DUF4872 - PFAM28P - GREMLIN Contacts

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DUF4872 - Domain of unknown function (DUF4872)

PFAM:	PF16169	Sequences: EDLARARFAKGAPAPKGNMYYPIDVPEKLPDLRKAIRKAIKKTARDMLNPPIPNFGVKGIRKLAKEIRKWPEKLGAKDARLYLGQIVRMQEEIGTGGGGFRFLYAAFLQEAAELLGNPELLEASEEMTEIGDLWREFALLAARISKGRDPEDYNEAADLLLEIADREEEAFKAL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	174 (173)
Sequences:	3767 (2654)
Seq/√Len:	201.7
META:	0.875

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
168_E	172_K	3.699	1.00
126_E	173_A	3.590	1.00
61_R	168_E	3.554	1.00
62_K	66_E	2.869	1.00
133_L	162_E	2.534	1.00
102_F	131_G	2.428	1.00
68_R	154_N	2.419	1.00
36_I	111_A	2.403	1.00
68_R	161_L	2.401	1.00
130_I	170_A	2.296	1.00
61_R	165_D	2.285	1.00
91_E	135_R	2.282	1.00
127_M	170_A	2.254	1.00
45_R	49_N	2.061	1.00
122_E	125_E	1.901	1.00
133_L	136_E	1.847	1.00
91_E	96_G	1.783	1.00
127_M	130_I	1.731	1.00
157_A	161_L	1.718	1.00
68_R	157_A	1.716	1.00
105_A	127_M	1.710	1.00
109_Q	128_T	1.710	1.00
61_R	164_A	1.710	1.00
91_E	95_T	1.699	1.00
126_E	130_I	1.688	1.00
40_I	104_Y	1.670	1.00
98_G	135_R	1.641	1.00
31_D	34_K	1.617	1.00
133_L	166_R	1.601	1.00
162_E	166_R	1.597	1.00
35_A	39_A	1.561	1.00
2_D	5_R	1.524	1.00
94_G	100_F	1.508	1.00
126_E	129_E	1.500	1.00
130_I	166_R	1.488	1.00
44_A	48_L	1.468	1.00
90_Q	138_A	1.468	1.00
37_R	41_K	1.437	1.00
169_E	173_A	1.428	1.00
159_L	162_E	1.425	1.00
123_A	170_A	1.423	1.00
154_N	158_D	1.412	1.00
89_M	93_I	1.400	1.00
36_I	114_L	1.395	1.00
94_G	97_G	1.389	1.00
66_E	69_K	1.383	1.00
123_A	126_E	1.374	1.00
37_R	117_N	1.374	1.00
8_F	18_N	1.366	1.00
33_R	37_R	1.355	1.00
48_L	57_V	1.352	1.00
64_A	157_A	1.339	1.00
61_R	161_L	1.313	1.00
97_G	100_F	1.305	1.00
47_M	127_M	1.296	1.00
86_I	141_A	1.282	1.00
83_L	141_A	1.282	1.00
123_A	173_A	1.275	1.00
60_I	164_A	1.261	1.00
165_D	168_E	1.244	1.00
43_T	104_Y	1.242	1.00
102_F	132_D	1.217	1.00
104_Y	107_F	1.207	1.00
129_E	166_R	1.204	1.00
133_L	159_L	1.197	1.00
70_W	82_Y	1.196	1.00
158_D	161_L	1.189	1.00
162_E	165_D	1.187	1.00
61_R	64_A	1.179	1.00
79_A	153_Y	1.166	1.00
119_E	122_E	1.156	1.00
166_R	169_E	1.147	1.00
112_A	121_L	1.141	1.00
125_E	129_E	1.137	1.00
118_P	122_E	1.136	1.00
60_I	134_W	1.135	1.00
111_A	115_L	1.126	1.00
113_E	121_L	1.121	1.00
