DUF4366 - PFAM28P - GREMLIN Contacts

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DUF4366 - Domain of unknown function (DUF4366)

PFAM:	PF14283	Sequences: MLAALLAALLLMGAFSVTAFAGGGEPTEETEPVTEETPEEEETETSEEEEEEEPLTPDGNGTLVDDITDADGKQFITVTTKSGNVFYLIIDRDRDGEEENVYFLNAVDEADLLALAEDDEEEEEPPAVCTCTEKCEAGAVNANNMTECTGKEPEPEPEPTEEPEEEPEPEPEKKKEKGGSGGGLLLLVLALAGIGGGAGYYFKIYKPKKEAKGEDDDEDYDYDEDDDDEEEEEEEDED	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	238 (222)
Sequences:	1116 (833)
Seq/√Len:	55.9
META:	0.823

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
78_V	88_L	4.534	1.00
94_R	99_E	3.310	1.00
201_Y	205_Y	3.086	1.00
222_Y	225_D	2.790	1.00
185_L	189_L	2.419	1.00
183_G	187_L	2.396	1.00
201_Y	204_I	2.392	1.00
55_L	73_K	2.286	1.00
182_G	186_L	2.282	1.00
24_G	27_T	2.250	1.00
84_N	109_E	2.212	1.00
66_D	76_I	2.194	1.00
144_N	147_E	2.097	1.00
206_K	210_E	2.093	1.00
66_D	74_Q	2.005	1.00
82_S	109_E	1.980	1.00
74_Q	94_R	1.969	1.00
61_G	78_V	1.956	1.00
205_Y	209_K	1.918	1.00
81_K	84_N	1.891	1.00
184_L	188_V	1.819	0.99
129_C	148_C	1.790	0.99
60_N	108_D	1.786	0.99
81_K	108_D	1.755	0.99
102_Y	106_A	1.750	0.99
32_P	36_E	1.686	0.99
76_I	88_L	1.681	0.99
184_L	187_L	1.659	0.99
60_N	63_L	1.654	0.99
67_I	71_D	1.627	0.99
76_I	94_R	1.620	0.99
105_N	114_A	1.617	0.99
90_I	103_F	1.611	0.98
160_T	163_P	1.602	0.98
94_R	100_N	1.584	0.98
57_P	64_V	1.581	0.98
57_P	105_N	1.578	0.98
109_E	116_A	1.570	0.98
201_Y	207_P	1.567	0.98
105_N	115_L	1.565	0.98
99_E	102_Y	1.562	0.98
138_G	141_N	1.548	0.98
96_G	100_N	1.541	0.98
55_L	67_I	1.502	0.98
57_P	62_T	1.492	0.97
84_N	105_N	1.481	0.97
157_P	160_T	1.478	0.97
197_G	201_Y	1.478	0.97
200_Y	205_Y	1.465	0.97
60_N	116_A	1.461	0.97
76_I	90_I	1.453	0.97
79_T	85_V	1.448	0.97
202_F	205_Y	1.441	0.97
231_E	234_E	1.427	0.97
81_K	106_A	1.419	0.97
60_N	106_A	1.416	0.97
72_G	95_D	1.413	0.97
6_L	11_L	1.410	0.96
34_T	37_T	1.400	0.96
61_G	102_Y	1.387	0.96
109_E	113_L	1.368	0.96
171_P	174_K	1.355	0.96
11_L	14_A	1.336	0.95
74_Q	83_G	1.333	0.95
35_E	38_P	1.330	0.95
60_N	81_K	1.314	0.95
67_I	76_I	1.298	0.94
180_S	183_G	1.292	0.94
66_D	94_R	1.285	0.94
9_L	14_A	1.279	0.94
65_D	73_K	1.272	0.94
82_S	114_A	1.253	0.93
103_F	115_L	1.228	0.93
42_E	45_T	1.223	0.92
120_E	123_E	1.219	0.92
204_I	207_P	1.219	0.92
54_P	73_K	1.216	0.92
26_P	30_T	1.213	0.92
106_A	116_A	1.211	0.92
39_E	43_T	1.210	0.92
217_D	220_Y	1.209	0.92
56_T	73_K	1.169	0.91
141_N	148_C	1.167	0.90
75_F	89_I	1.160	0.90
221_D	228_D	1.150	0.90
7_A	10_L	1.150	0.90
63_L	66_D	1.149	0.90
103_F	107_V	1.147	0.90
8_A	11_L	1.146	0.90
230_E	233_E	1.142	0.90
220_Y	223_D	1.140	0.89
87_Y	103_F	1.125	0.89
63_L	85_V	1.122	0.89
190_A	194_I	1.119	0.89
61_G	96_G	1.115	0.88
26_P	29_E	1.110	0.88
219_D	222_Y	1.109	0.88
71_D	99_E	1.106	0.88
6_L	10_L	1.105	0.88
129_C	138_G	1.091	0.87
145_M	148_C	1.088	0.87
