DUF3011 - PFAM28P - GREMLIN Contacts

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DUF3011 - Protein of unknown function (DUF3011)

PFAM:	PF11218	Sequences: VVRCESDDGRRRECPADTRGGVRLVRQLSDSPCIEGRTWGYDRGGIWVDRGCRAEFAVGGGGGGGGGGQTVRCESDDGRRRYCPADTRGGPVRLVRQLSGSPCVEGRTWGYDRGGIWVDRGCRAEFAVGGGGGGGGGGGGQTVTCESDDGRRRYCGADTRGGVRLVRQLSDSPCVEGRTWGYDRNGIWVDRGCRAEF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	197 (195)
Sequences:	671 (524)
Seq/√Len:	37.5
META:	0.893

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
110_G	117_W	2.813	1.00
40_G	47_W	2.778	1.00
30_D	100_G	2.621	1.00
18_T	21_G	2.577	1.00
165_L	195_A	2.522	1.00
93_R	127_A	2.510	1.00
100_G	171_D	2.380	1.00
179_T	191_R	2.287	0.99
101_S	172_S	2.264	0.99
82_Y	112_D	2.182	0.99
31_S	101_S	2.165	0.99
17_D	21_G	2.106	0.99
169_L	196_E	2.095	0.99
5_E	28_L	2.092	0.99
158_D	162_G	2.058	0.99
175_V	178_R	2.042	0.99
13_E	42_D	2.038	0.99
32_P	102_P	2.025	0.99
98_L	169_L	2.017	0.99
152_R	190_D	2.001	0.99
183_D	186_G	1.959	0.98
24_L	94_L	1.950	0.98
172_S	179_T	1.927	0.98
37_R	107_R	1.913	0.98
74_E	146_E	1.892	0.98
87_T	90_G	1.867	0.98
18_T	22_V	1.839	0.98
42_D	45_G	1.832	0.98
167_R	196_E	1.823	0.97
9_G	78_G	1.806	0.97
35_E	105_E	1.774	0.97
94_L	124_A	1.749	0.97
31_S	38_T	1.715	0.96
78_G	150_G	1.712	0.96
5_E	146_E	1.710	0.96
41_Y	111_Y	1.701	0.96
159_T	162_G	1.683	0.96
101_S	108_T	1.679	0.96
25_V	57_A	1.624	0.95
28_L	98_L	1.621	0.95
104_V	107_R	1.602	0.95
148_D	153_R	1.590	0.94
50_R	120_R	1.583	0.94
181_G	188_W	1.554	0.94
157_A	162_G	1.529	0.93
23_R	57_A	1.527	0.93
95_V	127_A	1.519	0.93
35_E	41_Y	1.517	0.93
31_S	172_S	1.489	0.92
159_T	182_Y	1.485	0.92
26_R	55_E	1.468	0.91
74_E	98_L	1.449	0.91
30_D	171_D	1.445	0.91
49_D	119_D	1.443	0.91
34_I	37_R	1.437	0.91
108_T	120_R	1.403	0.90
28_L	55_E	1.397	0.89
86_D	90_G	1.382	0.89
154_Y	183_D	1.380	0.89
87_T	92_V	1.373	0.88
11_R	152_R	1.365	0.88
96_R	125_E	1.352	0.88
125_E	196_E	1.343	0.87
38_T	108_T	1.306	0.86
178_R	191_R	1.295	0.85
53_R	123_R	1.283	0.85
9_G	150_G	1.282	0.85
74_E	123_R	1.277	0.85
175_V	179_T	1.269	0.84
156_G	159_T	1.263	0.84
28_L	169_L	1.244	0.83
3_R	28_L	1.222	0.82
11_R	42_D	1.219	0.82
159_T	163_V	1.209	0.81
72_R	144_T	1.200	0.81
123_R	194_R	1.194	0.80
98_L	125_E	1.186	0.80
11_R	80_R	1.184	0.80
13_E	45_G	1.182	0.80
103_C	122_C	1.167	0.79
143_V	187_I	1.160	0.78
52_C	56_F	1.151	0.78
40_G	110_G	1.145	0.77
162_G	182_Y	1.143	0.77
53_R	194_R	1.138	0.77
82_Y	114_G	1.130	0.76
144_T	169_L	1.128	0.76
11_R	49_D	1.126	0.76
106_G	177_G	1.120	0.76