40_I	120_L	1.116	1.00
41_K	45_R	1.096	1.00
164_A	168_E	1.090	1.00
68_R	158_D	1.088	1.00
140_L	159_L	1.072	1.00
88_R	93_I	1.063	1.00
50_P	55_F	1.061	1.00
96_G	100_F	1.052	1.00
118_P	121_L	1.051	1.00
95_T	100_F	1.043	1.00
42_K	46_D	1.040	1.00
126_E	169_E	1.038	1.00
123_A	130_I	1.035	1.00
165_D	169_E	1.032	1.00
53_P	62_K	1.008	1.00
115_L	118_P	0.993	1.00
105_A	124_S	0.979	1.00
105_A	128_T	0.976	1.00
33_R	114_L	0.970	0.99
46_D	55_F	0.967	0.99
85_Q	89_M	0.966	0.99
36_I	115_L	0.953	0.99
51_P	55_F	0.946	0.99
149_D	152_D	0.945	0.99
64_A	68_R	0.945	0.99
98_G	105_A	0.940	0.99
104_Y	127_M	0.939	0.99
140_L	155_E	0.938	0.99
126_E	170_A	0.937	0.99
139_L	142_A	0.934	0.99
160_L	163_I	0.914	0.99
59_G	62_K	0.913	0.99
141_A	145_S	0.912	0.99
47_M	56_G	0.910	0.99
85_Q	93_I	0.909	0.99
11_G	14_A	0.906	0.99
128_T	132_D	0.902	0.99
112_A	115_L	0.900	0.99
40_I	107_F	0.896	0.99
121_L	125_E	0.888	0.99
85_Q	88_R	0.887	0.99
52_I	55_F	0.885	0.99
39_A	43_T	0.883	0.99
13_P	22_P	0.875	0.99
84_G	88_R	0.870	0.99
90_Q	93_I	0.868	0.99
17_G	20_Y	0.867	0.99
91_E	97_G	0.863	0.99
63_L	160_L	0.862	0.99
109_Q	121_L	0.861	0.99
155_E	159_L	0.860	0.99
13_P	16_K	0.857	0.99
145_S	163_I	0.852	0.99
42_K	45_R	0.850	0.99
22_P	25_V	0.847	0.99
32_L	114_L	0.841	0.99
112_A	117_N	0.831	0.98
57_V	164_A	0.825	0.98
155_E	158_D	0.825	0.98
87_V	141_A	0.819	0.98
140_L	156_A	0.816	0.98
126_E	166_R	0.815	0.98
19_M	127_M	0.807	0.98
144_I	148_R	0.800	0.98
137_F	160_L	0.796	0.98
76_A	80_R	0.792	0.98
78_D	81_L	0.782	0.98
43_T	171_F	0.774	0.98
137_F	163_I	0.773	0.98
69_K	72_E	0.772	0.97
75_G	79_A	0.755	0.97
144_I	156_A	0.754	0.97
65_K	161_L	0.754	0.97
33_R	115_L	0.753	0.97
6_A	13_P	0.750	0.97
32_L	35_A	0.749	0.97
91_E	98_G	0.741	0.97
96_G	103_L	0.738	0.97
117_N	121_L	0.734	0.97
58_K	61_R	0.728	0.96
136_E	140_L	0.726	0.96
133_L	163_I	0.720	0.96
5_R	9_A	0.718	0.96
48_L	168_E	0.718	0.96
135_R	139_L	0.717	0.96
88_R	92_E	0.709	0.96
166_R	170_A	0.706	0.96
161_L	165_D	0.706	0.96
149_D	155_E	0.705	0.96
151_E	155_E	0.699	0.96
28_K	31_D	0.696	0.95
124_S	131_G	0.692	0.95
52_I	58_K	0.691	0.95
159_L	166_R	0.689	0.95
39_A	107_F	0.689	0.95
87_V	142_A	0.689	0.95
144_I	151_E	0.684	0.95
142_A	146_K	0.673	0.94
47_M	171_F	0.667	0.94
74_L	78_D	0.665	0.94
98_G	131_G	0.665	0.94
98_G	102_F	0.661	0.94
