DUF996 - PFAM28P - GREMLIN Contacts

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DUF996 - Protein of unknown function (DUF996)

PFAM:	PF06195	Sequences: LSIVGLILVLIALKGLSDYYKDPSIFNNALYGFILGIVGIVVAVVVVLAAFFSLLSGLGFTGPTGWSSLIGGIIVALVVAWVFLIISAIFLRKSFNLLAEKSGVGLFKTAGLLYLIGAILTIILIGLILIFIAWI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	135 (134)
Sequences:	1530 (1257)
Seq/√Len:	108.6
META:	0.932

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
14_K	18_D	5.088	1.00
112_L	116_I	3.889	1.00
92_R	96_N	3.666	1.00
22_D	101_K	3.538	1.00
23_P	27_N	3.023	1.00
28_N	93_K	2.588	1.00
89_I	115_L	2.536	1.00
22_D	97_L	2.481	1.00
20_Y	102_S	2.448	1.00
109_T	113_L	2.399	1.00
115_L	119_I	2.366	1.00
13_L	29_A	2.286	1.00
114_Y	133_A	2.148	1.00
16_L	102_S	1.958	1.00
4_V	8_L	1.782	1.00
121_T	127_L	1.746	1.00
13_L	98_L	1.746	1.00
105_G	108_K	1.681	1.00
99_A	108_K	1.673	1.00
24_S	97_L	1.667	1.00
100_E	108_K	1.605	1.00
10_L	33_F	1.588	1.00
26_F	30_L	1.577	1.00
20_Y	98_L	1.533	1.00
112_L	115_L	1.528	1.00
88_A	118_A	1.522	1.00
44_V	48_L	1.482	1.00
120_L	123_I	1.472	1.00
62_G	65_G	1.472	1.00
81_W	85_I	1.463	1.00
45_V	49_A	1.408	1.00
35_L	83_F	1.368	1.00
16_L	98_L	1.311	0.99
96_N	108_K	1.310	0.99
124_L	128_I	1.295	0.99
62_G	67_S	1.294	0.99
58_L	62_G	1.287	0.99
64_T	68_S	1.280	0.99
127_L	130_I	1.275	0.99
91_L	94_S	1.253	0.99
62_G	66_W	1.234	0.99
99_A	102_S	1.217	0.99
9_V	13_L	1.201	0.99
25_I	28_N	1.199	0.99
30_L	34_I	1.196	0.99
24_S	28_N	1.192	0.99
70_I	73_I	1.169	0.99
63_P	67_S	1.162	0.99
55_L	58_L	1.138	0.98
50_A	57_G	1.137	0.98
16_L	20_Y	1.137	0.98
36_G	87_S	1.135	0.98
4_V	7_I	1.130	0.98
96_N	112_L	1.126	0.98
111_G	115_L	1.122	0.98
89_I	93_K	1.088	0.98
13_L	95_F	1.082	0.98
15_G	19_Y	1.069	0.98
54_L	57_G	1.034	0.97
109_T	112_L	1.017	0.97
53_S	56_S	1.004	0.97
43_A	80_A	1.002	0.96
32_G	91_L	0.995	0.96
86_I	90_F	0.989	0.96
29_A	95_F	0.983	0.96
7_I	11_I	0.963	0.96
31_Y	90_F	0.961	0.96
63_P	125_I	0.953	0.95
37_I	41_V	0.951	0.95
59_G	63_P	0.932	0.95
106_L	110_A	0.921	0.94
14_K	26_F	0.909	0.94
12_A	19_Y	0.906	0.94
88_A	133_A	0.904	0.94
64_T	67_S	0.901	0.94
113_L	116_I	0.896	0.93
98_L	102_S	0.894	0.93
17_S	23_P	0.887	0.93
90_F	94_S	0.884	0.93
110_A	114_Y	0.881	0.93
54_L	61_T	0.878	0.93
81_W	98_L	0.876	0.93
29_A	94_S	0.871	0.93
50_A	54_L	0.867	0.92
32_G	87_S	0.866	0.92
90_F	112_L	0.865	0.92
94_S	98_L	0.865	0.92
58_L	63_P	0.853	0.92
117_G	126_G	0.847	0.91
51_F	54_L	0.842	0.91
50_A	76_A	0.838	0.91
3_I	7_I	0.838	0.91
46_V	50_A	0.829	0.91
53_S	60_F	0.824	0.90
17_S	25_I	0.819	0.90
104_V	109_T	0.816	0.90
14_K	17_S	0.807	0.89
70_I	74_I	0.800	0.89
87_S	91_L	0.796	0.89
35_L	86_I	0.790	0.88
57_G	61_T	0.789	0.88
61_T	64_T	0.788	0.88
