DUF4390 - PFAM28P - GREMLIN Contacts

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DUF4390 - Domain of unknown function (DUF4390)

PFAM:	PF14334	Sequences: AEGIEIRSAELELSDGGLLLSARLDFALSPELEEALQSGVPLTFVLEVELYRPRWYWFDEKVASLTRRYRLSYHALTRQYRVSRGGSGGLQQSFASLEEALRALGRVRGWPVADLSLLEPGERYYVRVRARLDTSQLPKPLQLLAFFSSDWDLESDWYRWT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	161 (157)
Sequences:	7491 (4949)
Seq/√Len:	395.0
META:	0.936

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
94_F	103_A	3.566	1.00
37_Q	80_Y	3.295	1.00
52_R	60_E	2.765	1.00
129_R	157_W	2.579	1.00
49_E	127_R	2.463	1.00
71_L	100_A	2.328	1.00
7_R	25_D	2.261	1.00
114_D	117_L	2.215	1.00
47_E	131_R	2.145	1.00
51_Y	61_K	2.000	1.00
46_L	130_A	1.973	1.00
33_E	37_Q	1.952	1.00
46_L	69_Y	1.948	1.00
96_S	99_E	1.911	1.00
22_A	128_V	1.904	1.00
49_E	64_S	1.896	1.00
17_G	111_P	1.879	1.00
61_K	64_S	1.828	1.00
127_R	159_R	1.795	1.00
79_Q	95_A	1.782	1.00
54_R	59_D	1.771	1.00
82_V	103_A	1.726	1.00
29_S	32_L	1.718	1.00
45_V	68_R	1.712	1.00
23_R	106_R	1.693	1.00
51_Y	59_D	1.682	1.00
92_Q	103_A	1.663	1.00
49_E	61_K	1.660	1.00
51_Y	125_Y	1.653	1.00
45_V	66_T	1.629	1.00
47_E	129_R	1.629	1.00
48_V	126_V	1.610	1.00
51_Y	127_R	1.608	1.00
107_V	110_W	1.586	1.00
41_P	70_R	1.525	1.00
22_A	107_V	1.519	1.00
82_V	100_A	1.469	1.00
36_L	42_L	1.468	1.00
8_S	23_R	1.465	1.00
26_F	105_G	1.450	1.00
52_R	122_E	1.444	1.00
12_E	21_S	1.416	1.00
62_V	124_Y	1.394	1.00
97_L	101_L	1.365	1.00
21_S	109_G	1.359	1.00
119_E	122_E	1.352	1.00
102_R	105_G	1.337	1.00
28_L	101_L	1.336	1.00
30_P	33_E	1.315	1.00
81_R	93_S	1.302	1.00
6_I	24_L	1.301	1.00
24_L	130_A	1.299	1.00
53_P	125_Y	1.290	1.00
32_L	42_L	1.277	1.00
14_S	19_L	1.262	1.00
73_Y	78_R	1.246	1.00
50_L	118_L	1.245	1.00
9_A	158_Y	1.242	1.00
23_R	108_R	1.241	1.00
149_S	152_D	1.229	1.00
125_Y	159_R	1.190	1.00
69_Y	84_R	1.184	1.00
47_E	66_T	1.179	1.00
139_K	142_Q	1.168	1.00
37_Q	97_L	1.164	1.00
121_G	124_Y	1.159	1.00
33_E	97_L	1.147	1.00
59_D	125_Y	1.138	1.00
54_R	60_E	1.138	1.00
49_E	157_W	1.127	1.00
140_P	143_L	1.124	1.00
4_I	24_L	1.124	1.00
144_L	147_F	1.107	1.00
30_P	34_E	1.104	1.00
79_Q	93_S	1.103	1.00
126_V	130_A	1.101	1.00
43_T	68_R	1.101	1.00
46_L	107_V	1.092	1.00
72_S	83_S	1.090	1.00
17_G	114_D	1.086	1.00
6_I	9_A	1.082	1.00
113_A	117_L	1.082	1.00
118_L	124_Y	1.082	1.00
13_L	115_L	1.065	1.00
50_L	113_A	1.046	1.00
6_I	128_V	1.043	1.00
45_V	131_R	1.034	1.00
70_R	83_S	1.024	1.00
118_L	121_G	1.023	1.00
119_E	124_Y	1.008	1.00
145_A	148_S	0.996	1.00
83_S	91_Q	0.991	1.00
72_S	81_R	0.984	1.00
26_F	130_A	0.966	1.00
36_L	71_L	0.964	1.00
127_R	157_W	0.959	1.00
102_R	106_R	0.938	1.00
34_E	37_Q	0.931	1.00
11_L	20_L	0.917	1.00
11_L	126_V	0.916	1.00
137_L	140_P	0.912	1.00
4_I	44_F	0.912	1.00
31_E	34_E	0.909	1.00
56_Y	59_D	0.908	1.00
16_G	115_L	0.895	1.00
19_L	109_G	0.886	1.00
133_D	136_Q	0.877	1.00
27_A	105_G	0.867	1.00
135_S	146_F	0.859	1.00
54_R	57_W	0.855	1.00
68_R	85_G	0.845	1.00
94_F	101_L	0.839	1.00
82_V	104_L	0.834	1.00
42_L	132_L	0.832	1.00
71_L	101_L	0.825	1.00
32_L	44_F	0.823	1.00
33_E	101_L	0.819	1.00
10_E	21_S	0.818	1.00
13_L	17_G	0.809	1.00
