DUF3296 - PFAM28P - GREMLIN Contacts

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DUF3296 - Protein of unknown function (DUF3296)

PFAM:	PF11726	Sequences: RIKEYLDAALSRYSRVLVVRVDLRYPKDYQDDDNKVISRFIESLKAKIKADLKRKLRRGKRVFKCLVGYVWVREQGESKGPHYHLLLFLNGDKYYSLGDYNQNDYNLAKRIGEAWASALGLDYEDYAGLVHFPKNPGYYLNRNDPDDKEKYENLFYRLSYLAKERTKGYGDGMRNFGCS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	179 (170)
Sequences:	2401 (1819)
Seq/√Len:	139.5
META:	0.578

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
86_L	158_L	3.883	1.00
15_R	92_D	3.197	1.00
18_V	154_L	3.089	1.00
21_V	85_L	2.938	1.00
23_L	115_W	2.702	1.00
14_S	92_D	2.517	1.00
71_W	177_G	2.487	1.00
9_A	16_V	2.408	1.00
76_G	79_K	2.372	1.00
24_R	79_K	2.286	1.00
71_W	83_Y	2.282	1.00
2_I	70_V	2.103	1.00
47_K	113_E	2.088	1.00
15_R	91_G	2.047	1.00
76_G	166_T	2.023	1.00
5_Y	68_G	2.003	1.00
108_A	132_F	1.964	1.00
143_N	147_D	1.852	1.00
73_R	83_Y	1.834	1.00
51_D	94_Y	1.805	1.00
43_S	47_K	1.798	1.00
37_I	40_F	1.762	1.00
18_V	86_L	1.752	1.00
18_V	88_F	1.693	1.00
109_K	113_E	1.690	1.00
75_Q	81_P	1.688	1.00
138_Y	157_R	1.655	1.00
128_G	133_P	1.652	1.00
25_Y	36_V	1.640	1.00
50_A	54_R	1.613	1.00
86_L	154_L	1.609	1.00
156_Y	159_S	1.586	1.00
90_N	93_K	1.581	1.00
12_R	66_L	1.576	1.00
27_K	80_G	1.576	1.00
82_H	160_Y	1.561	1.00
74_E	160_Y	1.541	1.00
103_N	106_N	1.538	1.00
116_A	126_Y	1.525	1.00
38_S	42_E	1.510	1.00
52_L	55_K	1.509	1.00
9_A	68_G	1.503	1.00
12_R	68_G	1.498	1.00
19_V	89_L	1.493	1.00
70_V	86_L	1.479	1.00
74_E	84_H	1.478	1.00
133_P	136_P	1.474	1.00
74_E	82_H	1.459	1.00
94_Y	107_L	1.450	1.00
125_D	128_G	1.408	1.00
84_H	160_Y	1.398	1.00
6_L	155_F	1.394	1.00
13_Y	67_V	1.345	1.00
5_Y	9_A	1.326	1.00
125_D	130_V	1.318	1.00
75_Q	80_G	1.310	1.00
42_E	45_K	1.303	1.00
72_V	176_F	1.253	1.00
3_K	7_D	1.223	1.00
165_R	168_G	1.219	1.00
72_V	167_K	1.217	1.00
121_L	126_Y	1.189	1.00
41_I	85_L	1.188	1.00
19_V	87_L	1.183	1.00
47_K	117_S	1.144	0.99
3_K	155_F	1.139	0.99
82_H	163_K	1.136	0.99
54_R	58_R	1.124	0.99
73_R	81_P	1.124	0.99
146_D	149_E	1.115	0.99
147_D	150_K	1.115	0.99
158_L	161_L	1.103	0.99
160_Y	163_K	1.099	0.99
13_Y	66_L	1.099	0.99
43_S	117_S	1.090	0.99
20_R	161_L	1.077	0.99
46_A	50_A	1.073	0.99
135_N	138_Y	1.070	0.99