36_I	40_I	0.661	0.94
141_A	156_A	0.659	0.94
64_A	164_A	0.655	0.94
119_E	173_A	0.652	0.94
91_E	94_G	0.650	0.93
14_A	90_Q	0.650	0.93
8_F	11_G	0.649	0.93
75_G	78_D	0.647	0.93
156_A	159_L	0.642	0.93
121_L	124_S	0.642	0.93
5_R	8_F	0.640	0.93
91_E	100_F	0.639	0.93
11_G	16_K	0.635	0.93
104_Y	111_A	0.632	0.92
107_F	111_A	0.629	0.92
14_A	18_N	0.625	0.92
44_A	123_A	0.622	0.92
159_L	163_I	0.621	0.92
46_D	50_P	0.619	0.92
33_R	116_G	0.613	0.91
87_V	92_E	0.613	0.91
127_M	171_F	0.610	0.91
102_F	135_R	0.608	0.91
63_L	66_E	0.604	0.91
161_L	164_A	0.598	0.90
112_A	118_P	0.597	0.90
171_F	174_L	0.593	0.90
140_L	144_I	0.590	0.90
47_M	57_V	0.587	0.89
84_G	145_S	0.582	0.89
169_E	172_K	0.581	0.89
16_K	20_Y	0.577	0.89
130_I	163_I	0.576	0.89
2_D	6_A	0.576	0.89
151_E	154_N	0.573	0.88
57_V	168_E	0.573	0.88
81_L	84_G	0.571	0.88
158_D	169_E	0.568	0.88
81_L	85_Q	0.565	0.88
76_A	79_A	0.565	0.88
104_Y	110_E	0.563	0.87
129_E	132_D	0.562	0.87
57_V	60_I	0.559	0.87
63_L	67_I	0.558	0.87
165_D	172_K	0.558	0.87
12_A	16_K	0.554	0.87
6_A	18_N	0.554	0.87
135_R	138_A	0.552	0.86
64_A	161_L	0.552	0.86
117_N	122_E	0.551	0.86
30_P	33_R	0.550	0.86
54_N	62_K	0.546	0.86
158_D	162_E	0.545	0.86
78_D	82_Y	0.543	0.85
30_P	35_A	0.541	0.85
8_F	17_G	0.537	0.85
91_E	99_G	0.536	0.85
70_W	78_D	0.536	0.85
93_I	97_G	0.532	0.84
67_I	86_I	0.532	0.84
61_R	65_K	0.531	0.84
74_L	77_K	0.530	0.84
56_G	99_G	0.527	0.84
15_P	20_Y	0.527	0.84
122_E	173_A	0.525	0.84
18_N	23_I	0.525	0.84
9_A	15_P	0.524	0.83
34_K	38_K	0.523	0.83
8_F	16_K	0.522	0.83
136_E	139_L	0.521	0.83
18_N	22_P	0.520	0.83
26_P	34_K	0.520	0.83
29_L	33_R	0.514	0.82
159_L	173_A	0.514	0.82
11_G	17_G	0.514	0.82
102_F	106_A	0.513	0.82
91_E	102_F	0.508	0.82
39_A	104_Y	0.506	0.81
62_K	65_K	0.502	0.81
83_L	144_I	0.500	0.81

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
1yviA	1	0.6207	18.6	0.927	Contact Map
3ikmA	1	0.7701	14.4	0.93	Contact Map
1nthA	5	0.7471	10.5	0.934	Contact Map
3pltA	2	0.3966	9	0.936	Contact Map
3us6A	1	0.6264	8.4	0.937	Contact Map
4eukB	1	0.6322	8.2	0.937	Contact Map
2wssS	1	0.7011	7.6	0.938	Contact Map
4g78A	1	0.592	7.4	0.939	Contact Map
2noxA	6	0.6437	6.4	0.941	Contact Map
2eqzA	1	0.408	6.2	0.941	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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