48_V	110_W	0.801	1.00
120_P	123_R	0.799	1.00
87_S	90_L	0.791	1.00
6_I	130_A	0.783	1.00
43_T	70_R	0.781	1.00
139_K	143_L	0.777	1.00
74_H	81_R	0.768	1.00
4_I	155_S	0.765	1.00
74_H	79_Q	0.764	1.00
18_L	36_L	0.760	1.00
74_H	77_T	0.756	1.00
85_G	88_G	0.751	1.00
18_L	115_L	0.751	1.00
24_L	46_L	0.750	1.00
84_R	87_S	0.750	1.00
28_L	33_E	0.749	1.00
82_V	94_F	0.748	1.00
5_E	25_D	0.748	1.00
12_E	109_G	0.745	1.00
128_V	157_W	0.743	1.00
96_S	100_A	0.726	1.00
81_R	91_Q	0.724	1.00
77_T	81_R	0.716	1.00
67_R	110_W	0.714	1.00
12_E	19_L	0.705	1.00
134_T	145_A	0.704	1.00
46_L	128_V	0.703	1.00
113_A	118_L	0.700	1.00
71_L	104_L	0.695	1.00
21_S	108_R	0.694	1.00
9_A	22_A	0.689	1.00
143_L	153_L	0.686	0.99
35_A	42_L	0.684	0.99
148_S	152_D	0.681	0.99
133_D	151_W	0.681	0.99
9_A	128_V	0.680	0.99
120_P	124_Y	0.674	0.99
137_L	142_Q	0.671	0.99
44_F	100_A	0.671	0.99
136_Q	143_L	0.664	0.99
99_E	102_R	0.664	0.99
139_K	144_L	0.664	0.99
90_L	93_S	0.659	0.99
10_E	13_L	0.658	0.99
65_L	110_W	0.654	0.99
97_L	100_A	0.653	0.99
98_E	102_R	0.648	0.99
7_R	10_E	0.648	0.99
69_Y	104_L	0.642	0.99
71_L	97_L	0.642	0.99
44_F	104_L	0.641	0.99
11_L	112_V	0.639	0.99
134_T	152_D	0.635	0.99
144_L	152_D	0.634	0.99
74_H	110_W	0.634	0.99
50_L	124_Y	0.633	0.99
9_A	126_V	0.630	0.99
104_L	130_A	0.630	0.99
44_F	105_G	0.630	0.99
34_E	38_S	0.629	0.99
94_F	99_E	0.629	0.99
32_L	35_A	0.625	0.99
138_P	151_W	0.624	0.99
36_L	80_Y	0.623	0.99
28_L	32_L	0.618	0.99
76_L	140_P	0.616	0.99
136_Q	146_F	0.613	0.99
20_L	48_V	0.611	0.99
69_Y	86_G	0.608	0.99
129_R	156_D	0.606	0.99
63_A	117_L	0.605	0.99
20_L	126_V	0.603	0.99
14_S	115_L	0.601	0.99
31_E	150_D	0.598	0.99
13_L	18_L	0.597	0.99
71_L	82_V	0.589	0.98
48_V	128_V	0.586	0.98
48_V	112_V	0.580	0.98
136_Q	142_Q	0.580	0.98
14_S	109_G	0.578	0.98
39_G	76_L	0.574	0.98
135_S	145_A	0.574	0.98
18_L	113_A	0.574	0.98
101_L	105_G	0.572	0.98
13_L	21_S	0.568	0.98
76_L	79_Q	0.565	0.98
66_T	133_D	0.565	0.98
41_P	72_S	0.564	0.98
92_Q	108_R	0.563	0.98
130_A	144_L	0.563	0.98
148_S	155_S	0.561	0.98
141_L	153_L	0.560	0.98
114_D	118_L	0.558	0.98
35_A	40_V	0.551	0.98
55_W	59_D	0.549	0.98
14_S	17_G	0.547	0.97
147_F	150_D	0.547	0.97
62_V	77_T	0.545	0.97
45_V	133_D	0.544	0.97
140_P	145_A	0.541	0.97
134_T	146_F	0.540	0.97
40_V	142_Q	0.534	0.97
78_R	95_A	0.531	0.97
52_R	57_W	0.527	0.97
135_S	144_L	0.515	0.96
101_L	104_L	0.514	0.96
8_S	21_S	0.512	0.96
70_R	81_R	0.512	0.96
98_E	106_R	0.512	0.96
54_R	58_F	0.511	0.96
43_T	104_L	0.511	0.96
65_L	114_D	0.509	0.96
47_E	64_S	0.508	0.96
145_A	149_S	0.507	0.96
6_I	22_A	0.503	0.96
67_R	84_R	0.502	0.96
144_L	148_S	0.500	0.96

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
2xcmC	1	0.3727	4.1	0.935	Contact Map
1sh8A	2	0.4534	4.1	0.935	Contact Map
4qqdA	1	0.6149	3.6	0.937	Contact Map
2llgA	1	0.4348	3.5	0.937	Contact Map
4pbdA	1	0.5839	3.4	0.937	Contact Map
3eudA	1	0.5963	3.3	0.938	Contact Map
4gioA	1	0.4658	3.3	0.938	Contact Map
2ffgA	1	0.4783	2.9	0.94	Contact Map
1y8xB	1	0.3665	2.8	0.94	Contact Map
4alzA	1	0.3354	2.7	0.941	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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