.00
10_P	71_V	0.639	1.00
51_W	54_R	0.634	1.00
70_R	73_A	0.632	1.00
4_F	83_C	0.628	1.00
45_G	62_I	0.598	1.00
22_D	26_I	0.591	1.00
23_I	63_P	0.586	1.00
14_R	17_R	0.582	1.00
24_L	75_L	0.581	1.00
43_E	46_R	0.578	1.00
81_E	84_F	0.576	1.00
5_A	8_P	0.575	1.00
39_V	42_A	0.558	1.00
22_D	58_L	0.556	1.00
7_L	10_P	0.549	1.00
82_A	85_L	0.547	1.00
9_D	16_K	0.545	1.00
40_A	43_E	0.542	1.00
81_E	88_V	0.532	1.00
42_A	45_G	0.518	1.00
50_E	54_R	0.513	1.00
31_V	35_A	0.512	1.00
35_A	48_K	0.512	1.00
20_L	24_L	0.505	1.00
22_D	53_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
2d74B	1	0.9886	19.2	0.863	Contact Map
1iufA	1	0.8182	17.1	0.866	Contact Map
3j81l	1	0.0568	13.6	0.872	Contact Map
1neeA	1	0.9773	11.6	0.875	Contact Map
3cw2K	1	0.9773	11.3	0.876	Contact Map
2k5eA	1	0.6932	10.7	0.877	Contact Map
2fsqA	1	1	9.7	0.88	Contact Map
1bm9A	2	0.8182	9.4	0.88	Contact Map
2p0vA	2	0.375	8.2	0.884	Contact Map
2k53A	1	0.6705	7.8	0.885	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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