105_N	108_D	1.085	0.87
185_L	188_V	1.082	0.87
37_T	41_E	1.078	0.87
76_I	108_D	1.064	0.86
118_D	121_E	1.063	0.86
166_E	170_E	1.061	0.86
8_A	13_G	1.060	0.86
57_P	72_G	1.054	0.85
174_K	177_K	1.045	0.85
25_E	31_E	1.045	0.85
63_L	81_K	1.042	0.85
182_G	189_L	1.040	0.85
60_N	66_D	1.035	0.84
231_E	235_E	1.033	0.84
199_G	205_Y	1.027	0.84
10_L	13_G	1.027	0.84
89_I	99_E	1.025	0.84
14_A	20_F	1.015	0.83
81_K	116_A	1.013	0.83
33_V	36_E	1.001	0.82
63_L	108_D	1.000	0.82
110_A	113_L	0.997	0.82
64_V	101_V	0.997	0.82
60_N	78_V	0.996	0.82
201_Y	206_K	0.994	0.82
108_D	116_A	0.985	0.81
68_T	71_D	0.984	0.81
175_K	178_G	0.979	0.81
38_P	44_E	0.978	0.81
85_V	108_D	0.974	0.80
64_V	79_T	0.967	0.80
23_G	26_P	0.962	0.80
143_N	146_T	0.961	0.80
209_K	213_G	0.948	0.79
114_A	117_E	0.944	0.78
57_P	63_L	0.943	0.78
73_K	91_D	0.941	0.78
198_A	202_F	0.939	0.78
213_G	217_D	0.938	0.78
129_C	141_N	0.932	0.77
79_T	99_E	0.927	0.77
183_G	193_G	0.926	0.77
76_I	96_G	0.917	0.76
63_L	106_A	0.912	0.76
200_Y	204_I	0.908	0.76
181_G	184_L	0.908	0.76
138_G	148_C	0.908	0.76
8_A	14_A	0.906	0.75
186_L	193_G	0.906	0.75
230_E	234_E	0.894	0.74
148_C	151_K	0.889	0.74
55_L	85_V	0.889	0.74
61_G	116_A	0.887	0.74
37_T	40_E	0.887	0.74
33_V	37_T	0.886	0.74
64_V	85_V	0.886	0.74
96_G	108_D	0.883	0.74
173_K	176_E	0.882	0.73
189_L	192_A	0.881	0.73
103_F	114_A	0.880	0.73
74_Q	81_K	0.870	0.72
25_E	28_E	0.868	0.72
31_E	34_T	0.866	0.72
34_T	38_P	0.864	0.72
82_S	113_L	0.864	0.72
153_P	161_E	0.855	0.71
55_L	65_D	0.852	0.71
38_P	41_E	0.851	0.71
110_A	119_D	0.849	0.71
28_E	33_V	0.848	0.70
7_A	20_F	0.847	0.70
6_L	13_G	0.841	0.70
183_G	186_L	0.841	0.70
220_Y	224_E	0.841	0.70
61_G	106_A	0.837	0.69
211_A	215_D	0.836	0.69
29_E	35_E	0.824	0.68
94_R	97_E	0.824	0.68
110_A	114_A	0.824	0.68
64_V	67_I	0.823	0.68
25_E	30_T	0.817	0.68
95_D	99_E	0.816	0.68
34_T	39_E	0.812	0.67
233_E	236_D	0.809	0.67
8_A	12_M	0.808	0.67
61_G	66_D	0.805	0.66
36_E	39_E	0.805	0.66
63_L	101_V	0.797	0.66
12_M	15_F	0.796	0.66
3_A	10_L	0.795	0.65
159_P	163_P	0.791	0.65
232_E	235_E	0.790	0.65
207_P	211_A	0.788	0.65
4_A	7_A	0.787	0.65
84_N	115_L	0.787	0.65
54_P	65_D	0.786	0.65
105_N	110_A	0.785	0.65
61_G	75_F	0.782	0.64
81_K	115_L	0.780	0.64
188_V	192_A	0.778	0.64
156_E	163_P	0.776	0.64
53_E	67_I	0.775	0.64
4_A	9_L	0.775	0.64
80_T	116_A	0.771	0.63
199_G	204_I	0.767	0.63
84_N	106_A	0.765	0.62
56_T	65_D	0.764	0.62
63_L	78_V	0.762	0.62
123_E	126_P	0.759	0.62
41_E	44_E	0.759	0.62
82_S	96_G	0.755	0.61
66_D	101_V	0.750	0.61
4_A	11_L	0.749	0.61
35_E	39_E	0.747	0.61
113_L	116_A	0.747	0.61
10_L	14_A	0.734	0.59
32_P	35_E	0.733	0.59
144_N	148_C	0.728	0.59
78_V	108_D	0.721	0.58
55_L	64_V	0.716	0.57
129_C	150_G	0.714	0.57
181_G	185_L	0.712	0.57
26_P	37_T	0.710	0.57
89_I	113_L	0.709	0.57
57_P	115_L	0.708	0.57
65_D	77_T	0.703	0.56
95_D	100_N	0.703	0.56
76_I	103_F	0.702	0.56
