DUF3566 - PFAM28P - GREMLIN Contacts

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DUF3566 - Transmembrane domain of unknown function (DUF3566)

PFAM:	PF12089	Sequences: PRRARLVLRRIDPWSVLKVSFLLSLALGIVLVVAVAVLWLVLDATGVFDSINSFVGDLGGSGSGFDLADYFSGGRVLGFAALIGLVNVVLLTALATLGAFLYNLIADLVGGIEVTLAE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	118 (117)
Sequences:	3018 (1715)
Seq/√Len:	158.5
META:	0.831

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
28_G	84_G	4.764	1.00
24_S	95_A	4.138	1.00
36_A	77_L	3.076	1.00
16_V	99_A	2.789	1.00
53_S	57_D	2.782	1.00
35_V	80_A	2.777	1.00
20_S	95_A	2.674	1.00
11_I	16_V	2.608	1.00
106_A	109_V	2.380	1.00
49_D	53_S	2.097	1.00
50_S	53_S	2.067	1.00
30_V	34_A	1.980	1.00
19_V	105_I	1.953	1.00
19_V	112_I	1.922	1.00
52_N	66_D	1.895	1.00
36_A	73_G	1.856	1.00
13_P	100_F	1.846	1.00
32_V	81_A	1.777	1.00
8_L	116_L	1.702	1.00
66_D	69_D	1.666	1.00
77_L	80_A	1.636	1.00
32_V	77_L	1.578	1.00
31_L	84_G	1.509	1.00
91_L	95_A	1.491	1.00
67_L	71_F	1.456	1.00
42_L	47_V	1.435	1.00
85_L	89_V	1.403	1.00
31_L	35_V	1.400	1.00
21_F	92_T	1.399	1.00
46_G	49_D	1.398	1.00
75_R	79_F	1.389	1.00
65_F	69_D	1.376	1.00
39_W	43_D	1.313	1.00
28_G	88_V	1.287	1.00
87_N	91_L	1.283	1.00
16_V	20_S	1.281	1.00
93_A	96_T	1.245	1.00
24_S	92_T	1.239	1.00
71_F	76_V	1.234	1.00
28_G	32_V	1.217	1.00
2_R	6_L	1.200	1.00
10_R	13_P	1.198	1.00
4_A	7_V	1.193	1.00
88_V	92_T	1.190	1.00
20_S	24_S	1.178	1.00
104_L	109_V	1.168	1.00
65_F	68_A	1.167	1.00
102_Y	106_A	1.142	1.00
25_L	29_I	1.101	1.00
17_L	21_F	1.091	0.99
20_S	96_T	1.086	0.99
73_G	77_L	1.081	0.99
16_V	95_A	1.074	0.99
83_I	87_N	1.063	0.99
73_G	81_A	1.055	0.99
52_N	56_G	1.051	0.99
14_W	18_K	1.048	0.99
56_G	61_S	1.038	0.99
5_R	113_E	1.000	0.99
21_F	24_S	1.000	0.99
40_L	118_E	0.998	0.99
9_R	117_A	0.993	0.99
8_L	114_V	0.990	0.99
86_V	90_L	0.963	0.99
49_D	52_N	0.962	0.99
21_F	88_V	0.955	0.99
39_W	101_L	0.906	0.98
47_V	50_S	0.898	0.98
81_A	85_L	0.896	0.98
54_F	58_L	0.890	0.98
59_G	64_G	0.881	0.98
57_D	60_G	0.878	0.98
3_R	8_L	0.872	0.97
58_L	61_S	0.860	0.97
51_I	55_V	0.848	0.97
6_L	116_L	0.839	0.97
49_D	62_G	0.832	0.97
12_D	18_K	0.831	0.97
2_R	13_P	0.819	0.96
17_L	96_T	0.806	0.96
40_L	43_D	0.803	0.96
17_L	20_S	0.774	0.95
39_W	75_R	0.770	0.95
93_A	108_L	0.769	0.95
40_L	44_A	0.764	0.95
18_K	108_L	0.758	0.94
8_L	11_I	0.756	0.94
24_S	91_L	0.756	0.94
64_G	68_A	0.756	0.94
