COPI_assoc - PFAM28P - GREMLIN Contacts

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COPI_assoc - COPI associated protein

PFAM:	PF08507	Sequences: HNIFRILNLVVGVLLILGGILQFISLFSDFFSIILGIYVILFGLLLVLLEFRIPFIRRYFGFLFSFLGRGLFYIFVGLLLLGGGLLGIIAGILLLAVGLLYIVLGFIPSIEPPRNMREADAEQAVKDLE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	129 (114)
Sequences:	905 (782)
Seq/√Len:	73.2
META:	0.529

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
70_G	98_G	4.178	1.00
85_L	89_I	3.394	1.00
74_I	98_G	3.179	1.00
78_L	81_L	3.062	1.00
19_G	43_G	2.402	1.00
91_G	95_L	2.383	1.00
88_I	92_I	2.187	1.00
42_F	75_F	2.183	1.00
12_G	43_G	2.170	1.00
13_V	17_L	2.098	1.00
77_G	95_L	2.094	1.00
62_F	72_F	2.024	1.00
46_L	73_Y	2.003	1.00
16_I	43_G	1.998	1.00
17_L	21_L	1.942	1.00
42_F	72_F	1.864	1.00
69_R	94_L	1.814	1.00
62_F	68_G	1.786	1.00
14_L	90_A	1.760	1.00
113_P	116_M	1.724	1.00
38_Y	75_F	1.617	0.99
12_G	19_G	1.608	0.99
50_E	69_R	1.595	0.99
70_G	102_I	1.532	0.99
79_L	82_G	1.515	0.99
15_L	19_G	1.457	0.99
8_N	73_Y	1.440	0.99
92_I	96_A	1.387	0.98
61_G	65_S	1.335	0.98
12_G	46_L	1.321	0.98
45_L	60_F	1.281	0.97
111_E	115_N	1.273	0.97
78_L	82_G	1.257	0.97
67_L	105_G	1.232	0.97
112_P	116_M	1.229	0.96
38_Y	42_F	1.228	0.96
50_E	73_Y	1.215	0.96
11_V	97_V	1.184	0.96
57_R	64_F	1.175	0.95
109_S	113_P	1.173	0.95
69_R	73_Y	1.166	0.95
77_G	91_G	1.156	0.95
80_L	83_G	1.146	0.95
86_L	90_A	1.140	0.95
109_S	115_N	1.136	0.95
21_L	24_I	1.134	0.95
35_L	38_Y	1.123	0.94
43_G	50_E	1.117	0.94
20_I	24_I	1.105	0.94
38_Y	63_L	1.087	0.93
46_L	76_V	1.082	0.93
111_E	114_R	1.081	0.93
7_L	11_V	1.054	0.92
43_G	62_F	1.046	0.92
101_Y	105_G	1.041	0.92
67_L	102_I	1.029	0.91
22_Q	36_G	1.022	0.91
12_G	47_V	0.994	0.90
73_Y	77_G	0.979	0.89
110_I	116_M	0.973	0.89
48_L	51_F	0.965	0.88
14_L	18_G	0.965	0.88
16_I	20_I	0.963	0.88
5_R	52_R	0.962	0.88
74_I	102_I	0.951	0.87
109_S	116_M	0.944	0.87
16_I	23_F	0.923	0.86
3_I	7_L	0.922	0.86
77_G	98_G	0.919	0.86
61_G	64_F	0.913	0.85
4_F	12_G	0.908	0.85
47_V	104_L	0.907	0.85
51_F	57_R	0.899	0.84
58_R	100_L	0.881	0.83
109_S	114_R	0.880	0.83
27_F	33_I	0.867	0.82
10_V	13_V	0.854	0.81
65_S	68_G	0.845	0.80
37_I	41_L	0.845	0.80
8_N	65_S	0.844	0.80
49_L	63_L	0.836	0.80
54_P	76_V	0.823	0.79
45_L	53_I	0.811	0.78
84_G	88_I	0.805	0.77
23_F	34_I	0.805	0.77
