DUF3159 - PFAM28P - GREMLIN Contacts

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DUF3159 - Protein of unknown function (DUF3159)

PFAM:	PF11361	Sequences: LGGVRGLVESALPVLVFVVVNAITAGLRPALIAALAVAVVLAVVRLVRRQPLQQALSGLLGVAIAALIALRTGSAEDYFLPGILTNAAYALAFLVSVLVRRPLVGVLAGALRGEPTAWRRDPALRRAYSRATWLWAAVFLLRLAVQLPLYLAGQVGALGVARLAMGWPLTALALAVTWWLLRRARRP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	187 (183)
Sequences:	3837 (2563)
Seq/√Len:	189.5
META:	0.758

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
97_V	133_W	4.405	1.00
67_L	71_R	3.590	1.00
76_E	153_G	3.430	1.00
135_W	177_T	3.408	1.00
90_A	140_L	3.025	1.00
20_V	33_A	2.737	1.00
84_L	88_A	2.695	1.00
138_V	173_A	2.665	1.00
26_G	29_P	2.308	1.00
82_G	162_R	2.251	1.00
28_R	32_I	2.227	1.00
32_I	36_A	2.164	1.00
100_R	125_R	2.091	1.00
92_A	95_V	2.080	1.00
146_Q	165_M	2.073	1.00
27_L	31_L	2.071	1.00
101_R	106_V	2.066	1.00
16_V	37_V	2.008	1.00
97_V	136_A	1.972	1.00
101_R	116_T	1.946	1.00
29_P	32_I	1.901	1.00
97_V	129_S	1.876	1.00
93_F	132_T	1.855	1.00
94_L	136_A	1.816	1.00
147_L	151_L	1.803	1.00
42_A	59_L	1.802	1.00
125_R	129_S	1.793	1.00
20_V	30_A	1.706	1.00
29_P	33_A	1.703	1.00
16_V	33_A	1.684	1.00
87_A	143_L	1.684	1.00
35_L	39_V	1.662	1.00
45_R	50_Q	1.647	1.00
40_V	44_V	1.644	1.00
141_L	165_M	1.641	1.00
143_L	147_L	1.630	1.00
104_V	131_A	1.592	1.00
95_V	99_V	1.567	1.00
20_V	29_P	1.556	1.00
96_S	132_T	1.500	1.00
97_V	132_T	1.500	1.00
36_A	40_V	1.494	1.00
74_S	77_D	1.472	1.00
31_L	66_A	1.423	1.00
154_Q	157_A	1.409	1.00
46_L	49_R	1.393	1.00
91_L	95_V	1.392	1.00
68_I	81_P	1.370	1.00
93_F	103_L	1.367	1.00
133_W	136_A	1.333	1.00
101_R	119_R	1.314	1.00
38_A	59_L	1.294	1.00
134_L	180_L	1.291	1.00
114_E	124_L	1.282	1.00
131_A	177_T	1.263	1.00
5_R	9_E	1.261	1.00
64_I	81_P	1.251	1.00
145_V	165_M	1.248	1.00
90_A	136_A	1.241	1.00
175_A	179_W	1.241	1.00
156_G	159_G	1.239	1.00
82_G	146_Q	1.230	1.00
100_R	129_S	1.227	1.00
67_L	70_L	1.207	1.00
136_A	140_L	1.194	1.00
26_G	30_A	1.191	1.00
126_R	130_R	1.182	1.00
24_T	30_A	1.178	1.00
66_A	69_A	1.175	1.00
33_A	36_A	1.170	1.00
146_Q	162_R	1.139	1.00
96_S	99_V	1.131	1.00
91_L	94_L	1.128	1.00
106_V	116_T	1.126	1.00
149_L	157_A	1.122	1.00
35_L	59_L	1.121	1.00
160_V	164_A	1.111	1.00
133_W	137_A	1.104	1.00
38_A	62_V	1.095	1.00
20_V	25_A	1.093	1.00
63_A	67_L	1.084	1.00
94_L	97_V	1.079	1.00
175_A	178_W	1.075	1.00