72_S	75_R	0.748	0.94
48_F	71_F	0.745	0.94
16_V	112_I	0.743	0.94
2_R	7_V	0.742	0.94
22_L	109_V	0.738	0.94
7_V	14_W	0.734	0.93
101_L	107_D	0.723	0.93
68_A	71_F	0.723	0.93
30_V	50_S	0.718	0.93
21_F	25_L	0.717	0.93
18_K	22_L	0.717	0.93
41_V	96_T	0.716	0.92
32_V	38_L	0.715	0.92
2_R	118_E	0.713	0.92
53_S	58_L	0.713	0.92
28_G	31_L	0.697	0.91
60_G	63_S	0.694	0.91
76_V	79_F	0.692	0.91
43_D	48_F	0.690	0.91
48_F	52_N	0.669	0.90
40_L	56_G	0.669	0.90
57_D	65_F	0.665	0.89
13_P	17_L	0.664	0.89
22_L	26_A	0.660	0.89
55_V	59_G	0.659	0.89
53_S	102_Y	0.653	0.89
10_R	90_L	0.649	0.88
102_Y	113_E	0.648	0.88
95_A	99_A	0.637	0.87
25_L	85_L	0.635	0.87
25_L	88_V	0.634	0.87
39_W	45_T	0.630	0.87
95_A	98_G	0.627	0.87
54_F	57_D	0.626	0.86
17_L	26_A	0.626	0.86
11_I	99_A	0.622	0.86
68_A	97_L	0.613	0.85
19_V	39_W	0.613	0.85
59_G	63_S	0.611	0.85
58_L	62_G	0.604	0.84
49_D	68_A	0.604	0.84
50_S	82_L	0.601	0.84
4_A	116_L	0.597	0.84
89_V	93_A	0.596	0.84
26_A	101_L	0.595	0.84
52_N	68_A	0.592	0.83
52_N	69_D	0.589	0.83
24_S	76_V	0.583	0.82
23_L	26_A	0.576	0.82
104_L	107_D	0.574	0.81
86_V	101_L	0.572	0.81
19_V	109_V	0.570	0.81
9_R	17_L	0.570	0.81
33_V	37_V	0.564	0.80
90_L	98_G	0.563	0.80
40_L	74_G	0.562	0.80
25_L	45_T	0.560	0.80
59_G	71_F	0.557	0.79
97_L	100_F	0.551	0.79
24_S	88_V	0.550	0.79
4_A	16_V	0.547	0.78
37_V	41_V	0.545	0.78
19_V	91_L	0.544	0.78
23_L	101_L	0.543	0.78
4_A	114_V	0.541	0.77
113_E	117_A	0.541	0.77
29_I	80_A	0.536	0.77
97_L	107_D	0.536	0.77
28_G	109_V	0.535	0.77
47_V	113_E	0.534	0.76
17_L	100_F	0.531	0.76
56_G	64_G	0.529	0.76
98_G	108_L	0.521	0.75
37_V	40_L	0.519	0.74
71_F	75_R	0.519	0.74
38_L	42_L	0.518	0.74
2_R	5_R	0.516	0.74
30_V	94_L	0.515	0.74
23_L	98_G	0.513	0.74
93_A	100_F	0.510	0.73
27_L	31_L	0.507	0.73
43_D	77_L	0.505	0.72
33_V	87_N	0.504	0.72
28_G	81_A	0.503	0.72
79_F	83_I	0.502	0.72
29_I	33_V	0.501	0.72
10_R	55_V	0.500	0.72

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
2onkC	2	0.7712	6.8	0.924	Contact Map
3d31C	2	0.7627	5.2	0.928	Contact Map
4f35D	2	0.339	3.8	0.933	Contact Map
4tquN	1	0.9322	2.9	0.936	Contact Map
2kogA	1	0.339	2.6	0.938	Contact Map
1vx77	1	0.2712	2.4	0.939	Contact Map
4v3iA	2	0	2.1	0.941	Contact Map
3zf7h	1	0.339	2.1	0.941	Contact Map
4j7cI	2	0.7881	2	0.942	Contact Map
3pjsK	4	0.8475	1.9	0.942	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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