DUF4272 - PFAM28P - GREMLIN Contacts

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DUF4272 - Domain of unknown function (DUF4272)

PFAM:	PF14094	Sequences: RKARSEAILKALGIPVNPHLPLIEDEEEVELRSAEEVARRALALLAVAARAESLEEGEPREEVEEWLKRYGLWDALTPKERAFLENPAPSEQDRINFSWRYEALWVLLWALGLVDELPFPDEICDVDLLVRLLPLGESPEEFIAKAKLRSKEEILDAADLIYRLHWAVRDARLNGKPAPGGLDPGVVYERHYALNWLIGYEDQDWDDV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	208 (203)
Sequences:	1882 (1607)
Seq/√Len:	112.8
META:	0.834

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
191_H	195_N	3.731	1.00
170_D	174_N	3.432	1.00
37_V	148_L	3.253	1.00
92_Q	96_N	2.922	1.00
39_R	75_A	2.833	1.00
67_L	76_L	2.793	1.00
110_A	197_L	2.736	1.00
2_K	6_E	2.681	1.00
43_A	76_L	2.585	1.00
158_A	198_I	2.583	1.00
38_A	143_I	2.527	1.00
188_Y	192_Y	2.431	1.00
6_E	17_N	2.408	1.00
90_S	93_D	2.337	1.00
169_R	172_R	2.161	1.00
165_H	191_H	1.997	1.00
200_Y	203_Q	1.996	1.00
165_H	169_R	1.990	1.00
100_R	192_Y	1.971	1.00
41_A	104_L	1.963	1.00
81_R	85_E	1.906	1.00
159_D	163_R	1.896	1.00
43_A	72_L	1.886	1.00
149_R	153_E	1.883	1.00
33_S	36_E	1.814	1.00
34_A	38_A	1.793	1.00
32_R	36_E	1.776	1.00
165_H	168_V	1.757	1.00
157_A	160_L	1.750	1.00
8_I	12_L	1.744	1.00
86_N	93_D	1.718	1.00
204_D	207_D	1.709	1.00
125_D	128_L	1.687	1.00
171_A	179_P	1.665	1.00
138_S	141_E	1.655	1.00
68_K	73_W	1.636	1.00
35_E	39_R	1.627	1.00
79_K	96_N	1.587	1.00
41_A	111_L	1.585	1.00
73_W	76_L	1.554	1.00
44_L	47_V	1.545	1.00
110_A	154_I	1.536	1.00
66_W	70_Y	1.535	1.00
6_E	16_V	1.509	1.00
12_L	119_F	1.498	1.00
161_I	194_L	1.483	1.00
6_E	18_P	1.483	1.00
51_A	97_F	1.461	1.00
38_A	146_A	1.458	1.00
105_W	129_L	1.445	1.00
168_V	184_P	1.440	1.00
92_Q	95_I	1.438	1.00
31_L	151_K	1.434	1.00
158_A	195_N	1.419	1.00
67_L	73_W	1.399	1.00
96_N	185_G	1.375	1.00
113_L	145_K	1.372	1.00
26_E	152_E	1.371	1.00
105_W	118_P	1.367	1.00
70_Y	139_P	1.365	1.00
83_F	97_F	1.359	1.00
40_R	80_E	1.359	1.00
172_R	184_P	1.354	1.00
103_A	106_V	1.330	1.00
52_E	101_Y	1.306	1.00
158_A	194_L	1.297	0.99
185_G	189_E	1.281	0.99
25_D	28_E	1.268	0.99
41_A	108_L	1.251	0.99
20_L	162_Y	1.242	0.99
105_W	114_V	1.235	0.99
64_E	73_W	1.232	0.99
39_R	143_I	1.214	0.99
123_I	126_V	1.214	0.99
47_V	97_F	1.209	0.99
107_L	197_L	1.205	0.99
52_E	126_V	1.177	0.99
83_F	89_P	1.176	0.99
99_W	185_G	1.172	0.99
49_A	52_E	1.162	0.99
31_L	154_I	1.156	0.99
65_E	69_R	1.153	0.99
51_A	83_F	1.132	0.99
141_E	145_K	1.105	0.98
137_E	145_K	1.104	0.98
77_T	206_D	1.102	0.98
166_W	170_D	1.098	0.98
50_R	89_P	1.094	0.98
112_G	147_K	1.093	0.98
70_Y	138_S	1.086	0.98
3_A	7_A	1.073	0.98
108_L	113_L	1.073	0.98
160_L	164_L	1.067	0.98
