DUF3841 - PFAM28P - GREMLIN Contacts

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DUF3841 - Domain of unknown function (DUF3841)

PFAM:	PF12952	Sequences: RLWTIQPEEVLEELEKTGVLRAKREYIEEKYGEIADIFLEAYDWMVEQMEKRVPKPEGVEYPIWAWYRREGHLPPGEGGVRLELEVPDEEVLLSDFDKWHYVLNYWYLPKDEEDEEAFEKELEKYGIDESDAYLSKGNFYPELKREIEKSWERIFDLDIWDKDKSIQATFWELRKEWVV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	179 (175)
Sequences:	652 (563)
Seq/√Len:	42.6
META:	0.779

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
43_D	61_Y	4.163	1.00
170_F	173_L	4.017	1.00
48_Q	152_E	3.407	1.00
121_E	146_E	3.338	1.00
11_L	15_E	3.318	1.00
48_Q	52_R	3.153	1.00
10_V	20_L	2.886	1.00
149_K	152_E	2.778	1.00
86_V	170_F	2.732	1.00
2_L	168_A	2.700	1.00
111_D	114_D	2.616	1.00
107_Y	114_D	2.457	1.00
48_Q	51_K	2.264	1.00
2_L	65_A	2.175	1.00
73_L	79_G	2.049	0.99
107_Y	150_S	2.016	0.99
15_E	175_K	1.997	0.99
24_R	28_E	1.959	0.99
101_Y	106_W	1.949	0.99
11_L	178_V	1.895	0.99
49_M	169_T	1.888	0.99
14_L	178_V	1.886	0.99
8_E	12_E	1.879	0.99
1_R	85_E	1.841	0.98
109_P	114_D	1.821	0.98
45_M	94_S	1.817	0.98
175_K	178_V	1.795	0.98
65_A	168_A	1.774	0.98
20_L	63_I	1.773	0.98
21_R	58_G	1.766	0.98
86_V	177_W	1.753	0.98
3_W	83_E	1.691	0.97
145_R	149_K	1.689	0.97
88_D	168_A	1.688	0.97
90_E	172_E	1.669	0.97
7_P	10_V	1.630	0.97
174_R	177_W	1.606	0.96
50_E	55_K	1.598	0.96
117_A	146_E	1.591	0.96
100_H	103_L	1.551	0.95
21_R	172_E	1.541	0.95
19_V	58_G	1.540	0.95
19_V	172_E	1.521	0.95
13_E	17_T	1.520	0.95
45_M	169_T	1.477	0.94
173_L	178_V	1.465	0.94
157_L	166_I	1.459	0.94
94_S	100_H	1.424	0.93
102_V	154_I	1.412	0.93
65_A	170_F	1.360	0.91
66_W	96_F	1.356	0.91
22_A	27_I	1.352	0.91
68_R	72_H	1.334	0.90
113_E	117_A	1.305	0.89
2_L	91_V	1.272	0.88
10_V	63_I	1.231	0.86
1_R	89_E	1.208	0.85
65_A	86_V	1.201	0.85
45_M	92_L	1.184	0.84
121_E	143_L	1.183	0.84
23_K	26_Y	1.181	0.84
143_L	147_I	1.179	0.84
138_N	142_E	1.161	0.83
100_H	104_N	1.160	0.83
52_R	152_E	1.133	0.81
49_M	53_V	1.127	0.81
14_L	173_L	1.123	0.81
25_E	146_E	1.121	0.80
128_D	131_D	1.119	0.80
67_Y	93_L	1.110	0.80
108_L	159_I	1.078	0.78
9_E	12_E	1.078	0.78
45_M	49_M	1.076	0.78
143_L	146_E	1.070	0.77
154_I	157_L	1.066	0.77
56_P	59_V	1.052	0.76
95_D	171_W	1.049	0.76
148_E	152_E	1.045	0.75
50_E	56_P	1.014	0.73
71_G	76_G	1.011	0.73