173_P	179_T	1.108	0.75
45_G	115_G	1.106	0.75
32_P	38_T	1.103	0.75
16_A	58_V	1.086	0.73
58_V	128_V	1.084	0.73
22_V	40_G	1.075	0.73
72_R	98_L	1.070	0.72
108_T	195_A	1.062	0.72
29_S	170_S	1.052	0.71
80_R	119_D	1.050	0.71
3_R	26_R	1.048	0.71
144_T	196_E	1.047	0.71
87_T	111_Y	1.044	0.70
74_E	169_L	1.040	0.70
7_D	12_R	1.039	0.70
5_E	74_E	1.038	0.70
158_D	163_V	1.032	0.70
13_E	82_Y	1.013	0.68
149_D	153_R	1.000	0.67
142_T	183_D	0.993	0.67
37_R	50_R	0.976	0.65
77_D	149_D	0.973	0.65
73_C	83_C	0.971	0.65
94_L	165_L	0.968	0.65
82_Y	115_G	0.959	0.64
47_W	117_W	0.948	0.63
99_S	123_R	0.948	0.63
97_Q	102_P	0.944	0.63
76_D	148_D	0.943	0.62
47_W	110_G	0.934	0.62
66_G	137_G	0.929	0.61
43_R	113_R	0.928	0.61
179_T	190_D	0.923	0.61
79_R	151_R	0.922	0.61
82_Y	154_Y	0.918	0.60
38_T	50_R	0.916	0.60
81_R	153_R	0.915	0.60
39_W	46_I	0.914	0.60
107_R	120_R	0.914	0.60
36_G	177_G	0.902	0.59
77_D	119_D	0.894	0.58
24_L	54_A	0.891	0.58
8_D	12_R	0.890	0.58
48_V	52_C	0.879	0.57
7_D	76_D	0.871	0.56
70_T	95_V	0.862	0.56
193_C	197_F	0.860	0.55
17_D	59_G	0.856	0.55
77_D	81_R	0.854	0.55
89_G	161_G	0.853	0.55
99_S	170_S	0.849	0.54
72_R	125_E	0.844	0.54
16_A	21_G	0.827	0.52
60_G	130_G	0.823	0.52
21_G	59_G	0.818	0.52
104_V	127_A	0.818	0.52
189_V	193_C	0.817	0.52
25_V	166_V	0.816	0.51
39_W	109_W	0.812	0.51
3_R	55_E	0.805	0.50
34_I	104_V	0.805	0.50
33_C	52_C	0.804	0.50
90_G	111_Y	0.800	0.50
3_R	72_R	0.797	0.50
57_A	127_A	0.795	0.50
10_R	79_R	0.795	0.50
4_C	14_C	0.792	0.49
2_V	16_A	0.791	0.49
15_P	84_P	0.791	0.49
12_R	153_R	0.781	0.48
112_D	115_G	0.779	0.48
97_Q	168_Q	0.775	0.48
24_L	124_A	0.773	0.48
83_C	103_C	0.769	0.47
83_C	122_C	0.766	0.47
115_G	186_G	0.752	0.46
53_R	167_R	0.749	0.46
48_V	56_F	0.748	0.45
16_A	46_I	0.745	0.45
73_C	126_F	0.741	0.45
134_G	137_G	0.741	0.45
166_V	178_R	0.740	0.45
63_G	132_G	0.740	0.45
46_I	58_V	0.738	0.45
35_E	42_D	0.734	0.44
17_D	22_V	0.731	0.44
88_R	106_G	0.718	0.43
108_T	179_T	0.715	0.43
165_L	168_Q	0.699	0.41
25_V	95_V	0.697	0.41
87_T	128_V	0.696	0.41
65_G	134_G	0.694	0.41
106_G	109_W	0.693	0.41
64_G	133_G	0.690	0.40
157_A	160_R	0.689	0.40
44_G	185_N	0.683	0.40
131_G	136_G	0.682	0.40
99_S	168_Q	0.677	0.39
105_E	176_E	0.676	0.39
140_G	143_V	0.676	0.39
40_G	117_W	0.673	0.39
13_E	44_G	0.665	0.38
192_G	197_F	0.662	0.38
127_A	130_G	0.657	0.38
150_G	153_R	0.656	0.38
33_C	56_F	0.653	0.37
3_R	36_G	0.650	0.37
11_R	47_W	0.648	0.37
76_D	81_R	0.648	0.37
54_A	112_D	0.646	0.37
118_V	126_F	0.645	0.37
83_C	117_W	0.639	0.36
22_V	47_W	0.632	0.36
178_R	182_Y	0.632	0.36