60_F	63_P	0.787	0.88
77_L	125_I	0.786	0.88
30_L	47_V	0.785	0.88
2_S	6_L	0.783	0.88
74_I	125_I	0.771	0.87
112_L	119_I	0.770	0.87
52_F	57_G	0.768	0.87
63_P	66_W	0.766	0.87
78_V	82_V	0.765	0.87
33_F	91_L	0.764	0.87
85_I	119_I	0.760	0.86
25_I	94_S	0.753	0.86
33_F	47_V	0.752	0.86
85_I	89_I	0.751	0.86
9_V	12_A	0.746	0.85
95_F	134_W	0.742	0.85
82_V	86_I	0.740	0.85
3_I	16_L	0.737	0.85
51_F	55_L	0.732	0.84
49_A	53_S	0.719	0.83
35_L	90_F	0.717	0.83
124_L	127_L	0.714	0.83
62_G	68_S	0.702	0.82
51_F	64_T	0.701	0.82
61_T	66_W	0.695	0.81
38_V	109_T	0.685	0.80
50_A	53_S	0.682	0.80
128_I	135_I	0.678	0.79
69_L	78_V	0.676	0.79
57_G	67_S	0.673	0.79
31_Y	35_L	0.671	0.79
52_F	56_S	0.670	0.79
96_N	119_I	0.669	0.78
95_F	99_A	0.663	0.78
64_T	74_I	0.661	0.78
11_I	15_G	0.655	0.77
52_F	55_L	0.654	0.77
15_G	18_D	0.654	0.77
44_V	49_A	0.650	0.76
10_L	26_F	0.647	0.76
107_F	110_A	0.646	0.76
89_I	102_S	0.644	0.76
87_S	114_Y	0.641	0.75
65_G	68_S	0.631	0.74
39_G	83_F	0.631	0.74
121_T	134_W	0.625	0.74
55_L	59_G	0.625	0.74
61_T	65_G	0.625	0.74
129_L	133_A	0.620	0.73
69_L	72_G	0.620	0.73
35_L	43_A	0.619	0.73
95_F	98_L	0.617	0.73
68_S	124_L	0.611	0.72
88_A	115_L	0.606	0.71
105_G	109_T	0.602	0.71
47_V	55_L	0.599	0.70
16_L	106_L	0.595	0.70
52_F	59_G	0.589	0.69
49_A	58_L	0.589	0.69
10_L	29_A	0.588	0.69
45_V	62_G	0.579	0.68
40_I	84_L	0.577	0.68
116_I	119_I	0.576	0.67
10_L	32_G	0.572	0.67
56_S	62_G	0.567	0.66
131_F	135_I	0.567	0.66
50_A	55_L	0.564	0.66
81_W	91_L	0.563	0.66
94_S	108_K	0.562	0.66
109_T	116_I	0.561	0.65
32_G	88_A	0.560	0.65
53_S	57_G	0.558	0.65
17_S	27_N	0.557	0.65
95_F	120_L	0.554	0.65
69_L	75_V	0.550	0.64
45_V	53_S	0.549	0.64
22_D	122_I	0.547	0.64
53_S	68_S	0.543	0.63
60_F	64_T	0.543	0.63
12_A	15_G	0.542	0.63
60_F	65_G	0.540	0.63
81_W	121_T	0.539	0.62
77_L	81_W	0.535	0.62
52_F	58_L	0.534	0.62
6_L	12_A	0.533	0.62
59_G	64_T	0.532	0.61
56_S	59_G	0.529	0.61
23_P	103_G	0.528	0.61
10_L	14_K	0.524	0.60
28_N	31_Y	0.523	0.60
40_I	53_S	0.518	0.59
109_T	131_F	0.513	0.59
31_Y	34_I	0.512	0.59
47_V	50_A	0.510	0.58
5_G	13_L	0.510	0.58
95_F	114_Y	0.510	0.58
9_V	14_K	0.505	0.57
120_L	126_G	0.502	0.57
93_K	111_G	0.500	0.57

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
3j1zP	8	0.9481	37.4	0.874	Contact Map
3h90A	3	0.9481	28.8	0.881	Contact Map
3x29A	1	0.6444	5.1	0.916	Contact Map
4lz6A	1	0.8519	3.5	0.922	Contact Map
2nq2A	2	0.9185	3.3	0.923	Contact Map
4p79A	1	0.7111	3.1	0.924	Contact Map
3v5uA	1	0.4963	2.9	0.925	Contact Map
4g1uA	2	0.9333	2.9	0.925	Contact Map
2qi9A	2	0.9259	2.2	0.93	Contact Map
3w4tA	1	0.8	1.5	0.936	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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