DUF2080 - PFAM28P - GREMLIN Contacts

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DUF2080 - Putative transposon-encoded protein (DUF2080)

PFAM:	PF09853	Sequences: IKIKKKKLLLVDNIEGFFEKKVTPFGTGAKVDCPKEYLGKKVYVIILKDE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	50 (48)
Sequences:	1628 (910)
Seq/√Len:	131.4
META:	0.98

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
15_E	48_K	3.065	1.00
19_E	41_K	2.918	1.00
23_T	30_K	2.796	1.00
8_L	12_D	2.469	1.00
31_V	44_V	2.135	1.00
20_K	32_D	2.127	1.00
21_K	41_K	1.811	1.00
23_T	32_D	1.758	1.00
25_F	32_D	1.754	1.00
33_C	44_V	1.695	1.00
7_K	13_N	1.673	1.00
7_K	11_V	1.650	1.00
42_V	46_I	1.599	1.00
25_F	28_G	1.512	1.00
22_V	33_C	1.435	1.00
15_E	40_K	1.306	1.00
37_Y	40_K	1.209	1.00
29_A	38_L	1.205	0.99
18_F	44_V	1.204	0.99
17_F	43_Y	1.167	0.99
31_V	42_V	1.013	0.98
16_G	37_Y	0.955	0.97
41_K	47_L	0.941	0.97
18_F	31_V	0.938	0.97
18_F	37_Y	0.929	0.97
20_K	28_G	0.899	0.96
2_K	9_L	0.840	0.95
24_P	38_L	0.824	0.94
9_L	45_I	0.822	0.94
18_F	32_D	0.820	0.94
8_L	11_V	0.800	0.93
5_K	11_V	0.787	0.92
20_K	25_F	0.764	0.91
28_G	33_C	0.759	0.91
4_K	9_L	0.749	0.90
4_K	7_K	0.748	0.90
16_G	28_G	0.737	0.90
3_I	18_F	0.727	0.89
5_K	8_L	0.704	0.87
28_G	47_L	0.701	0.87
26_G	39_G	0.695	0.87
18_F	33_C	0.687	0.86
46_I	49_D	0.687	0.86
22_V	29_A	0.680	0.86
16_G	33_C	0.670	0.85
13_N	17_F	0.663	0.84
30_K	43_Y	0.661	0.84
12_D	15_E	0.657	0.84
20_K	30_K	0.637	0.82
35_K	38_L	0.632	0.81
27_T	38_L	0.622	0.80
19_E	48_K	0.619	0.80
20_K	31_V	0.619	0.80
18_F	46_I	0.615	0.79
13_N	48_K	0.609	0.79
13_N	34_P	0.602	0.78
16_G	22_V	0.597	0.77
4_K	8_L	0.586	0.76
30_K	33_C	0.573	0.75
21_K	39_G	0.571	0.74
41_K	48_K	0.568	0.74
18_F	34_P	0.566	0.74
6_K	37_Y	0.556	0.72
3_I	6_K	0.552	0.72
29_A	35_K	0.546	0.71
3_I	37_Y	0.545	0.71
10_L	17_F	0.527	0.68
22_V	31_V	0.507	0.65
2_K	5_K	0.507	0.65
5_K	13_N	0.501	0.64
15_E	36_E	0.500	0.64
22_V	42_V	0.500	0.64

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
2mrnA	2	0.98	69.5	0.744	Contact Map
1mvfD	1	0.6	68.4	0.747	Contact Map
3zvkE	2	0.68	64.9	0.752	Contact Map
3tndB	3	0.66	10.9	0.837	Contact Map
4ujrS	1	1	9.4	0.841	Contact Map
3o27A	2	0.72	8.8	0.844	Contact Map
1vx79	1	0.96	8.2	0.846	Contact Map
2l66A	2	0.66	7.5	0.848	Contact Map
4wpmA	1	0.9	6.2	0.854	Contact Map
3j61f	1	1	5.4	0.858	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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