DUF3093 - PFAM28P - GREMLIN Contacts

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DUF3093 - Protein of unknown function (DUF3093)

PFAM:	PF11292	Sequences: RYRERLWVPLWWWLLALLLALSAALVAAPVGLGAALVVYAVLLALAAALLLWLGRPRIEVTDGELRAGRARIPLSYLGEVEALDAEAARAARGPDADPRAFLLLRPWIKTAVRVEVDDPADPTPYWLVSTRRPEELAAAL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	140 (139)
Sequences:	3023 (2089)
Seq/√Len:	177.2
META:	0.767

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
88_A	111_A	3.936	1.00
90_A	95_D	3.554	1.00
132_R	135_E	3.308	1.00
64_E	71_R	3.119	1.00
59_E	66_R	2.751	1.00
73_P	76_Y	2.750	1.00
3_R	57_R	2.466	1.00
90_A	94_P	2.403	1.00
72_I	77_L	2.372	1.00
84_D	87_A	2.333	1.00
100_A	125_Y	2.241	1.00
78_G	116_V	2.129	1.00
91_A	95_D	1.998	1.00
72_I	116_V	1.988	1.00
81_E	115_E	1.934	1.00
67_A	128_V	1.900	1.00
3_R	59_E	1.893	1.00
81_E	113_R	1.700	1.00
118_D	121_D	1.692	1.00
92_R	104_L	1.680	1.00
56_P	103_L	1.675	1.00
78_G	117_D	1.670	1.00
25_L	29_P	1.659	1.00
78_G	115_E	1.618	1.00
79_E	115_E	1.591	1.00
67_A	103_L	1.549	1.00
65_L	128_V	1.527	1.00
80_V	115_E	1.519	1.00
108_I	129_S	1.483	1.00
80_V	137_A	1.467	1.00
15_L	19_L	1.412	1.00
26_V	29_P	1.406	1.00
91_A	113_R	1.391	1.00
111_A	130_T	1.378	1.00
82_A	137_A	1.373	1.00
56_P	67_A	1.366	1.00
65_L	114_V	1.363	1.00
83_L	111_A	1.329	1.00
58_I	128_V	1.328	1.00
91_A	96_A	1.301	1.00
88_A	92_R	1.294	1.00
86_E	89_R	1.286	1.00
23_A	26_V	1.272	1.00
31_G	36_L	1.259	1.00
66_R	71_R	1.232	1.00
33_G	37_V	1.231	1.00
34_A	38_V	1.225	1.00
64_E	74_L	1.214	1.00
24_A	27_A	1.209	1.00
8_V	12_W	1.204	1.00
70_A	101_F	1.196	1.00
85_A	109_K	1.184	1.00
135_E	138_A	1.184	1.00
31_G	34_A	1.167	1.00
32_L	35_A	1.155	1.00
9_P	12_W	1.143	1.00
32_L	36_L	1.138	1.00
25_L	28_A	1.118	1.00
24_A	28_A	1.095	1.00
82_A	130_T	1.095	1.00
134_E	138_A	1.095	1.00
118_D	123_T	1.083	1.00
61_T	64_E	1.066	1.00
48_A	52_W	1.033	0.99
28_A	32_L	1.025	0.99
72_I	76_Y	1.012	0.99
13_W	21_L	1.010	0.99
58_I	65_L	1.009	0.99
29_P	32_L	1.006	0.99
84_D	134_E	0.991	0.99
30_V	34_A	0.986	0.99
70_A	121_D	0.983	0.99
23_A	27_A	0.982	0.99
61_T	66_R	0.980	0.99
74_L	77_L	0.979	0.99
77_L	80_V	0.971	0.99
81_E	87_A	0.948	0.99
96_A	111_A	0.945	0.99
31_G	37_V	0.944	0.99
128_V	136_L	0.937	0.99
74_L	140_L	0.935	0.99
87_A	95_D	0.933	0.99
88_A	104_L	0.929	0.99
76_Y	117_D	0.927	0.99
56_P	105_R	0.921	0.99
31_G	35_A	0.918	0.99
83_L	91_A	0.915	0.99
23_A	29_P	0.904	0.99
31_G	38_V	0.892	0.98
45_L	49_L	0.892	0.98
27_A	35_A	0.889	0.98
46_A	50_L	0.877	0.98
30_V	36_L	0.875	0.98
22_S	26_V	0.868	0.98
10_L	14_L	0.868	0.98
27_A	31_G	0.863	0.98
85_A	110_T	0.844	0.98
92_R	127_L	0.840	0.98
83_L	88_A	0.839	0.98
26_V	31_G	0.834	0.98
87_A	90_A	0.823	0.97
27_A	33_G	0.823	0.97
111_A	127_L	0.820	0.97
27_A	32_L	0.819	0.97
49_L	53_L	0.819	0.97