65_A	173_L	1.010	0.73
151_W	155_F	1.004	0.73
135_S	147_I	0.998	0.72
115_E	119_E	0.997	0.72
121_E	125_Y	0.993	0.72
93_L	166_I	0.987	0.71
90_E	177_W	0.984	0.71
116_E	120_K	0.967	0.70
66_W	94_S	0.960	0.69
56_P	171_W	0.949	0.68
49_M	52_R	0.939	0.67
4_T	22_A	0.913	0.65
145_R	148_E	0.912	0.65
49_M	92_L	0.911	0.65
14_L	20_L	0.904	0.64
151_W	154_I	0.897	0.64
98_K	109_P	0.894	0.63
141_P	145_R	0.886	0.63
91_V	168_A	0.875	0.62
54_P	117_A	0.870	0.61
22_A	63_I	0.867	0.61
24_R	43_D	0.863	0.61
160_W	163_D	0.860	0.60
16_K	46_V	0.858	0.60
87_P	177_W	0.858	0.60
96_F	100_H	0.857	0.60
103_L	167_Q	0.857	0.60
76_G	79_G	0.857	0.60
24_R	39_L	0.852	0.60
110_K	153_R	0.850	0.60
94_S	167_Q	0.846	0.59
68_R	71_G	0.845	0.59
38_F	103_L	0.844	0.59
142_E	145_R	0.844	0.59
53_V	101_Y	0.817	0.57
127_I	142_E	0.816	0.56
99_W	151_W	0.810	0.56
81_R	159_I	0.807	0.56
117_A	120_K	0.807	0.56
87_P	90_E	0.797	0.55
47_E	145_R	0.796	0.55
41_A	100_H	0.795	0.54
114_D	117_A	0.794	0.54
51_K	174_R	0.791	0.54
22_A	30_K	0.789	0.54
11_L	14_L	0.789	0.54
44_W	48_Q	0.779	0.53
119_E	123_E	0.775	0.53
41_A	102_V	0.770	0.52
97_D	115_E	0.766	0.52
49_M	94_S	0.764	0.52
101_Y	105_Y	0.758	0.51
140_Y	144_K	0.753	0.50
10_V	22_A	0.752	0.50
119_E	124_K	0.750	0.50
114_D	153_R	0.750	0.50
27_I	31_Y	0.743	0.50
101_Y	109_P	0.739	0.49
98_K	118_F	0.739	0.49
7_P	85_E	0.737	0.49
45_M	103_L	0.735	0.49
11_L	65_A	0.729	0.48
112_E	115_E	0.725	0.48
144_K	148_E	0.723	0.48
57_E	85_E	0.722	0.48
21_R	59_V	0.720	0.47
58_G	168_A	0.713	0.47
112_E	116_E	0.711	0.47
108_L	123_E	0.709	0.46
1_R	83_E	0.701	0.46
9_E	13_E	0.693	0.45
75_P	79_G	0.691	0.45
31_Y	38_F	0.690	0.45
51_K	152_E	0.688	0.44
28_E	87_P	0.684	0.44
92_L	156_D	0.678	0.43
52_R	116_E	0.677	0.43
128_D	134_L	0.676	0.43
6_Q	10_V	0.671	0.43
121_E	142_E	0.669	0.43
11_L	80_V	0.664	0.42
28_E	31_Y	0.663	0.42
33_E	36_D	0.657	0.41
66_W	128_D	0.656	0.41
11_L	175_K	0.648	0.41
113_E	124_K	0.645	0.40
51_K	116_E	0.645	0.40
53_V	106_W	0.644	0.40
37_I	102_V	0.643	0.40
20_L	152_E	0.642	0.40
26_Y	30_K	0.641	0.40
112_E	117_A	0.636	0.40
71_G	75_P	0.634	0.39
63_I	85_E	0.634	0.39
166_I	170_F	0.634	0.39
102_V	158_D	0.633	0.39
55_K	59_V	0.632	0.39
60_E	126_G	0.632	0.39
1_R	15_E	0.631	0.39
19_V	174_R	0.630	0.39
47_E	148_E	0.630	0.39
101_Y	108_L	0.630	0.39
