DUF417 - PFAM28P - GREMLIN Contacts

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DUF417 - Protein of unknown function, DUF417

PFAM:	PF04224	Sequences: MKLLELAARLERLGYHLLRYGLVIVLLWIGGLKFTAYEAEGIVPLVANSPLMSWLYPVFSYKYHMNKEGEVPANRAWHEANGVYGFSYLLGVVEILIALLLALGPWSPKLGALGSLLAVGMFLTTLSFLFTTPGVWVPSLGGFPALSGAGQFLLKDVVLLGASLWLLADSAKRIL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	175 (143)
Sequences:	2048 (855)
Seq/√Len:	71.5
META:	0.808

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
115_S	166_L	3.647	1.00
84_Y	88_Y	3.466	1.00
97_I	117_L	3.392	1.00
48_N	132_T	3.034	1.00
100_L	110_L	2.867	1.00
55_L	86_F	2.708	1.00
23_V	102_A	2.573	1.00
18_L	162_A	2.556	1.00
43_V	47_A	2.364	1.00
14_G	168_A	2.221	1.00
23_V	27_L	2.204	1.00
158_V	162_A	2.191	1.00
118_A	163_S	2.184	1.00
111_G	166_L	2.153	1.00
40_E	43_V	2.148	1.00
21_G	161_G	2.045	1.00
119_V	164_L	2.034	1.00
86_F	90_L	2.022	1.00
36_A	40_E	1.876	1.00
97_I	121_M	1.851	1.00
116_L	120_G	1.790	1.00
104_G	111_G	1.790	1.00
17_L	164_L	1.724	1.00
92_V	96_L	1.707	1.00
100_L	114_G	1.674	1.00
119_V	160_L	1.610	0.99
115_S	167_L	1.578	0.99
25_V	158_V	1.577	0.99
26_L	122_F	1.531	0.99
111_G	115_S	1.481	0.99
26_L	121_M	1.450	0.99
121_M	124_T	1.447	0.99
146_L	150_G	1.421	0.99
60_S	82_G	1.399	0.98
116_L	167_L	1.378	0.98
24_I	157_V	1.376	0.98
17_L	161_G	1.364	0.98
34_F	92_V	1.359	0.98
22_L	162_A	1.348	0.98
126_L	130_F	1.333	0.98
36_A	84_Y	1.290	0.97
112_A	167_L	1.285	0.97
115_S	119_V	1.250	0.97
57_P	82_G	1.234	0.96
147_S	150_G	1.233	0.96
39_A	87_S	1.212	0.96
32_L	37_Y	1.205	0.96
27_L	95_I	1.200	0.96
15_Y	165_W	1.164	0.95
94_E	152_F	1.157	0.95
119_V	167_L	1.135	0.94
59_F	82_G	1.126	0.94
135_V	150_G	1.120	0.94
103_L	107_S	1.114	0.94
45_L	153_L	1.110	0.93
32_L	139_S	1.098	0.93
18_L	158_V	1.091	0.93
57_P	85_G	1.082	0.93
20_Y	105_P	1.062	0.92
136_W	141_G	1.061	0.92
93_V	121_M	1.057	0.92
127_S	131_T	1.056	0.92
27_L	98_A	1.054	0.92
120_G	124_T	1.047	0.91
31_G	95_I	1.044	0.91
95_I	99_L	1.040	0.91
43_V	83_V	1.034	0.91
55_L	89_L	1.028	0.91
140_L	145_A	1.027	0.90
148_G	151_Q	1.025	0.90
97_I	118_A	1.017	0.90
42_I	49_S	1.017	0.90
93_V	97_I	1.003	0.89
46_V	86_F	0.999	0.89
93_V	124_T	0.999	0.89
25_V	29_I	0.986	0.89
85_G	89_L	0.986	0.89
9_R	12_R	0.962	0.87
98_A	102_A	0.959	0.87
37_Y	140_L	0.955	0.87
52_M	128_F	0.951	0.87
39_A	42_I	0.944	0.86
29_I	151_Q	0.928	0.85
102_A	105_P	0.926	0.85
118_A	122_F	0.924	0.85
34_F	95_I	0.920	0.85
14_G	164_L	0.918	0.85
88_Y	92_V	0.906	0.84
154_L	158_V	0.903	0.84
28_W	32_L	0.900	0.84
34_F	88_Y	0.888	0.83
104_G	170_S	0.883	0.82
112_A	171_A	0.857	0.81
35_T	41_G	0.856	0.80
19_R	166_L	0.853	0.80
21_G	26_L	0.849	0.80
104_G	169_D	0.847	0.80
82_G	85_G	0.846	0.80
116_L	119_V	0.844	0.79
113_L	117_L	0.841	0.79
19_R	105_P	0.836	0.79
97_I	124_T	0.833	0.79
104_G	107_S	0.823	0.78
42_I	128_F	0.820	0.77
104_G	166_L	0.819	0.77
13_L	16_H	0.815	0.77
26_L	124_T	0.815	0.77