8_I	11_A	1.067	0.98
170_D	176_K	1.061	0.98
142_F	146_A	1.049	0.98
38_A	142_F	1.048	0.98
98_S	123_I	1.045	0.98
48_A	101_Y	1.040	0.97
43_A	67_L	1.035	0.97
99_W	189_E	1.033	0.97
168_V	172_R	1.031	0.97
91_E	94_R	1.027	0.97
48_A	104_L	1.027	0.97
8_I	157_A	1.027	0.97
5_S	159_D	1.026	0.97
169_R	173_L	1.011	0.97
179_P	182_L	0.998	0.97
155_L	159_D	0.998	0.97
14_I	167_A	0.993	0.97
170_D	173_L	0.989	0.97
161_I	191_H	0.989	0.97
185_G	188_Y	0.986	0.97
158_A	161_I	0.983	0.96
119_F	164_L	0.978	0.96
150_S	153_E	0.971	0.96
157_A	161_I	0.970	0.96
106_V	117_L	0.966	0.96
105_W	124_C	0.964	0.96
5_S	8_I	0.964	0.96
51_A	98_S	0.962	0.96
4_R	156_D	0.956	0.96
21_P	162_Y	0.953	0.96
2_K	163_R	0.939	0.95
2_K	5_S	0.939	0.95
47_V	84_L	0.930	0.95
143_I	146_A	0.927	0.95
111_L	146_A	0.926	0.95
9_L	14_I	0.917	0.95
165_H	187_V	0.911	0.95
91_E	95_I	0.907	0.94
103_A	193_A	0.904	0.94
42_L	72_L	0.903	0.94
67_L	84_L	0.903	0.94
157_A	194_L	0.900	0.94
46_A	66_W	0.892	0.94
37_V	197_L	0.890	0.94
83_F	94_R	0.886	0.94
165_H	188_Y	0.880	0.94
77_T	107_L	0.880	0.94
67_L	72_L	0.870	0.93
81_R	84_L	0.868	0.93
50_R	63_V	0.866	0.93
7_A	11_A	0.866	0.93
15_P	179_P	0.863	0.93
199_G	202_D	0.863	0.93
35_E	143_I	0.862	0.93
184_P	188_Y	0.848	0.92
120_P	161_I	0.844	0.92
48_A	52_E	0.835	0.92
169_R	188_Y	0.833	0.92
100_R	189_E	0.825	0.91
128_L	133_L	0.815	0.91
72_L	75_A	0.812	0.90
10_K	18_P	0.809	0.90
162_Y	191_H	0.809	0.90
12_L	164_L	0.800	0.90
168_V	187_V	0.795	0.90
78_P	207_D	0.787	0.89
106_V	193_A	0.787	0.89
47_V	100_R	0.780	0.89
4_R	7_A	0.777	0.88
45_L	104_L	0.774	0.88
104_L	129_L	0.771	0.88
17_N	20_L	0.767	0.88
59_P	62_E	0.762	0.87
157_A	190_R	0.758	0.87
163_R	167_A	0.756	0.87
2_K	20_L	0.754	0.87
105_W	128_L	0.753	0.87
154_I	194_L	0.748	0.87
103_A	185_G	0.746	0.86
166_W	173_L	0.739	0.86
8_I	160_L	0.732	0.85
106_V	194_L	0.730	0.85
120_P	164_L	0.728	0.85
168_V	171_A	0.727	0.85
161_I	190_R	0.724	0.85
7_A	10_K	0.721	0.84
48_A	127_D	0.719	0.84
106_V	191_H	0.716	0.84
20_L	24_E	0.715	0.84
107_L	110_A	0.708	0.83
167_A	171_A	0.701	0.83
107_L	193_A	0.699	0.83
42_L	139_P	0.698	0.83
34_A	148_L	0.697	0.82
48_A	51_A	0.694	0.82
37_V	111_L	0.686	0.81
76_L	84_L	0.685	0.81
48_A	191_H	0.685	0.81
50_R	84_L	0.680	0.81
162_Y	165_H	0.680	0.81
23_I	29_V	0.676	0.80
195_N	198_I	0.676	0.80
183_D	187_V	0.675	0.80
130_V	133_L	0.674	0.80
113_L	146_A	0.668	0.80
15_P	170_D	0.667	0.80
190_R	194_L	0.665	0.79
44_L	104_L	0.665	0.79
50_R	60_R	0.651	0.78
72_L	76_L	0.651	0.78
100_R	103_A	0.651	0.78
22_L	25_D	0.648	0.78
29_V	151_K	0.644	0.77
10_K	15_P	0.639	0.77
51_A	94_R	0.639	0.77
17_N	166_W	0.636	0.76
2_K	17_N	0.631	0.76