130_T	133_P	0.819	0.97
27_A	30_V	0.814	0.97
25_L	31_G	0.808	0.97
22_S	25_L	0.808	0.97
61_T	74_L	0.801	0.97
60_V	139_A	0.798	0.97
70_A	118_D	0.797	0.97
70_A	123_T	0.796	0.97
60_V	136_L	0.793	0.97
30_V	35_A	0.790	0.97
97_D	124_P	0.774	0.96
13_W	16_A	0.772	0.96
24_A	31_G	0.770	0.96
114_V	128_V	0.764	0.96
135_E	139_A	0.759	0.96
25_L	34_A	0.759	0.96
88_A	127_L	0.750	0.96
118_D	122_P	0.746	0.95
10_L	107_W	0.743	0.95
85_A	88_A	0.736	0.95
133_P	139_A	0.736	0.95
23_A	28_A	0.734	0.95
76_Y	116_V	0.734	0.95
113_R	123_T	0.729	0.95
33_G	38_V	0.725	0.95
20_A	43_L	0.722	0.95
63_G	74_L	0.712	0.94
82_A	112_V	0.702	0.94
83_L	96_A	0.696	0.93
32_L	38_V	0.696	0.93
28_A	35_A	0.695	0.93
15_L	18_L	0.694	0.93
84_D	96_A	0.684	0.93
54_G	107_W	0.679	0.93
96_A	102_L	0.678	0.93
101_F	123_T	0.669	0.92
2_Y	132_R	0.667	0.92
14_L	18_L	0.662	0.92
11_W	14_L	0.659	0.92
44_A	48_A	0.646	0.91
72_I	80_V	0.628	0.89
23_A	31_G	0.628	0.89
76_Y	123_T	0.628	0.89
12_W	83_L	0.626	0.89
15_L	21_L	0.622	0.89
40_A	44_A	0.621	0.89
28_A	31_G	0.619	0.89
20_A	24_A	0.617	0.89
18_L	21_L	0.613	0.88
65_L	136_L	0.611	0.88
24_A	29_P	0.607	0.88
97_D	125_Y	0.603	0.87
75_S	117_D	0.600	0.87
70_A	122_P	0.599	0.87
19_L	22_S	0.598	0.87
133_P	138_A	0.591	0.86
96_A	125_Y	0.589	0.86
12_W	16_A	0.587	0.86
29_P	37_V	0.585	0.86
30_V	33_G	0.583	0.86
114_V	137_A	0.582	0.86
21_L	24_A	0.581	0.86
8_V	50_L	0.574	0.85
58_I	67_A	0.564	0.84
82_A	106_P	0.562	0.84
116_V	123_T	0.557	0.83
62_D	74_L	0.556	0.83
52_W	55_R	0.555	0.83
64_E	73_P	0.554	0.83
26_V	32_L	0.554	0.83
80_V	114_V	0.553	0.83
26_V	30_V	0.553	0.83
102_L	107_W	0.549	0.82
25_L	38_V	0.548	0.82
88_A	110_T	0.547	0.82
40_A	43_L	0.547	0.82
113_R	127_L	0.547	0.82
39_Y	42_L	0.545	0.82
50_L	54_G	0.545	0.82
92_R	111_A	0.543	0.81
30_V	38_V	0.539	0.81
35_A	39_Y	0.538	0.81
28_A	38_V	0.534	0.80
73_P	116_V	0.532	0.80
29_P	33_G	0.531	0.80
100_A	124_P	0.530	0.80
32_L	37_V	0.529	0.80
67_A	97_D	0.528	0.80
14_L	120_A	0.527	0.80
29_P	35_A	0.521	0.79
65_L	77_L	0.516	0.78
90_A	134_E	0.513	0.78
20_A	44_A	0.513	0.78
136_L	139_A	0.511	0.77
92_R	102_L	0.510	0.77
89_R	94_P	0.510	0.77
76_Y	79_E	0.510	0.77
104_L	129_S	0.505	0.77
2_Y	60_V	0.502	0.76
77_L	116_V	0.502	0.76
133_P	137_A	0.501	0.76
25_L	33_G	0.500	0.76
8_V	15_L	0.500	0.76

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
1ynfA	2	0.2929	14.7	0.935	Contact Map
4c5eA	3	0.4	8.6	0.942	Contact Map
3ut1A	2	0.3786	8.4	0.942	Contact Map
3f70A	2	0.4214	8.3	0.942	Contact Map
1oz2A	1	0.3857	7.2	0.944	Contact Map
2bivA	1	0.4	6.7	0.944	Contact Map
3pmiA	4	0.2571	6.3	0.945	Contact Map
2jlnA	1	0.4714	5.4	0.947	Contact Map
1bxnI	3	0.4429	5.2	0.947	Contact Map
2r58A	1	0.3786	4.2	0.95	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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