DUF359 - PFAM28P - GREMLIN Contacts

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DUF359 - Protein of unknown function (DUF359)

PFAM:	PF04019	Sequences: VTENLLKAGIIPDLAIVDGKTKRKPVDPEVKIKIELIKSKFEKVLRVKNPPGTITEELWEAIKEALKSKEPVLIVVDGEEDLLVLPAILLAPEGSVVVYGQPGEGVVVVKVTEEKKEKARELLKRME	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	127 (123)
Sequences:	3261 (2367)
Seq/√Len:	213.4
META:	0.924

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
58_L	83_L	5.294	1.00
22_K	103_G	3.742	1.00
101_Q	107_V	3.293	1.00
48_K	77_D	3.043	1.00
50_P	55_T	2.946	1.00
115_K	118_K	2.700	1.00
2_T	15_A	2.347	1.00
3_E	7_K	2.190	1.00
93_E	116_K	2.076	1.00
45_L	72_V	2.069	1.00
47_V	76_V	1.926	1.00
59_W	90_L	1.896	1.00
46_R	75_V	1.814	1.00
17_V	73_L	1.789	1.00
96_V	108_V	1.767	1.00
46_R	77_D	1.726	1.00
87_A	91_A	1.656	1.00
109_V	115_K	1.633	1.00
92_P	95_S	1.600	1.00
63_K	90_L	1.580	1.00
98_V	108_V	1.561	1.00
97_V	111_V	1.548	1.00
61_A	74_I	1.530	1.00
19_G	75_V	1.525	1.00
88_I	119_A	1.485	1.00
42_E	71_P	1.476	1.00
65_A	74_I	1.412	1.00
47_V	61_A	1.404	1.00
98_V	106_V	1.392	1.00
44_V	75_V	1.388	1.00
16_I	62_I	1.379	1.00
101_Q	104_E	1.379	1.00
88_I	97_V	1.377	1.00
61_A	65_A	1.366	1.00
5_L	98_V	1.349	1.00
120_R	124_K	1.321	1.00
16_I	87_A	1.304	1.00
93_E	113_E	1.301	1.00
15_A	73_L	1.297	1.00
12_P	15_A	1.287	1.00
65_A	72_V	1.262	1.00
91_A	95_S	1.236	1.00
84_V	88_I	1.234	1.00
1_V	4_N	1.216	1.00
66_L	91_A	1.213	1.00
54_I	83_L	1.196	1.00
112_T	115_K	1.157	1.00
50_P	53_T	1.153	1.00
45_L	61_A	1.147	1.00
117_E	121_E	1.143	1.00
85_L	119_A	1.142	1.00
6_L	12_P	1.100	1.00
87_A	97_V	1.081	1.00
17_V	75_V	1.077	1.00
66_L	87_A	1.052	1.00
44_V	73_L	1.041	1.00
62_I	87_A	1.035	1.00
1_V	106_V	1.024	1.00
84_V	97_V	1.024	1.00
1_V	98_V	1.015	1.00
41_F	73_L	1.014	1.00
115_K	119_A	1.006	1.00
121_E	125_R	1.005	1.00
93_E	112_T	1.004	1.00
4_N	7_K	1.004	1.00
14_L	65_A	0.999	1.00
99_Y	107_V	0.993	1.00
4_N	106_V	0.981	1.00
16_I	74_I	0.978	1.00
89_L	120_R	0.975	1.00
3_E	26_V	0.970	1.00
88_I	109_V	0.969	1.00
4_N	8_A	0.946	1.00
13_D	71_P	0.934	0.99
48_K	57_E	0.932	0.99
13_D	95_S	0.928	0.99
89_L	123_L	0.927	0.99
43_K	70_E	0.918	0.99
47_V	55_T	0.891	0.99
21_T	24_K	0.887	0.99
26_V	30_V	0.887	0.99
57_E	61_A	0.869	0.99
20_K	25_P	0.864	0.99
123_L	126_M	0.864	0.99
10_I	13_D	0.855	0.99
54_I	62_I	0.854	0.99
117_E	120_R	0.853	0.99
21_T	26_V	0.851	0.99
56_E	60_E	0.847	0.99
43_K	72_V	0.828	0.99
20_K	51_P	0.826	0.99
118_K	122_L	0.822	0.99
55_T	58_L	0.800	0.98
84_V	101_Q	0.795	0.98
