DUF2160 - PFAM28P - GREMLIN Contacts

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DUF2160 - Predicted small integral membrane protein (DUF2160)

PFAM:	PF09928	Sequences: WMAWTWPTAIFFIVIALLLAGMTVWEIRSPGAPRRGILPIETTRGDRLFISLLGSAFIHLAWLGLVGTPLWIALAISLVYAAAVFRWV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	88 (88)
Sequences:	3355 (1418)
Seq/√Len:	151.1
META:	0.885

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
25_W	29_S	2.912	1.00
54_G	80_Y	2.802	1.00
23_T	27_I	2.763	1.00
83_A	87_W	2.639	1.00
51_S	81_A	2.591	1.00
26_E	31_G	2.357	1.00
59_H	73_A	2.075	1.00
58_I	80_Y	2.068	1.00
14_V	18_L	2.038	1.00
33_P	41_E	1.980	1.00
52_L	56_A	1.860	1.00
59_H	77_S	1.842	1.00
35_R	39_P	1.820	1.00
10_I	14_V	1.775	1.00
35_R	41_E	1.762	1.00
17_L	21_G	1.740	1.00
6_W	10_I	1.739	1.00
59_H	74_L	1.720	1.00
80_Y	84_V	1.656	1.00
18_L	48_L	1.623	1.00
55_S	77_S	1.621	1.00
22_M	48_L	1.553	1.00
59_H	70_L	1.553	1.00
19_L	23_T	1.512	1.00
53_L	57_F	1.455	1.00
13_I	17_L	1.347	1.00
7_P	10_I	1.345	1.00
24_V	28_R	1.307	1.00
69_P	72_I	1.278	1.00
29_S	44_R	1.264	1.00
40_I	50_I	1.219	1.00
22_M	25_W	1.202	1.00
21_G	25_W	1.191	1.00
16_A	20_A	1.185	1.00
85_F	88_V	1.183	1.00
54_G	84_V	1.151	1.00
29_S	32_A	1.140	1.00
74_L	78_L	1.134	1.00
54_G	58_I	1.124	0.99
75_A	79_V	1.104	0.99
6_W	9_A	1.051	0.99
31_G	43_T	1.050	0.99
61_A	64_G	1.023	0.99
57_F	61_A	1.022	0.99
31_G	44_R	1.016	0.99
11_F	14_V	1.015	0.99
13_I	16_A	0.984	0.99
42_T	46_D	0.979	0.99
68_T	72_I	0.979	0.99
62_W	66_V	0.955	0.98
63_L	70_L	0.954	0.98
78_L	82_A	0.952	0.98
71_W	74_L	0.910	0.98
37_I	88_V	0.871	0.97
15_I	18_L	0.869	0.97
30_P	44_R	0.869	0.97
20_A	24_V	0.867	0.97
26_E	44_R	0.867	0.97
35_R	40_I	0.866	0.97
18_L	21_G	0.854	0.97
72_I	75_A	0.839	0.96
21_G	29_S	0.831	0.96
82_A	87_W	0.821	0.96
11_F	56_A	0.820	0.96
26_E	32_A	0.817	0.96
74_L	77_S	0.808	0.95
81_A	85_F	0.807	0.95
69_P	74_L	0.803	0.95
1_W	4_W	0.773	0.94
55_S	59_H	0.759	0.94
84_V	88_V	0.749	0.93
37_I	83_A	0.742	0.93
43_T	49_F	0.742	0.93
61_A	65_L	0.736	0.93
20_A	23_T	0.723	0.92
62_W	68_T	0.713	0.91
62_W	72_I	0.710	0.91
80_Y	83_A	0.701	0.91
75_A	81_A	0.699	0.91
66_V	69_P	0.697	0.90
25_W	82_A	0.682	0.89
39_P	88_V	0.680	0.89
60_L	64_G	0.678	0.89
22_M	26_E	0.670	0.89
22_M	30_P	0.667	0.88
79_V	82_A	0.664	0.88
21_G	28_R	0.659	0.88
34_R	47_R	0.656	0.88
55_S	81_A	0.651	0.87
69_P	75_A	0.645	0.87
25_W	31_G	0.642	0.86
62_W	76_I	0.635	0.86
10_I	17_L	0.633	0.86
70_L	77_S	0.628	0.85
5_T	8_T	0.627	0.85
72_I	76_I	0.625	0.85
26_E	35_R	0.624	0.85
55_S	80_Y	0.623	0.85
71_W	78_L	0.614	0.84
13_I	20_A	0.608	0.83
7_P	39_P	0.590	0.81
14_V	74_L	0.580	0.80
70_L	74_L	0.576	0.80
11_F	19_L	0.574	0.80
7_P	13_I	0.567	0.79
62_W	70_L	0.564	0.79
22_M	50_I	0.562	0.78
51_S	55_S	0.561	0.78
12_F	56_A	0.560	0.78
63_L	74_L	0.560	0.78
39_P	85_F	0.556	0.78
73_A	77_S	0.556	0.78
22_M	44_R	0.548	0.77
17_L	28_R	0.547	0.76
21_G	24_V	0.541	0.76
16_A	56_A	0.536	0.75
82_A	86_R	0.535	0.75
10_I	13_I	0.527	0.74
25_W	32_A	0.527	0.74
73_A	78_L	0.523	0.73
37_I	54_G	0.522	0.73
19_L	22_M	0.520	0.73
22_M	29_S	0.517	0.72
43_T	63_L	0.517	0.72
33_P	43_T	0.513	0.72
15_I	52_L	0.510	0.71
19_L	30_P	0.509	0.71
31_G	39_P	0.507	0.71
38_L	80_Y	0.506	0.71
32_A	50_I	0.502	0.70
83_A	86_R	0.501	0.70
46_D	50_I	0.500	0.70

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
4p02B	1	0.3523	2.5	0.94	Contact Map
1jb0M	1	0.2955	2.3	0.941	Contact Map
4ev6A	3	0.3523	1.8	0.944	Contact Map
4c7rA	3	0.9432	1.7	0.945	Contact Map
4pd6A	3	0.4318	1.4	0.948	Contact Map
2wswA	3	0.9886	1.4	0.948	Contact Map
4i0uA	4	0.3295	1.3	0.948	Contact Map
3s8fC	1	0.3523	1.2	0.949	Contact Map
3s0xA	1	0.8068	1.2	0.95	Contact Map
3c02A	3	0.3182	1	0.952	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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