7_D	151_Y	1.061	0.99
72_V	161_L	1.050	0.99
164_E	167_K	1.047	0.99
40_F	43_S	1.045	0.99
35_K	39_R	1.043	0.99
2_I	162_A	1.042	0.99
47_K	110_R	1.022	0.99
114_A	119_L	1.015	0.99
22_D	82_H	1.014	0.99
6_L	154_L	1.012	0.99
40_F	44_L	1.010	0.99
75_Q	78_S	1.004	0.98
128_G	131_H	0.997	0.98
166_T	170_G	0.989	0.98
37_I	41_I	0.987	0.98
55_K	58_R	0.982	0.98
130_V	133_P	0.980	0.98
91_G	139_Y	0.973	0.98
63_F	89_L	0.972	0.98
167_K	170_G	0.969	0.98
127_A	132_F	0.960	0.98
166_T	169_Y	0.957	0.98
155_F	159_S	0.952	0.98
43_S	46_A	0.950	0.98
135_N	140_L	0.937	0.98
174_R	178_C	0.927	0.97
121_L	125_D	0.924	0.97
65_C	93_K	0.918	0.97
129_L	133_P	0.908	0.97
29_Y	32_D	0.892	0.97
74_E	163_K	0.884	0.97
9_A	12_R	0.882	0.96
41_I	45_K	0.881	0.96
42_E	46_A	0.873	0.96
138_Y	141_N	0.869	0.96
84_H	163_K	0.859	0.96
10_L	16_V	0.854	0.96
52_L	56_L	0.852	0.96
39_R	43_S	0.848	0.96
54_R	57_R	0.836	0.95
127_A	131_H	0.835	0.95
21_V	87_L	0.833	0.95
123_Y	127_A	0.832	0.95
108_A	112_G	0.830	0.95
144_D	150_K	0.829	0.95
164_E	169_Y	0.817	0.95
168_G	171_D	0.816	0.95
41_I	69_Y	0.811	0.94
106_N	110_R	0.803	0.94
38_S	41_I	0.800	0.94
22_D	160_Y	0.797	0.94
13_Y	16_V	0.797	0.94
107_L	110_R	0.797	0.94
124_E	127_A	0.795	0.94
44_L	87_L	0.788	0.94
16_V	88_F	0.788	0.94
147_D	151_Y	0.787	0.93
170_G	175_N	0.785	0.93
53_K	56_L	0.784	0.93
18_V	158_L	0.781	0.93
4_E	7_D	0.778	0.93
5_Y	70_V	0.774	0.93
44_L	111_I	0.764	0.92
23_L	85_L	0.763	0.92
119_L	133_P	0.757	0.92
138_Y	142_R	0.756	0.92
122_D	125_D	0.747	0.92
113_E	117_S	0.743	0.91
129_L	132_F	0.741	0.91
40_F	45_K	0.736	0.91
121_L	127_A	0.734	0.91
55_K	60_K	0.734	0.91
65_C	94_Y	0.732	0.91
114_A	118_A	0.725	0.90
126_Y	131_H	0.720	0.90
68_G	178_C	0.716	0.90
51_D	54_R	0.715	0.90
18_V	157_R	0.713	0.90
6_L	18_V	0.711	0.89
87_L	111_I	0.707	0.89
76_G	81_P	0.702	0.89
170_G	173_M	0.701	0.89
159_S	162_A	0.698	0.89
146_D	150_K	0.696	0.88
40_F	47_K	0.695	0.88
148_K	151_Y	0.692	0.88
49_K	53_K	0.691	0.88
66_L	89_L	0.679	0.87
137_G	142_R	0.675	0.87
127_A	130_V	0.674	0.87
16_V	67_V	0.674	0.87
174_R	177_G	0.673	0.87
53_K	57_R	0.670	0.87
17_L	139_Y	0.668	0.86
123_Y	126_Y	0.668	0.86
45_K	49_K	0.668	0.86
41_I	44_L	0.666	0.86
168_G	175_N	0.663	0.86
121_L	124_E	0.662	0.86
137_G	141_N	0.660	0.86
