DUF3611 - PFAM28P - GREMLIN Contacts

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DUF3611 - Protein of unknown function (DUF3611)

PFAM:	PF12263	Sequences: PPALQRLARAFRRLGWIGFWLQLVLGVVSALLLLFALVFRRSASGTNPGLGFGLFLAIAGLLVLLFSIYWSFRYTRLARRLRSADPALRPSKAEVIRLLRIGLIASLLGMLLSLLGAQAEVGSLLAKALSQPQGVPVIQPTSWVSALDIFVVQANTNTLFAHFVGLVFSLWLLFRVN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	177 (174)
Sequences:	791 (574)
Seq/√Len:	43.5
META:	0.671

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
16_W	75_T	4.773	1.00
153_Q	157_N	3.600	1.00
74_Y	102_G	3.352	1.00
66_F	105_A	3.320	1.00
139_Q	142_S	3.317	1.00
70_W	102_G	3.079	1.00
75_T	78_A	3.054	1.00
60_G	113_S	2.923	1.00
171_W	175_R	2.571	1.00
129_L	133_Q	2.387	1.00
85_D	88_L	2.307	1.00
14_L	168_F	2.254	1.00
66_F	70_W	2.232	1.00
77_L	95_V	2.136	1.00
99_L	169_S	2.022	0.99
133_Q	137_V	2.018	0.99
140_P	143_W	2.002	0.99
106_S	122_G	1.970	0.99
47_N	53_G	1.954	0.99
125_L	149_I	1.916	0.99
72_F	75_T	1.873	0.99
65_L	68_I	1.829	0.98
35_F	126_A	1.801	0.98
102_G	172_L	1.692	0.97
57_A	151_V	1.641	0.97
26_G	64_L	1.612	0.97
133_Q	138_I	1.606	0.96
50_L	53_G	1.604	0.96
73_R	90_P	1.579	0.96
116_G	162_H	1.535	0.95
132_P	136_P	1.530	0.95
132_P	135_V	1.513	0.95
47_N	50_L	1.512	0.95
53_G	101_I	1.506	0.95
169_S	172_L	1.501	0.95
59_A	63_V	1.478	0.94
162_H	165_G	1.470	0.94
119_A	122_G	1.438	0.94
67_S	162_H	1.420	0.93
114_L	165_G	1.400	0.93
114_L	163_F	1.352	0.91
137_V	144_V	1.336	0.91
125_L	133_Q	1.328	0.90
122_G	153_Q	1.324	0.90
125_L	150_F	1.304	0.90
8_A	78_A	1.299	0.89
55_F	59_A	1.298	0.89
129_L	148_D	1.288	0.89
8_A	152_V	1.286	0.89
64_L	144_V	1.263	0.88
126_A	159_L	1.259	0.88
62_L	66_F	1.259	0.88
92_K	95_V	1.252	0.88
14_L	21_L	1.250	0.88
134_G	137_V	1.247	0.87
81_L	154_A	1.247	0.87
32_L	56_L	1.241	0.87
12_R	78_A	1.228	0.87
124_L	152_V	1.220	0.86
142_S	146_A	1.220	0.86
67_S	106_S	1.207	0.86
36_A	149_I	1.195	0.85
18_G	71_S	1.161	0.83
154_A	157_N	1.152	0.83
15_G	74_Y	1.150	0.83
118_Q	157_N	1.143	0.82
15_G	18_G	1.138	0.82
39_F	129_L	1.128	0.82
56_L	145_S	1.122	0.81
70_W	101_I	1.120	0.81
41_R	78_A	1.117	0.81
3_A	8_A	1.113	0.81
132_P	137_V	1.110	0.80
16_W	76_R	1.101	0.80
136_P	140_P	1.092	0.79
91_S	176_V	1.091	0.79
25_L	69_Y	1.090	0.79
123_S	127_K	1.086	0.79
121_V	153_Q	1.074	0.78