54_A	96_R	0.631	0.35
122_C	126_F	0.628	0.35
116_I	128_V	0.628	0.35
25_V	54_A	0.624	0.35
24_L	165_L	0.622	0.35
77_D	101_S	0.617	0.34
83_C	109_W	0.616	0.34
42_D	115_G	0.613	0.34
119_D	190_D	0.612	0.34
85_A	128_V	0.610	0.34
68_G	140_G	0.609	0.34
18_T	41_Y	0.606	0.33
102_P	108_T	0.604	0.33
92_V	163_V	0.603	0.33
62_G	134_G	0.601	0.33
182_Y	187_I	0.599	0.33
87_T	115_G	0.598	0.33
159_T	187_I	0.598	0.33
71_V	116_I	0.598	0.33
160_R	164_R	0.597	0.33
13_E	18_T	0.596	0.33
22_V	46_I	0.594	0.33
73_C	122_C	0.594	0.33
44_G	114_G	0.594	0.33
83_C	126_F	0.593	0.32
26_R	96_R	0.593	0.32
61_G	65_G	0.593	0.32
70_T	125_E	0.591	0.32
53_R	124_A	0.591	0.32
102_P	173_P	0.589	0.32
103_C	126_F	0.586	0.32
74_E	97_Q	0.584	0.32
105_E	111_Y	0.583	0.32
194_R	197_F	0.580	0.31
74_E	144_T	0.578	0.31
33_C	39_W	0.577	0.31
13_E	35_E	0.576	0.31
9_G	26_R	0.575	0.31
80_R	152_R	0.575	0.31
10_R	15_P	0.571	0.31
5_E	53_R	0.570	0.31
116_I	124_A	0.570	0.31
13_E	40_G	0.569	0.31
142_T	154_Y	0.563	0.30
21_G	42_D	0.562	0.30
156_G	162_G	0.562	0.30
173_P	178_R	0.562	0.30
92_V	128_V	0.561	0.30
43_R	184_R	0.561	0.30
27_Q	55_E	0.557	0.30
73_C	103_C	0.557	0.30
156_G	160_R	0.556	0.30
62_G	71_V	0.555	0.30
104_V	108_T	0.554	0.29
165_L	170_S	0.554	0.29
74_E	152_R	0.552	0.29
18_T	45_G	0.551	0.29
73_C	118_V	0.548	0.29
75_S	121_G	0.548	0.29
145_C	180_W	0.548	0.29
146_E	196_E	0.545	0.29
54_A	194_R	0.542	0.29
152_R	162_G	0.539	0.28
90_G	129_G	0.539	0.28
178_R	187_I	0.537	0.28
27_Q	51_G	0.534	0.28
47_W	52_C	0.534	0.28
68_G	84_P	0.532	0.28
92_V	111_Y	0.530	0.28
6_S	14_C	0.529	0.28
170_S	192_G	0.527	0.28
11_R	40_G	0.525	0.27
118_V	122_C	0.525	0.27
61_G	131_G	0.524	0.27
11_R	45_G	0.523	0.27
165_L	179_T	0.521	0.27
189_V	192_G	0.521	0.27
124_A	161_G	0.519	0.27
33_C	40_G	0.518	0.27
73_C	109_W	0.517	0.27
158_D	176_E	0.517	0.27
39_W	180_W	0.513	0.27
168_Q	192_G	0.512	0.26
33_C	48_V	0.511	0.26
155_C	180_W	0.511	0.26
145_C	155_C	0.509	0.26
48_V	54_A	0.505	0.26
26_R	32_P	0.503	0.26
45_G	186_G	0.500	0.26

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
2kn0A	1	0.1421	5.7	0.965	Contact Map
2kmzA	1	0.1624	3.9	0.968	Contact Map
2eqpA	1	0.198	1.4	0.974	Contact Map
2kjxA	1	0.1117	1.1	0.976	Contact Map
3d3zA	1	0.3147	0.9	0.978	Contact Map
2mfaA	1	0.2081	0.8	0.978	Contact Map
2j5hA	1	0.1066	0.8	0.978	Contact Map
2m35A	1	0.1015	0.8	0.978	Contact Map
2kerA	1	0.1421	0.8	0.978	Contact Map
1ok0A	1	0.1523	0.8	0.978	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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