DUF4290 - PFAM28P - GREMLIN Contacts

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DUF4290 - Domain of unknown function (DUF4290)

PFAM:	PF14123	Sequences: MEYNTQREKLILPEYGRNIQKMVDHAKTIEDREERNRCAKAIIEVMGNLNPHLRDVEDFKHKLWDHLFIMSDFKLDVDSPYPIPTKEELEEKPEPLPYPQNKIKYRHYGKNIELMIDKAIEMEDGEEKEALIRLIANHMKKSYLNWNKDSVDDEVIFKDLKELSDGKLKLDEE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	173 (172)
Sequences:	4067 (2350)
Seq/√Len:	179.2
META:	0.916

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
27_K	74_K	4.968	1.00
36_N	40_K	3.590	1.00
32_R	76_D	3.494	1.00
118_K	121_E	3.424	1.00
161_K	169_K	3.363	1.00
32_R	78_D	3.314	1.00
26_A	42_I	3.169	1.00
25_H	28_T	2.774	1.00
71_S	74_K	2.558	1.00
39_A	67_L	2.448	1.00
29_I	38_C	2.406	1.00
2_E	7_R	2.231	1.00
26_A	38_C	2.202	1.00
73_F	89_L	2.197	1.00
120_I	167_K	2.151	1.00
122_M	125_G	2.073	1.00
68_F	79_S	2.058	1.00
27_K	71_S	2.051	1.00
8_E	24_D	2.008	1.00
107_H	159_D	2.000	1.00
138_H	141_K	1.991	1.00
72_D	86_K	1.989	1.00
68_F	83_I	1.969	1.00
105_Y	162_E	1.874	1.00
125_G	129_E	1.810	1.00
26_A	39_A	1.737	1.00
34_E	37_R	1.725	1.00
158_K	161_K	1.720	1.00
116_I	164_S	1.709	1.00
117_D	121_E	1.611	1.00
34_E	38_C	1.604	1.00
31_D	34_E	1.591	1.00
125_G	128_K	1.584	1.00
101_N	110_K	1.573	1.00
79_S	82_P	1.513	1.00
47_G	53_L	1.493	1.00
130_A	133_R	1.483	1.00
119_A	135_I	1.472	1.00
23_V	71_S	1.469	1.00
21_K	24_D	1.413	1.00
85_T	88_E	1.398	1.00
124_D	128_K	1.385	1.00
79_S	83_I	1.376	1.00
132_I	168_L	1.335	1.00
33_E	37_R	1.303	1.00
25_H	29_I	1.300	1.00
91_E	94_E	1.298	1.00
2_E	21_K	1.290	1.00
43_I	63_L	1.280	1.00
61_H	65_D	1.278	1.00
155_V	159_D	1.232	1.00
140_K	153_D	1.219	1.00
43_I	67_L	1.218	1.00
116_I	160_L	1.192	1.00
103_I	113_E	1.183	1.00
112_I	135_I	1.176	1.00
111_N	114_L	1.174	1.00
4_N	7_R	1.174	1.00
29_I	34_E	1.172	1.00
22_M	38_C	1.166	1.00
45_V	48_N	1.164	1.00
116_I	135_I	1.161	1.00
45_V	49_L	1.157	1.00
38_C	41_A	1.149	1.00
138_H	142_S	1.143	1.00
128_K	132_I	1.128	1.00
112_I	142_S	1.125	1.00
47_G	59_F	1.111	1.00
68_F	77_V	1.091	1.00
130_A	134_L	1.090	1.00
83_I	86_K	1.068	1.00
15_Y	66_H	1.063	1.00
33_E	36_N	1.062	1.00
154_E	158_K	1.050	1.00
126_E	129_E	1.049	1.00
23_V	67_L	1.049	1.00
159_D	162_E	1.048	1.00
110_K	113_E	1.045	1.00
46_M	63_L	1.021	0.99
