DUF3408 - PFAM28P - GREMLIN Contacts

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DUF3408 - Protein of unknown function (DUF3408)

PFAM:	PF11888	Sequences: EIDEELLREMMAGGIPLKEKPEEEETPAPEEEEEEEEEEEEEEEPEPEPETKEVQKRESSKRRKESLEDYRETFLKPPKITDRKPVYISRETHERLDRIVRVIGGRKVSVSGYIDNILRHHLEEYKEEINELYNKK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	136 (126)
Sequences:	1411 (993)
Seq/√Len:	88.5
META:	0.782

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
74_F	120_H	4.199	1.00
89_S	115_D	3.251	1.00
120_H	125_Y	2.839	1.00
120_H	124_E	2.537	1.00
98_R	102_V	2.504	1.00
89_S	92_T	2.245	1.00
35_E	39_E	2.095	1.00
5_E	8_R	2.049	1.00
24_E	27_P	2.044	1.00
21_P	24_E	2.004	1.00
27_P	33_E	1.958	1.00
31_E	39_E	1.947	1.00
8_R	11_M	1.905	1.00
70_Y	121_H	1.790	1.00
47_P	51_T	1.766	1.00
34_E	37_E	1.742	1.00
22_E	25_E	1.740	1.00
94_E	106_R	1.708	1.00
93_H	122_L	1.631	1.00
83_R	87_Y	1.577	1.00
59_S	63_R	1.567	1.00
59_S	62_R	1.561	1.00
114_I	126_K	1.541	1.00
28_A	31_E	1.528	1.00
42_E	46_E	1.489	1.00
84_K	111_S	1.478	1.00
6_L	10_M	1.464	0.99
33_E	38_E	1.443	0.99
30_E	33_E	1.432	0.99
85_P	93_H	1.424	0.99
97_D	112_G	1.417	0.99
58_E	62_R	1.355	0.99
25_E	36_E	1.348	0.99
43_E	46_E	1.317	0.99
39_E	44_E	1.308	0.99
86_V	114_I	1.301	0.99
70_Y	113_Y	1.288	0.99
91_E	95_R	1.280	0.99
130_N	134_N	1.264	0.98
87_Y	93_H	1.250	0.98
78_P	112_G	1.246	0.98
106_R	115_D	1.236	0.98
90_R	111_S	1.234	0.98
5_E	11_M	1.222	0.98
23_E	26_T	1.217	0.98
27_P	30_E	1.193	0.98
9_E	12_A	1.184	0.98
122_L	126_K	1.184	0.98
25_E	30_E	1.173	0.97
26_T	30_E	1.170	0.97
108_V	114_I	1.154	0.97
57_R	60_S	1.150	0.97
24_E	31_E	1.128	0.97
92_T	115_D	1.126	0.97
92_T	119_R	1.094	0.96
82_D	90_R	1.088	0.96
26_T	42_E	1.087	0.96
38_E	41_E	1.084	0.96
126_K	129_I	1.078	0.96
9_E	13_G	1.061	0.95
32_E	41_E	1.048	0.95
37_E	40_E	1.046	0.95
26_T	39_E	1.041	0.95
6_L	9_E	1.023	0.94
32_E	45_P	1.021	0.94
28_A	32_E	1.015	0.94
84_K	110_V	1.014	0.94
58_E	61_K	1.006	0.94
35_E	38_E	1.003	0.94
33_E	36_E	1.003	0.94
42_E	45_P	0.999	0.94
36_E	40_E	0.993	0.93
113_Y	117_I	0.993	0.93
108_V	115_D	0.991	0.93
90_R	110_V	0.982	0.93
28_A	42_E	0.956	0.92
85_P	100_V	0.956	0.92
36_E	39_E	0.951	0.92
31_E	34_E	0.942	0.91
107_K	111_S	0.933	0.91
86_V	93_H	0.931	0.91
84_K	95_R	0.930	0.91
93_H	115_D	0.923	0.91
92_T	122_L	0.921	0.91
35_E	45_P	0.916	0.90
130_N	133_Y	0.914	0.90
119_R	123_E	0.912	0.90
113_Y	118_L	0.905	0.90
70_Y	99_I	0.880	0.88
24_E	28_A	0.878	0.88
32_E	37_E	0.875	0.88
29_P	43_E	0.869	0.88
57_R	61_K	0.862	0.87
27_P	39_E	0.854	0.87
36_E	41_E	0.848	0.86