127_A	131_A	1.074	1.00
83_I	143_L	1.040	1.00
139_F	142_R	1.026	1.00
60_L	64_I	1.022	1.00
178_W	182_R	1.019	1.00
35_L	63_A	1.011	1.00
176_V	180_L	1.006	1.00
16_V	20_V	1.006	1.00
134_L	173_A	1.001	0.99
104_V	177_T	0.989	0.99
90_A	93_F	0.989	0.99
93_F	104_V	0.983	0.99
57_S	65_A	0.981	0.99
104_V	132_T	0.979	0.99
4_V	8_V	0.974	0.99
90_A	94_L	0.973	0.99
43_V	47_V	0.961	0.99
80_L	150_Y	0.959	0.99
113_G	116_T	0.959	0.99
61_G	65_A	0.946	0.99
171_A	175_A	0.943	0.99
84_L	87_A	0.938	0.99
73_G	77_D	0.937	0.99
55_A	58_G	0.935	0.99
53_Q	57_S	0.933	0.99
103_L	106_V	0.931	0.99
177_T	180_L	0.922	0.99
129_S	133_W	0.908	0.99
148_P	151_L	0.903	0.99
112_R	128_Y	0.903	0.99
149_L	161_A	0.901	0.99
56_L	60_L	0.887	0.99
155_V	159_G	0.880	0.99
86_N	142_R	0.875	0.99
52_L	56_L	0.870	0.99
38_A	42_A	0.866	0.99
31_L	70_L	0.864	0.99
72_T	77_D	0.860	0.98
44_V	48_R	0.847	0.98
157_A	164_A	0.841	0.98
145_V	161_A	0.836	0.98
148_P	152_A	0.833	0.98
77_D	81_P	0.832	0.98
122_P	125_R	0.831	0.98
172_L	175_A	0.830	0.98
73_G	76_E	0.828	0.98
39_V	59_L	0.828	0.98
1_L	4_V	0.822	0.98
42_A	56_L	0.822	0.98
170_T	174_L	0.822	0.98
157_A	161_A	0.810	0.98
162_R	165_M	0.806	0.98
83_I	147_L	0.803	0.98
144_A	148_P	0.797	0.97
157_A	160_V	0.792	0.97
144_A	147_L	0.791	0.97
51_P	54_Q	0.787	0.97
18_V	65_A	0.787	0.97
156_G	160_V	0.782	0.97
12_L	37_V	0.780	0.97
149_L	154_Q	0.780	0.97
21_N	24_T	0.778	0.97
30_A	34_A	0.776	0.97
104_V	128_Y	0.771	0.97
79_F	159_G	0.767	0.97
74_S	153_G	0.765	0.97
81_P	85_T	0.762	0.97
109_G	114_E	0.761	0.97
108_A	112_R	0.759	0.97
11_A	14_V	0.758	0.97
134_L	176_V	0.757	0.97
62_V	78_Y	0.752	0.96
1_L	10_S	0.750	0.96
88_A	92_A	0.749	0.96
8_V	12_L	0.730	0.96
43_V	46_L	0.730	0.96
161_A	165_M	0.730	0.96
106_V	110_A	0.727	0.96
90_A	143_L	0.722	0.96
80_L	83_I	0.718	0.95
159_G	163_L	0.716	0.95
15_L	19_V	0.704	0.95
116_T	120_R	0.697	0.95
143_L	148_P	0.697	0.95
39_V	43_V	0.697	0.95
89_Y	93_F	0.684	0.94
93_F	96_S	0.684	0.94
37_V	41_L	0.679	0.94
170_T	177_T	0.676	0.94
62_V	65_A	0.676	0.94
130_R	134_L	0.676	0.94
57_S	60_L	0.672	0.93
127_A	130_R	0.671	0.93
71_R	77_D	0.669	0.93
135_W	170_T	0.669	0.93
167_W	171_A	0.664	0.93
42_A	55_A	0.664	0.93
60_L	63_A	0.664	0.93
176_V	179_W	0.660	0.93
168_P	174_L	0.660	0.93
85_T	89_Y	0.658	0.93
46_L	52_L	0.657	0.93
105_G	119_R	0.655	0.93
128_Y	131_A	0.654	0.93
179_W	183_R	0.652	0.92
2_G	6_G	0.652	0.92
36_A	39_V	0.652	0.92