110_K	114_L	1.019	0.99
119_A	131_L	1.016	0.99
36_N	78_D	1.011	0.99
52_H	56_V	1.010	0.99
108_Y	159_D	1.010	0.99
129_E	132_I	1.010	0.99
155_V	158_K	1.003	0.99
7_R	21_K	1.001	0.99
44_E	60_K	1.001	0.99
144_L	151_V	0.997	0.99
119_A	132_I	0.991	0.99
67_L	75_L	0.990	0.99
164_S	168_L	0.976	0.99
104_K	113_E	0.967	0.99
140_K	151_V	0.962	0.99
114_L	117_D	0.960	0.99
58_D	61_H	0.957	0.99
25_H	38_C	0.952	0.99
11_I	20_Q	0.936	0.99
18_N	21_K	0.934	0.99
122_M	127_E	0.932	0.99
53_L	59_F	0.929	0.99
52_H	55_D	0.924	0.99
114_L	118_K	0.924	0.99
119_A	168_L	0.907	0.99
124_D	129_E	0.902	0.99
69_I	73_F	0.900	0.99
117_D	120_I	0.896	0.99
118_K	122_M	0.886	0.98
132_I	160_L	0.880	0.98
143_Y	156_I	0.879	0.98
24_D	72_D	0.878	0.98
29_I	32_R	0.868	0.98
99_P	110_K	0.866	0.98
35_R	39_A	0.864	0.98
121_E	167_K	0.855	0.98
23_V	42_I	0.849	0.98
113_E	117_D	0.836	0.98
102_K	110_K	0.834	0.98
151_V	156_I	0.829	0.98
143_Y	151_V	0.823	0.98
47_G	54_R	0.815	0.97
136_A	170_L	0.812	0.97
59_F	63_L	0.809	0.97
52_H	59_F	0.809	0.97
61_H	81_Y	0.808	0.97
81_Y	84_P	0.804	0.97
79_S	84_P	0.802	0.97
88_E	91_E	0.797	0.97
107_H	139_M	0.797	0.97
136_A	160_L	0.796	0.97
11_I	72_D	0.792	0.97
111_N	138_H	0.784	0.97
116_I	168_L	0.783	0.97
160_L	164_S	0.782	0.97
141_K	144_L	0.782	0.97
8_E	12_L	0.779	0.97
50_N	53_L	0.778	0.97
137_N	140_K	0.760	0.96
55_D	60_K	0.755	0.96
50_N	70_M	0.754	0.96
20_Q	24_D	0.745	0.96
126_E	130_A	0.742	0.95
129_E	171_D	0.737	0.95
120_I	128_K	0.729	0.95
32_R	36_N	0.725	0.95
161_K	164_S	0.716	0.95
65_D	84_P	0.716	0.95
108_Y	147_N	0.710	0.94
36_N	68_F	0.709	0.94
100_Q	103_I	0.702	0.94
113_E	163_L	0.695	0.94
65_D	82_P	0.682	0.93
47_G	60_K	0.680	0.93
86_K	90_E	0.680	0.93
30_E	34_E	0.679	0.93
11_I	70_M	0.678	0.93
144_L	150_S	0.678	0.93
102_K	113_E	0.677	0.93
14_E	62_K	0.676	0.93
53_L	61_H	0.667	0.92
47_G	55_D	0.666	0.92
101_N	115_M	0.661	0.92
65_D	81_Y	0.661	0.92
24_D	70_M	0.660	0.92
143_Y	146_W	0.660	0.92
93_P	96_L	0.657	0.92
10_L	13_P	0.655	0.91
152_D	155_V	0.655	0.91
30_E	33_E	0.654	0.91
44_E	47_G	0.651	0.91
30_E	123_E	0.646	0.91
35_R	78_D	0.643	0.91
104_K	165_D	0.639	0.90
52_H	61_H	0.637	0.90
142_S	146_W	0.637	0.90
143_Y	148_K	0.637	0.90
144_L	149_D	0.636	0.90
78_D	81_Y	0.636	0.90
38_C	42_I	0.634	0.90
87_E	91_E	0.630	0.90