59_F	85_G	0.800	0.76
107_S	110_L	0.799	0.76
40_E	83_V	0.785	0.74
112_A	116_L	0.784	0.74
24_I	28_W	0.780	0.74
29_I	158_V	0.776	0.74
35_T	98_A	0.775	0.73
21_G	29_I	0.774	0.73
46_V	52_M	0.762	0.72
58_V	82_G	0.761	0.72
49_S	54_W	0.760	0.72
96_L	100_L	0.760	0.72
29_I	146_L	0.753	0.71
54_W	58_V	0.752	0.71
99_L	103_L	0.746	0.71
137_V	151_Q	0.743	0.70
20_Y	102_A	0.741	0.70
29_I	154_L	0.733	0.69
37_Y	137_V	0.729	0.69
27_L	102_A	0.728	0.69
123_L	160_L	0.716	0.67
38_E	87_S	0.716	0.67
9_R	13_L	0.713	0.67
50_P	133_P	0.710	0.67
90_L	167_L	0.707	0.66
41_G	148_G	0.705	0.66
22_L	49_S	0.701	0.66
20_Y	165_W	0.697	0.65
13_L	164_L	0.692	0.65
129_L	135_V	0.692	0.65
131_T	135_V	0.690	0.65
137_V	140_L	0.685	0.64
136_W	144_P	0.685	0.64
45_L	149_A	0.679	0.63
28_W	98_A	0.676	0.63
19_R	115_S	0.671	0.62
32_L	146_L	0.668	0.62
132_T	151_Q	0.666	0.62
18_L	161_G	0.665	0.62
36_A	88_Y	0.664	0.62
32_L	145_A	0.659	0.61
136_W	142_G	0.656	0.61
20_Y	161_G	0.656	0.61
94_E	122_F	0.651	0.60
18_L	21_G	0.645	0.59
93_V	96_L	0.643	0.59
26_L	29_I	0.641	0.59
101_L	118_A	0.640	0.59
20_Y	23_V	0.628	0.57
25_V	159_L	0.627	0.57
135_V	149_A	0.625	0.57
105_P	111_G	0.614	0.56
20_Y	115_S	0.612	0.55
97_I	120_G	0.611	0.55
11_E	172_K	0.601	0.54
137_V	145_A	0.601	0.54
49_S	131_T	0.598	0.54
86_F	93_V	0.598	0.54
59_F	89_L	0.598	0.54
42_I	46_V	0.596	0.53
32_L	140_L	0.594	0.53
105_P	170_S	0.586	0.52
58_V	152_F	0.584	0.52
55_L	59_F	0.582	0.52
32_L	137_V	0.581	0.52
165_W	169_D	0.579	0.51
18_L	22_L	0.575	0.51
93_V	114_G	0.575	0.51
32_L	148_G	0.574	0.51
44_P	149_A	0.569	0.50
82_G	86_F	0.568	0.50
39_A	47_A	0.567	0.50
12_R	109_K	0.565	0.50
84_Y	87_S	0.565	0.50
52_M	98_A	0.564	0.50
35_T	145_A	0.561	0.49
49_S	132_T	0.557	0.49
11_E	14_G	0.557	0.49
90_L	93_V	0.554	0.48
102_A	112_A	0.554	0.48
23_V	101_L	0.552	0.48
25_V	146_L	0.551	0.48
19_R	22_L	0.549	0.48
129_L	150_G	0.546	0.47
13_L	17_L	0.546	0.47
100_L	111_G	0.539	0.46
26_L	118_A	0.539	0.46
104_G	108_P	0.537	0.46
11_E	169_D	0.535	0.46
40_E	98_A	0.532	0.46
28_W	154_L	0.529	0.45
28_W	148_G	0.528	0.45
167_L	170_S	0.526	0.45
90_L	121_M	0.515	0.44
30_G	34_F	0.513	0.43
114_G	117_L	0.512	0.43
46_V	56_Y	0.510	0.43
31_G	145_A	0.510	0.43
14_G	26_L	0.509	0.43
17_L	21_G	0.508	0.43
108_P	166_L	0.505	0.42
101_L	115_S	0.505	0.42
53_S	108_P	0.504	0.42
149_A	154_L	0.503	0.42
146_L	151_Q	0.502	0.42
95_I	106_W	0.501	0.42
101_L	104_G	0.500	0.42

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
3rkoL	1	0.7029	7.2	0.963	Contact Map
2fyuK	1	0.3029	5.6	0.965	Contact Map
3wu2Z	1	0.32	3.9	0.968	Contact Map
4he8L	1	0.7029	3.4	0.969	Contact Map
4ezcA	3	0.6286	3	0.969	Contact Map
4bwzA	2	0.3714	2.7	0.97	Contact Map
3tx3A	2	0.6686	2.2	0.971	Contact Map
4q25A	2	0.1771	2.2	0.972	Contact Map
3wajA	1	0.7486	1.6	0.974	Contact Map
4o93A	2	0.48	1.5	0.974	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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