121_E	124_K	0.781	0.98
86_P	89_L	0.778	0.98
61_A	64_E	0.772	0.98
14_L	62_I	0.752	0.98
5_L	106_V	0.752	0.98
47_V	58_L	0.752	0.98
45_L	65_A	0.752	0.98
54_I	59_W	0.751	0.98
9_G	12_P	0.748	0.97
62_I	74_I	0.718	0.97
88_I	111_V	0.708	0.96
91_A	111_V	0.700	0.96
89_L	119_A	0.700	0.96
55_T	83_L	0.696	0.96
6_L	41_F	0.693	0.96
82_L	101_Q	0.692	0.96
101_Q	105_G	0.690	0.96
5_L	8_A	0.689	0.96
54_I	86_P	0.689	0.96
47_V	57_E	0.687	0.96
14_L	87_A	0.683	0.96
85_L	89_L	0.675	0.95
49_N	65_A	0.672	0.95
11_I	71_P	0.671	0.95
85_L	88_I	0.671	0.95
114_E	117_E	0.670	0.95
14_L	66_L	0.668	0.95
59_W	86_P	0.653	0.94
5_L	12_P	0.652	0.94
17_V	42_E	0.651	0.94
6_L	11_I	0.651	0.94
29_E	32_I	0.647	0.94
15_A	106_V	0.647	0.94
94_G	111_V	0.643	0.94
84_V	89_L	0.641	0.94
52_G	105_G	0.640	0.94
47_V	65_A	0.640	0.94
94_G	110_K	0.640	0.94
97_V	109_V	0.639	0.94
39_S	42_E	0.637	0.94
76_V	80_E	0.631	0.93
113_E	116_K	0.630	0.93
22_K	102_P	0.626	0.93
5_L	10_I	0.622	0.93
102_P	105_G	0.617	0.93
42_E	73_L	0.606	0.92
6_L	15_A	0.604	0.92
84_V	87_A	0.593	0.91
122_L	126_M	0.591	0.91
21_T	80_E	0.588	0.91
40_K	46_R	0.585	0.91
60_E	70_E	0.575	0.90
43_K	68_S	0.572	0.90
57_E	60_E	0.571	0.89
3_E	30_V	0.570	0.89
60_E	64_E	0.566	0.89
111_V	116_K	0.563	0.89
77_D	96_V	0.561	0.89
84_V	109_V	0.561	0.89
8_A	103_G	0.561	0.89
111_V	119_A	0.556	0.88
84_V	119_A	0.554	0.88
102_P	107_V	0.553	0.88
39_S	46_R	0.551	0.88
11_I	15_A	0.544	0.87
27_D	44_V	0.544	0.87
67_K	114_E	0.543	0.87
16_I	83_L	0.542	0.87
72_V	75_V	0.540	0.87
45_L	64_E	0.539	0.87
88_I	116_K	0.536	0.86
8_A	106_V	0.535	0.86
44_V	62_I	0.534	0.86
88_I	115_K	0.534	0.86
8_A	21_T	0.534	0.86
3_E	104_E	0.527	0.85
49_N	98_V	0.524	0.85
84_V	122_L	0.524	0.85
49_N	53_T	0.520	0.85
2_T	6_L	0.516	0.84
9_G	121_E	0.514	0.84
4_N	96_V	0.514	0.84
5_L	13_D	0.510	0.84
104_E	107_V	0.507	0.83
110_K	126_M	0.507	0.83
50_P	65_A	0.506	0.83
114_E	126_M	0.506	0.83
64_E	68_S	0.506	0.83
68_S	72_V	0.503	0.83
93_E	111_V	0.500	0.82

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
3oryA	3	0.9685	87.6	0.869	Contact Map
1rxwA	1	0.9449	86.1	0.872	Contact Map
4wa8A	1	0.7323	85	0.874	Contact Map
2izoA	1	0.6693	82.8	0.878	Contact Map
1a76A	1	0.9685	77.9	0.883	Contact Map
1b43A	2	0.9606	61.6	0.896	Contact Map
4q0wA	1	0.8661	39.8	0.909	Contact Map
1ul1X	1	0.8031	31.9	0.914	Contact Map
3q8kA	1	0.9685	31.6	0.914	Contact Map
2p62A	2	0.4173	31.4	0.914	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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