20_R	82_H	0.658	0.86
145_P	150_K	0.655	0.85
136_P	140_L	0.655	0.85
36_V	40_F	0.654	0.85
37_I	45_K	0.653	0.85
150_K	153_N	0.650	0.85
44_L	47_K	0.645	0.84
135_N	141_N	0.645	0.84
17_L	91_G	0.641	0.84
141_N	144_D	0.639	0.84
23_L	130_V	0.637	0.84
24_R	129_L	0.635	0.83
142_R	145_P	0.635	0.83
88_F	111_I	0.629	0.83
63_F	93_K	0.627	0.83
28_D	31_D	0.626	0.83
52_L	62_V	0.624	0.82
139_Y	144_D	0.622	0.82
60_K	63_F	0.622	0.82
171_D	175_N	0.618	0.82
43_S	50_A	0.615	0.81
38_S	45_K	0.606	0.81
55_K	114_A	0.606	0.81
22_D	161_L	0.604	0.80
114_A	117_S	0.602	0.80
7_D	155_F	0.597	0.80
122_D	128_G	0.593	0.79
86_L	157_R	0.591	0.79
55_K	59_G	0.587	0.78
136_P	139_Y	0.581	0.78
135_N	144_D	0.578	0.77
11_S	32_D	0.574	0.77
51_D	55_K	0.573	0.77
153_N	156_Y	0.565	0.76
10_L	23_L	0.562	0.75
91_G	102_Q	0.560	0.75
154_L	157_R	0.559	0.75
110_R	113_E	0.557	0.75
83_Y	163_K	0.557	0.75
35_K	43_S	0.555	0.74
126_Y	130_V	0.555	0.74
10_L	18_V	0.553	0.74
37_I	47_K	0.552	0.74
19_V	108_A	0.551	0.74
12_R	16_V	0.549	0.74
165_R	171_D	0.546	0.73
149_E	153_N	0.543	0.73
111_I	114_A	0.543	0.73
47_K	51_D	0.543	0.73
16_V	68_G	0.540	0.72
172_G	175_N	0.539	0.72
104_D	108_A	0.539	0.72
142_R	146_D	0.536	0.72
47_K	50_A	0.536	0.72
72_V	178_C	0.535	0.72
15_R	163_K	0.532	0.71
25_Y	119_L	0.531	0.71
126_Y	129_L	0.531	0.71
163_K	167_K	0.526	0.71
6_L	10_L	0.523	0.70
8_A	68_G	0.519	0.70
30_Q	81_P	0.519	0.70
153_N	157_R	0.515	0.69
113_E	116_A	0.514	0.69
165_R	169_Y	0.510	0.68
6_L	88_F	0.508	0.68
8_A	11_S	0.507	0.68
2_I	158_L	0.507	0.68
57_R	60_K	0.506	0.68
10_L	13_Y	0.505	0.67
41_I	47_K	0.505	0.67
16_V	142_R	0.505	0.67
4_E	8_A	0.504	0.67
48_I	67_V	0.503	0.67
48_I	52_L	0.502	0.67
142_R	151_Y	0.502	0.67
135_N	139_Y	0.500	0.67

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
4pp4A	1	0.8547	38.1	0.912	Contact Map
4ht4A	1	0.6648	20.4	0.923	Contact Map
2ns6A	1	0.6201	11.9	0.931	Contact Map
2v6eA	2	0.419	10.6	0.933	Contact Map
2pa4A	3	0.3464	10.5	0.933	Contact Map
4le5A	2	0.2514	6.9	0.938	Contact Map
3fovA	2	0.2402	6	0.94	Contact Map
3dkxA	3	0.7598	5.9	0.94	Contact Map
3h4lA	2	0.905	5.8	0.94	Contact Map
1p7lA	4	0.3352	4.4	0.943	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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