7_L	11_F	1.059	0.77
4_L	89_R	1.057	0.77
34_L	43_A	1.054	0.77
159_L	165_G	1.039	0.76
23_L	85_D	1.034	0.76
109_G	162_H	1.021	0.75
118_Q	156_T	1.020	0.75
16_W	22_Q	1.017	0.74
112_L	151_V	0.997	0.73
25_L	119_A	0.990	0.72
157_N	168_F	0.985	0.72
118_Q	160_F	0.980	0.72
114_L	160_F	0.957	0.70
12_R	16_W	0.954	0.69
47_N	54_L	0.952	0.69
29_S	125_L	0.949	0.69
130_S	136_P	0.942	0.68
31_L	96_I	0.938	0.68
136_P	143_W	0.936	0.68
122_G	154_A	0.936	0.68
20_W	75_T	0.934	0.68
156_T	166_L	0.931	0.68
123_S	149_I	0.920	0.67
86_P	121_V	0.920	0.67
8_A	124_L	0.918	0.66
7_L	17_I	0.918	0.66
90_P	105_A	0.917	0.66
57_A	155_N	0.911	0.66
16_W	124_L	0.909	0.66
70_W	74_Y	0.895	0.64
135_V	150_F	0.891	0.64
5_Q	9_R	0.881	0.63
14_L	18_G	0.877	0.63
124_L	149_I	0.876	0.63
145_S	149_I	0.867	0.62
20_W	24_V	0.867	0.62
30_A	89_R	0.867	0.62
151_V	155_N	0.866	0.62
50_L	54_L	0.866	0.62
33_L	37_L	0.848	0.60
120_E	148_D	0.847	0.60
108_L	112_L	0.844	0.60
64_L	106_S	0.843	0.60
32_L	152_V	0.841	0.60
63_V	105_A	0.840	0.60
89_R	95_V	0.839	0.59
36_A	123_S	0.839	0.59
131_Q	143_W	0.837	0.59
36_A	40_R	0.827	0.58
25_L	28_V	0.826	0.58
85_D	144_V	0.804	0.56
11_F	99_L	0.801	0.56
64_L	153_Q	0.799	0.56
101_I	125_L	0.798	0.56
76_R	93_A	0.794	0.55
130_S	147_L	0.794	0.55
27_V	95_V	0.787	0.55
11_F	38_V	0.787	0.55
34_L	62_L	0.787	0.55
34_L	159_L	0.784	0.54
5_Q	8_A	0.775	0.53
116_G	127_K	0.773	0.53
39_F	42_S	0.768	0.53
26_G	145_S	0.767	0.53
131_Q	138_I	0.763	0.52
30_A	174_F	0.758	0.52
13_R	78_A	0.757	0.52
15_G	165_G	0.752	0.51
120_E	145_S	0.750	0.51
144_V	175_R	0.744	0.50
145_S	151_V	0.735	0.50
82_R	86_P	0.731	0.49
61_L	65_L	0.727	0.49
31_L	150_F	0.725	0.49
7_L	10_A	0.718	0.48
125_L	129_L	0.717	0.48
23_L	96_I	0.716	0.48
52_F	93_A	0.711	0.47
135_V	138_I	0.710	0.47
120_E	152_V	0.710	0.47
28_V	53_G	0.708	0.47
114_L	122_G	0.707	0.47
96_I	161_A	0.706	0.47
90_P	94_E	0.705	0.47
143_W	149_I	0.704	0.47
71_S	97_R	0.700	0.46
107_L	165_G	0.692	0.45
3_A	38_V	0.691	0.45
3_A	6_R	0.690	0.45
72_F	92_K	0.687	0.45
17_I	26_G	0.685	0.45
113_S	134_G	0.680	0.44
88_L	166_L	0.677	0.44
161_A	164_V	0.672	0.44
11_F	70_W	0.672	0.44
17_I	27_V	0.672	0.44
113_S	176_V	0.665	0.43
70_W	176_V	0.665	0.43
10_A	13_R	0.664	0.43
64_L	173_L	0.663	0.43
120_E	143_W	0.662	0.43
86_P	158_T	0.662	0.43
6_R	110_M	0.659	0.42