1_L	5_R	0.649	0.92
21_N	25_A	0.647	0.92
138_V	169_L	0.646	0.92
121_D	124_L	0.645	0.92
49_R	56_L	0.642	0.92
37_V	40_V	0.641	0.92
41_L	44_V	0.640	0.92
64_I	67_L	0.638	0.92
36_A	43_V	0.635	0.91
21_N	155_V	0.634	0.91
31_L	34_A	0.634	0.91
110_A	113_G	0.634	0.91
165_M	168_P	0.632	0.91
110_A	116_T	0.629	0.91
27_L	75_A	0.627	0.91
7_L	11_A	0.623	0.91
86_N	143_L	0.620	0.90
82_G	165_M	0.620	0.90
102_P	132_T	0.618	0.90
114_E	117_A	0.618	0.90
172_L	176_V	0.615	0.90
62_V	66_A	0.615	0.90
150_Y	158_L	0.614	0.90
132_T	135_W	0.611	0.90
84_L	143_L	0.609	0.90
18_V	22_A	0.606	0.89
44_V	47_V	0.597	0.89
64_I	69_A	0.596	0.89
101_R	113_G	0.594	0.88
94_L	98_L	0.593	0.88
70_L	78_Y	0.590	0.88
11_A	41_L	0.590	0.88
68_I	77_D	0.588	0.88
170_T	175_A	0.584	0.88
53_Q	59_L	0.583	0.88
137_A	140_L	0.582	0.87
108_A	128_Y	0.581	0.87
117_A	121_D	0.580	0.87
21_N	30_A	0.578	0.87
97_V	101_R	0.578	0.87
135_W	139_F	0.577	0.87
83_I	150_Y	0.575	0.87
71_R	161_A	0.574	0.87
83_I	151_L	0.571	0.86
127_A	180_L	0.568	0.86
68_I	72_T	0.568	0.86
20_V	24_T	0.563	0.86
9_E	135_W	0.563	0.86
15_L	22_A	0.561	0.85
19_V	24_T	0.560	0.85
106_V	115_P	0.559	0.85
4_V	9_E	0.553	0.85
34_A	62_V	0.553	0.85
104_V	135_W	0.551	0.84
25_A	29_P	0.549	0.84
83_I	87_A	0.549	0.84
181_L	184_A	0.548	0.84
145_V	148_P	0.546	0.84
5_R	8_V	0.545	0.84
81_P	84_L	0.543	0.84
139_F	165_M	0.542	0.83
122_P	126_R	0.542	0.83
89_Y	92_A	0.541	0.83
14_V	18_V	0.540	0.83
101_R	109_G	0.538	0.83
167_W	170_T	0.536	0.83
95_V	136_A	0.535	0.83
98_L	136_A	0.525	0.82
167_W	175_A	0.524	0.81
165_M	169_L	0.524	0.81
53_Q	86_N	0.524	0.81
106_V	119_R	0.522	0.81
138_V	141_L	0.520	0.81
28_R	70_L	0.519	0.81
70_L	74_S	0.515	0.80
86_N	89_Y	0.512	0.80
45_R	49_R	0.509	0.80
142_R	168_P	0.507	0.79
26_G	32_I	0.507	0.79
173_A	181_L	0.505	0.79
52_L	55_A	0.503	0.79
76_E	155_V	0.502	0.79
175_A	183_R	0.501	0.78
174_L	181_L	0.500	0.78

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
2xq2A	2	0.8556	27.4	0.925	Contact Map
4gc0A	1	0.6738	13.5	0.935	Contact Map
3wdoA	1	0.6524	4.1	0.949	Contact Map
2wswA	3	0.9572	3.9	0.949	Contact Map
2mofA	1	0.1872	3.7	0.95	Contact Map
4pypA	1	0.6471	3.7	0.95	Contact Map
2jlnA	1	0.8342	3.4	0.951	Contact Map
1kf6C	1	0.4439	3.4	0.951	Contact Map
3j45G	1	0.3422	2.7	0.953	Contact Map
4c7rA	3	0.9412	2.6	0.954	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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