24_G	28_E	0.692	0.55
57_P	96_G	0.692	0.55
34_T	45_T	0.692	0.55
217_D	223_D	0.691	0.55
189_L	193_G	0.684	0.54
9_L	13_G	0.681	0.54
11_L	15_F	0.681	0.54
22_G	26_P	0.678	0.53
45_T	48_E	0.677	0.53
183_G	190_A	0.673	0.53
55_L	61_G	0.671	0.53
120_E	126_P	0.668	0.52
141_N	145_M	0.667	0.52
20_F	23_G	0.662	0.52
91_D	102_Y	0.655	0.51
66_D	81_K	0.650	0.50
36_E	41_E	0.650	0.50
85_V	106_A	0.649	0.50
185_L	193_G	0.644	0.50
56_T	59_G	0.643	0.50
40_E	44_E	0.642	0.49
71_D	80_T	0.642	0.49
71_D	96_G	0.641	0.49
62_T	100_N	0.641	0.49
210_E	215_D	0.640	0.49
84_N	114_A	0.639	0.49
85_V	116_A	0.637	0.49
129_C	140_V	0.633	0.48
185_L	197_G	0.633	0.48
67_I	101_V	0.632	0.48
64_V	102_Y	0.630	0.48
38_P	43_T	0.628	0.48
83_G	109_E	0.627	0.48
83_G	107_V	0.626	0.48
67_I	96_G	0.625	0.48
63_L	71_D	0.624	0.47
68_T	89_I	0.623	0.47
27_T	30_T	0.618	0.47
71_D	101_V	0.617	0.47
89_I	102_Y	0.616	0.47
27_T	33_V	0.615	0.47
54_P	67_I	0.610	0.46
72_G	101_V	0.608	0.46
76_I	106_A	0.604	0.45
28_E	31_E	0.604	0.45
56_T	105_N	0.600	0.45
223_D	229_E	0.600	0.45
7_A	16_S	0.600	0.45
85_V	102_Y	0.598	0.45
76_I	81_K	0.593	0.44
190_A	193_G	0.587	0.44
82_S	115_L	0.587	0.44
79_T	102_Y	0.584	0.43
222_Y	229_E	0.583	0.43
31_E	37_T	0.581	0.43
174_K	179_G	0.580	0.43
61_G	67_I	0.579	0.43
182_G	185_L	0.579	0.43
142_A	145_M	0.577	0.42
98_E	101_V	0.576	0.42
122_E	125_P	0.568	0.41
31_E	41_E	0.568	0.41
7_A	11_L	0.567	0.41
36_E	50_E	0.565	0.41
210_E	222_Y	0.564	0.41
36_E	52_E	0.563	0.41
189_L	196_G	0.563	0.41
142_A	148_C	0.562	0.41
59_G	64_V	0.561	0.41
227_D	234_E	0.558	0.40
19_A	43_T	0.558	0.40
96_G	106_A	0.555	0.40
60_N	96_G	0.555	0.40
31_E	35_E	0.554	0.40
204_I	208_K	0.554	0.40
153_P	171_P	0.550	0.40
75_F	79_T	0.548	0.39
5_L	10_L	0.547	0.39
89_I	104_L	0.546	0.39
47_E	51_E	0.546	0.39
94_R	102_Y	0.544	0.39
63_L	96_G	0.543	0.39
67_I	72_G	0.542	0.39
59_G	100_N	0.541	0.39
99_E	106_A	0.539	0.38
225_D	229_E	0.538	0.38
71_D	94_R	0.535	0.38
72_G	94_R	0.534	0.38
161_E	171_P	0.530	0.38
16_S	22_G	0.527	0.37
129_C	145_M	0.524	0.37
43_T	48_E	0.523	0.37
117_E	120_E	0.523	0.37
78_V	81_K	0.518	0.36
61_G	115_L	0.517	0.36
186_L	189_L	0.516	0.36
96_G	102_Y	0.511	0.36
113_L	119_D	0.510	0.36
61_G	80_T	0.509	0.35
191_L	194_I	0.509	0.35
201_Y	209_K	0.509	0.35
71_D	95_D	0.506	0.35
124_E	127_A	0.501	0.35
54_P	91_D	0.500	0.35

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
2l2tA	2	0.1849	70.2	0.935	Contact Map
2ks1B	1	0.1849	58.2	0.94	Contact Map
2jwaA	2	0.1849	56.4	0.94	Contact Map
4u7aA	1	0	55.8	0.941	Contact Map
2rddB	1	0.1555	36.7	0.947	Contact Map
2micA	2	0.1723	33.5	0.948	Contact Map
2m20A	2	0.2395	28.6	0.95	Contact Map
2kncA	1	0.2143	26.8	0.951	Contact Map
1iijA	1	0.1471	26.5	0.951	Contact Map
2k1kA	2	0.1555	23.9	0.952	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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