94_S	169_T	0.630	0.39
104_N	108_L	0.629	0.39
89_E	117_A	0.625	0.39
68_R	81_R	0.624	0.39
109_P	115_E	0.622	0.38
30_K	87_P	0.620	0.38
138_N	145_R	0.619	0.38
96_F	167_Q	0.618	0.38
122_L	127_I	0.616	0.38
68_R	73_L	0.616	0.38
27_I	30_K	0.616	0.38
111_D	149_K	0.614	0.38
52_R	158_D	0.613	0.38
104_N	109_P	0.611	0.37
85_E	88_D	0.605	0.37
59_V	178_V	0.602	0.37
45_M	72_H	0.602	0.37
3_W	62_P	0.602	0.37
34_I	37_I	0.601	0.36
2_L	5_I	0.600	0.36
65_A	169_T	0.595	0.36
27_I	39_L	0.589	0.35
22_A	26_Y	0.585	0.35
9_E	21_R	0.583	0.35
45_M	100_H	0.582	0.35
67_Y	102_V	0.581	0.35
58_G	162_K	0.580	0.35
160_W	164_K	0.579	0.35
71_G	81_R	0.577	0.34
101_Y	169_T	0.577	0.34
45_M	69_R	0.575	0.34
111_D	147_I	0.574	0.34
38_F	100_H	0.574	0.34
88_D	177_W	0.574	0.34
98_K	101_Y	0.574	0.34
54_P	135_S	0.572	0.34
90_E	145_R	0.567	0.34
139_F	144_K	0.566	0.33
96_F	154_I	0.565	0.33
71_G	96_F	0.564	0.33
30_K	139_F	0.563	0.33
5_I	68_R	0.558	0.33
113_E	149_K	0.557	0.33
78_G	115_E	0.552	0.32
17_T	57_E	0.551	0.32
107_Y	147_I	0.551	0.32
3_W	95_D	0.550	0.32
70_E	75_P	0.550	0.32
18_G	64_W	0.549	0.32
114_D	122_L	0.547	0.32
71_G	79_G	0.545	0.32
89_E	158_D	0.545	0.32
18_G	175_K	0.544	0.32
2_L	178_V	0.542	0.31
58_G	172_E	0.539	0.31
17_T	25_E	0.539	0.31
66_W	100_H	0.537	0.31
34_I	44_W	0.533	0.31
53_V	173_L	0.528	0.30
2_L	84_L	0.527	0.30
16_K	75_P	0.527	0.30
94_S	154_I	0.526	0.30
73_L	76_G	0.526	0.30
160_W	169_T	0.525	0.30
10_V	82_L	0.521	0.30
77_E	152_E	0.521	0.30
34_I	71_G	0.521	0.30
146_E	177_W	0.519	0.30
67_Y	165_S	0.515	0.29
48_Q	154_I	0.513	0.29
10_V	177_W	0.513	0.29
129_E	167_Q	0.512	0.29
51_K	128_D	0.512	0.29
68_R	75_P	0.512	0.29
8_E	80_V	0.511	0.29
59_V	118_F	0.508	0.29
28_E	39_L	0.506	0.29
60_E	140_Y	0.505	0.29
4_T	15_E	0.504	0.28
11_L	84_L	0.500	0.28

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
3lr0A	2	0.4302	5.1	0.957	Contact Map
4g2kA	3	0.2849	4.7	0.958	Contact Map
3te8A	2	0.4804	4.5	0.959	Contact Map
1h12A	1	0.3575	3.3	0.961	Contact Map
4oayA	2	0.1564	3	0.962	Contact Map
4jprA	3	0.2849	2.8	0.963	Contact Map
1guuA	1	0.2793	2.5	0.964	Contact Map
4n21A	3	0.3073	2.5	0.964	Contact Map
2gzsA	1	0.2626	2.4	0.964	Contact Map
1w36C	1	0.8827	2.3	0.965	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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