20_W	35_F	0.655	0.42
24_V	111_L	0.648	0.41
107_L	122_G	0.646	0.41
7_L	15_G	0.646	0.41
91_S	96_I	0.645	0.41
110_M	160_F	0.643	0.41
31_L	114_L	0.638	0.40
39_F	145_S	0.636	0.40
60_G	161_A	0.632	0.40
72_F	80_R	0.631	0.40
7_L	92_K	0.626	0.39
155_N	162_H	0.626	0.39
85_D	91_S	0.625	0.39
63_V	135_V	0.622	0.39
98_L	156_T	0.621	0.39
84_A	95_V	0.617	0.39
39_F	134_G	0.617	0.39
28_V	61_L	0.614	0.38
121_V	142_S	0.613	0.38
10_A	86_P	0.610	0.38
7_L	30_A	0.609	0.38
116_G	128_A	0.609	0.38
58_I	107_L	0.608	0.38
78_A	82_R	0.608	0.38
115_L	119_A	0.605	0.37
137_V	140_P	0.598	0.37
51_G	54_L	0.596	0.37
23_L	68_I	0.592	0.36
62_L	153_Q	0.591	0.36
58_I	161_A	0.585	0.36
64_L	166_L	0.579	0.35
131_Q	144_V	0.574	0.35
60_G	150_F	0.571	0.34
141_T	166_L	0.569	0.34
35_F	147_L	0.568	0.34
10_A	32_L	0.568	0.34
116_G	139_Q	0.563	0.34
34_L	130_S	0.562	0.34
92_K	99_L	0.561	0.34
14_L	66_F	0.560	0.33
96_I	176_V	0.559	0.33
28_V	31_L	0.559	0.33
64_L	143_W	0.558	0.33
110_M	115_L	0.558	0.33
40_R	111_L	0.558	0.33
61_L	89_R	0.555	0.33
38_V	124_L	0.553	0.33
21_L	164_V	0.552	0.33
159_L	163_F	0.541	0.32
113_S	128_A	0.541	0.32
26_G	62_L	0.538	0.32
99_L	114_L	0.537	0.32
57_A	158_T	0.532	0.31
24_V	68_I	0.532	0.31
124_L	137_V	0.532	0.31
149_I	160_F	0.531	0.31
47_N	51_G	0.529	0.31
56_L	129_L	0.529	0.31
161_A	165_G	0.528	0.31
154_A	167_V	0.528	0.31
18_G	165_G	0.524	0.30
133_Q	143_W	0.523	0.30
119_A	123_S	0.523	0.30
128_A	162_H	0.519	0.30
101_I	107_L	0.518	0.30
122_G	157_N	0.516	0.30
144_V	150_F	0.516	0.30
109_G	116_G	0.516	0.30
12_R	34_L	0.516	0.30
10_A	141_T	0.515	0.30
144_V	148_D	0.512	0.30
81_L	117_A	0.512	0.30
4_L	92_K	0.509	0.29
7_L	168_F	0.508	0.29
26_G	126_A	0.508	0.29
87_A	147_L	0.507	0.29
9_R	111_L	0.502	0.29
94_E	115_L	0.500	0.29
70_W	75_T	0.500	0.29

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
3ayfA	2	0.887	34.1	0.939	Contact Map
3o7qA	1	0.8983	13.6	0.949	Contact Map
2m20A	2	0.2938	7.8	0.955	Contact Map
4ev6A	3	0.3785	7.8	0.955	Contact Map
2ljbA	3	0.1412	7.6	0.955	Contact Map
2l2tA	2	0.2486	6.7	0.956	Contact Map
3s8fA	1	0.774	6.4	0.956	Contact Map
4i0uA	4	0.3672	6	0.957	Contact Map
1ytrA	1	0.0904	5.3	0.958	Contact Map
3bkdA	4	0.1412	4.8	0.959	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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