129_E	133_R	0.629	0.90
69_I	89_L	0.623	0.89
124_D	167_K	0.610	0.88
122_M	131_L	0.610	0.88
12_L	23_V	0.610	0.88
56_V	59_F	0.609	0.88
143_Y	155_V	0.608	0.88
1_M	143_Y	0.607	0.88
85_T	89_L	0.605	0.88
74_K	86_K	0.603	0.88
55_D	58_D	0.602	0.88
53_L	62_K	0.601	0.88
120_I	168_L	0.597	0.87
120_I	165_D	0.596	0.87
30_E	121_E	0.591	0.87
112_I	115_M	0.591	0.87
55_D	59_F	0.589	0.87
73_F	85_T	0.587	0.86
73_F	93_P	0.586	0.86
8_E	11_I	0.585	0.86
137_N	141_K	0.583	0.86
36_N	79_S	0.582	0.86
47_G	63_L	0.581	0.86
132_I	170_L	0.580	0.86
22_M	26_A	0.579	0.86
19_I	45_V	0.578	0.86
138_H	159_D	0.577	0.85
53_L	56_V	0.575	0.85
127_E	141_K	0.573	0.85
112_I	139_M	0.572	0.85
158_K	162_E	0.572	0.85
54_R	59_F	0.572	0.85
161_K	165_D	0.571	0.85
68_F	85_T	0.568	0.85
150_S	155_V	0.566	0.84
37_R	41_A	0.561	0.84
101_N	114_L	0.561	0.84
47_G	56_V	0.556	0.83
38_C	45_V	0.553	0.83
127_E	130_A	0.552	0.83
157_F	168_L	0.546	0.82
147_N	164_S	0.544	0.82
9_K	72_D	0.544	0.82
120_I	164_S	0.543	0.82
157_F	161_K	0.543	0.82
22_M	45_V	0.542	0.82
24_D	27_K	0.540	0.81
68_F	71_S	0.539	0.81
68_F	159_D	0.536	0.81
20_Q	70_M	0.535	0.81
117_D	165_D	0.534	0.81
107_H	152_D	0.530	0.80
101_N	106_R	0.529	0.80
161_K	166_G	0.527	0.80
148_K	153_D	0.526	0.80
52_H	58_D	0.524	0.80
9_K	20_Q	0.524	0.80
141_K	145_N	0.524	0.80
28_T	38_C	0.523	0.79
133_R	171_D	0.522	0.79
152_D	157_F	0.521	0.79
8_E	70_M	0.520	0.79
115_M	139_M	0.520	0.79
105_Y	163_L	0.519	0.79
106_R	138_H	0.518	0.79
157_F	172_E	0.518	0.79
141_K	159_D	0.515	0.78
23_V	26_A	0.513	0.78
46_M	70_M	0.510	0.78
47_G	61_H	0.510	0.78
82_P	85_T	0.510	0.78
154_E	172_E	0.509	0.78
2_E	6_Q	0.506	0.77
11_I	18_N	0.505	0.77
157_F	169_K	0.505	0.77
47_G	50_N	0.505	0.77
94_E	97_P	0.501	0.76
39_A	77_V	0.500	0.76

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
1kxgA	5	0.2428	11.1	0.96	Contact Map
3k49A	1	0.3757	6.3	0.965	Contact Map
2ve7A	1	0.8092	5.8	0.965	Contact Map
3bwtA	1	0.3699	5	0.966	Contact Map
2hinA	2	0.3237	4.7	0.967	Contact Map
1b4aA	5	0.2832	4.6	0.967	Contact Map
1rq6A	1	0.2139	3.9	0.968	Contact Map
3j20S	1	0.2428	3.3	0.969	Contact Map
1stzA	3	0.3006	3.3	0.969	Contact Map
2tnfA	3	0.2601	3.2	0.969	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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