58_E	62_E	0.628	0.75
142_F	145_K	0.625	0.75
10_K	16_V	0.623	0.75
86_N	89_P	0.621	0.75
151_K	154_I	0.621	0.75
14_I	23_I	0.613	0.74
160_L	182_L	0.608	0.73
109_W	149_R	0.607	0.73
15_P	19_H	0.607	0.73
47_V	83_F	0.606	0.73
23_I	158_A	0.604	0.73
60_R	63_V	0.601	0.72
26_E	151_K	0.600	0.72
49_A	97_F	0.599	0.72
76_L	81_R	0.596	0.72
119_F	187_V	0.593	0.71
38_A	99_W	0.593	0.71
47_V	86_N	0.592	0.71
9_L	164_L	0.591	0.71
137_E	141_E	0.588	0.71
6_E	19_H	0.587	0.70
46_A	104_L	0.585	0.70
95_I	99_W	0.580	0.70
165_H	173_L	0.578	0.69
123_I	127_D	0.578	0.69
45_L	130_V	0.578	0.69
96_N	189_E	0.577	0.69
41_A	129_L	0.577	0.69
60_R	67_L	0.574	0.69
41_A	107_L	0.572	0.68
22_L	26_E	0.572	0.68
7_A	12_L	0.570	0.68
95_I	98_S	0.566	0.68
201_E	204_D	0.566	0.68
60_R	64_E	0.564	0.67
129_L	133_L	0.563	0.67
51_A	105_W	0.563	0.67
43_A	47_V	0.562	0.67
6_E	15_P	0.561	0.67
26_E	31_L	0.559	0.67
37_V	110_A	0.559	0.67
25_D	29_V	0.558	0.67
159_D	162_Y	0.557	0.66
126_V	133_L	0.557	0.66
45_L	133_L	0.555	0.66
178_A	184_P	0.554	0.66
154_I	163_R	0.552	0.66
39_R	84_L	0.552	0.66
126_V	131_R	0.551	0.66
27_E	30_E	0.551	0.66
116_E	176_K	0.551	0.66
2_K	22_L	0.549	0.65
91_E	116_E	0.548	0.65
73_W	81_R	0.548	0.65
78_P	204_D	0.547	0.65
162_Y	166_W	0.547	0.65
44_L	103_A	0.546	0.65
159_D	187_V	0.545	0.65
140_E	144_A	0.545	0.65
104_L	124_C	0.542	0.64
118_P	121_D	0.542	0.64
133_L	142_F	0.539	0.64
3_A	11_A	0.539	0.64
202_D	208_V	0.537	0.64
106_V	195_N	0.536	0.63
16_V	19_H	0.536	0.63
64_E	85_E	0.535	0.63
129_L	132_L	0.535	0.63
158_A	164_L	0.535	0.63
10_K	65_E	0.532	0.63
118_P	122_E	0.532	0.63
194_L	205_W	0.531	0.63
73_W	85_E	0.529	0.62
9_L	171_A	0.528	0.62
159_D	164_L	0.527	0.62
120_P	156_D	0.527	0.62
199_G	203_Q	0.524	0.62
101_Y	134_P	0.522	0.61
139_P	142_F	0.522	0.61
79_K	93_D	0.521	0.61
118_P	190_R	0.520	0.61
127_D	183_D	0.518	0.61
23_I	27_E	0.516	0.61
97_F	100_R	0.515	0.60
3_A	10_K	0.515	0.60
6_E	163_R	0.511	0.60
21_P	24_E	0.508	0.59
36_E	39_R	0.508	0.59
69_R	147_K	0.506	0.59
99_W	169_R	0.505	0.59
35_E	38_A	0.502	0.59
43_A	135_L	0.502	0.59
58_E	94_R	0.502	0.59
6_E	10_K	0.500	0.58

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
2c9oA	3	0.3702	10.6	0.947	Contact Map
2zf8A	1	0.1683	4.9	0.954	Contact Map
3o0kA	1	0.4087	4.2	0.956	Contact Map
3wbwA	1	0.4663	4.1	0.956	Contact Map
3vxgA	1	0.4615	3.7	0.957	Contact Map
2i82A	1	0.2885	3.3	0.958	Contact Map
1ohuA	1	0.4519	2.9	0.959	Contact Map
4lgtA	1	0.2885	2.8	0.959	Contact Map
3axsA	2	0.375	2.7	0.96	Contact Map
1vioA	2	0.2404	2.6	0.96	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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