45_P	52_K	0.846	0.86
84_K	93_H	0.841	0.86
7_L	14_G	0.835	0.86
39_E	45_P	0.831	0.85
27_P	38_E	0.831	0.85
40_E	46_E	0.826	0.85
32_E	46_E	0.821	0.85
80_I	89_S	0.819	0.85
6_L	13_G	0.811	0.84
108_V	119_R	0.809	0.84
34_E	45_P	0.789	0.82
90_R	94_E	0.789	0.82
115_D	119_R	0.787	0.82
89_S	93_H	0.784	0.82
23_E	29_P	0.781	0.82
33_E	45_P	0.780	0.82
49_P	52_K	0.775	0.81
21_P	34_E	0.769	0.81
24_E	39_E	0.762	0.80
25_E	28_A	0.760	0.80
33_E	39_E	0.754	0.79
30_E	37_E	0.751	0.79
89_S	122_L	0.748	0.79
34_E	38_E	0.738	0.78
35_E	41_E	0.735	0.78
37_E	44_E	0.724	0.77
39_E	43_E	0.722	0.76
23_E	30_E	0.718	0.76
88_I	95_R	0.694	0.73
24_E	37_E	0.686	0.73
25_E	33_E	0.671	0.71
30_E	40_E	0.667	0.70
48_E	51_T	0.665	0.70
7_L	11_M	0.664	0.70
44_E	47_P	0.663	0.70
5_E	9_E	0.663	0.70
6_L	11_M	0.660	0.70
40_E	43_E	0.657	0.69
45_P	48_E	0.656	0.69
30_E	34_E	0.653	0.69
23_E	37_E	0.648	0.68
22_E	31_E	0.645	0.68
7_L	10_M	0.638	0.67
26_T	29_P	0.637	0.67
8_R	12_A	0.634	0.67
71_R	111_S	0.632	0.66
99_I	122_L	0.630	0.66
29_P	32_E	0.625	0.65
93_H	97_D	0.625	0.65
21_P	26_T	0.622	0.65
73_T	120_H	0.620	0.65
78_P	92_T	0.619	0.65
44_E	53_E	0.616	0.64
20_K	23_E	0.613	0.64
28_A	38_E	0.612	0.64
37_E	47_P	0.610	0.64
38_E	43_E	0.606	0.63
46_E	51_T	0.603	0.63
5_E	12_A	0.602	0.63
21_P	29_P	0.601	0.62
26_T	44_E	0.599	0.62
49_P	53_E	0.598	0.62
34_E	39_E	0.598	0.62
85_P	111_S	0.589	0.61
26_T	36_E	0.587	0.61
77_P	109_S	0.581	0.60
103_I	132_L	0.581	0.60
50_E	54_V	0.578	0.59
24_E	29_P	0.578	0.59
28_A	35_E	0.566	0.58
132_L	135_K	0.566	0.58
33_E	51_T	0.560	0.57
39_E	46_E	0.559	0.57
33_E	37_E	0.554	0.56
21_P	30_E	0.549	0.56
31_E	44_E	0.544	0.55
84_K	89_S	0.543	0.55
30_E	38_E	0.536	0.54
75_L	129_I	0.532	0.53
36_E	44_E	0.531	0.53
25_E	29_P	0.531	0.53
22_E	34_E	0.530	0.53
36_E	43_E	0.527	0.53
26_T	32_E	0.525	0.52
98_R	106_R	0.524	0.52
33_E	40_E	0.523	0.52
84_K	130_N	0.523	0.52
97_D	106_R	0.523	0.52
100_V	106_R	0.521	0.52
32_E	38_E	0.513	0.51
74_F	96_L	0.513	0.51
46_E	49_P	0.510	0.50
26_T	43_E	0.504	0.50
22_E	33_E	0.500	0.49

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
1p94A	2	0.5588	72.6	0.875	Contact Map
2cpgA	2	0.3309	71.9	0.876	Contact Map
2kelA	2	0.3382	68.5	0.878	Contact Map
1bazA	4	0.3676	65.6	0.881	Contact Map
3omyA	2	0.3529	56.9	0.887	Contact Map
1dp3A	1	0.3676	56.2	0.888	Contact Map
2mdvA	2	0.2794	54.8	0.888	Contact Map
2k9iA	2	0.4044	54.1	0.889	Contact Map
4hv0A	1	0.3456	52.7	0.89	Contact Map
4qpoA	4	0.3529	50.9	0.891	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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