105_G	108_P	0.804	0.77
108_P	112_P	0.801	0.77
91_G	94_L	0.791	0.76
18_G	90_A	0.764	0.73
26_L	92_I	0.764	0.73
110_I	113_P	0.755	0.72
104_L	107_I	0.755	0.72
106_F	113_P	0.753	0.72
59_Y	72_F	0.752	0.72
16_I	76_V	0.751	0.72
10_V	89_I	0.747	0.72
53_I	65_S	0.745	0.71
106_F	111_E	0.743	0.71
109_S	112_P	0.736	0.70
49_L	69_R	0.727	0.70
110_I	114_R	0.726	0.69
72_F	76_V	0.725	0.69
18_G	49_L	0.723	0.69
60_F	73_Y	0.722	0.69
112_P	115_N	0.719	0.69
17_L	20_I	0.716	0.68
89_I	92_I	0.716	0.68
85_L	92_I	0.711	0.68
19_G	42_F	0.709	0.68
15_L	39_V	0.704	0.67
84_G	102_I	0.696	0.66
48_L	54_P	0.690	0.66
107_I	110_I	0.685	0.65
57_R	61_G	0.678	0.64
108_P	116_M	0.676	0.64
73_Y	97_V	0.675	0.64
30_F	33_I	0.667	0.63
46_L	80_L	0.666	0.63
74_I	77_G	0.662	0.62
63_L	72_F	0.660	0.62
43_G	68_G	0.654	0.61
48_L	106_F	0.649	0.61
9_L	13_V	0.646	0.60
31_F	61_G	0.629	0.58
60_F	69_R	0.622	0.58
4_F	7_L	0.620	0.57
31_F	37_I	0.617	0.57
77_G	94_L	0.613	0.56
48_L	67_L	0.609	0.56
16_I	47_V	0.606	0.56
40_I	92_I	0.605	0.55
10_V	41_L	0.605	0.55
13_V	33_I	0.604	0.55
13_V	86_L	0.593	0.54
33_I	37_I	0.585	0.53
45_L	103_V	0.582	0.53
79_L	101_Y	0.571	0.51
46_L	63_L	0.570	0.51
10_V	21_L	0.570	0.51
17_L	24_I	0.567	0.51
70_G	92_I	0.562	0.50
34_I	51_F	0.555	0.49
99_L	103_V	0.554	0.49
14_L	74_I	0.552	0.49
35_L	91_G	0.552	0.49
27_F	103_V	0.551	0.49
63_L	68_G	0.551	0.49
58_R	90_A	0.549	0.49
19_G	22_Q	0.547	0.48
6_I	37_I	0.541	0.48
83_G	86_L	0.539	0.47
24_I	100_L	0.539	0.47
40_I	43_G	0.535	0.47
4_F	98_G	0.533	0.47
53_I	86_L	0.532	0.46
27_F	90_A	0.532	0.46
53_I	56_I	0.530	0.46
70_G	105_G	0.527	0.46
38_Y	50_E	0.526	0.46
32_S	94_L	0.525	0.46
9_L	14_L	0.523	0.45
85_L	88_I	0.515	0.44
44_L	97_V	0.512	0.44
16_I	37_I	0.511	0.44
32_S	103_V	0.508	0.43
28_S	71_L	0.505	0.43
77_G	90_A	0.505	0.43
70_G	77_G	0.505	0.43
64_F	110_I	0.501	0.43
36_G	66_F	0.500	0.43
78_L	91_G	0.500	0.43

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
4o6yA	2	0.8295	40.4	0.868	Contact Map
4pypA	1	0.8372	26.4	0.88	Contact Map
4ev6A	3	0.4574	18.8	0.888	Contact Map
3l1lA	2	0.8372	16.5	0.891	Contact Map
4i0uA	4	0.4496	15.5	0.892	Contact Map
4bgnA	3	0.845	13.5	0.895	Contact Map
3rvyA	3	0.7907	12.9	0.896	Contact Map
2jlnA	1	0.876	9.7	0.902	Contact Map
4zw9A	1	0.938	8.5	0.904	Contact Map
2xq2A	2	0.969	8.1	0.905	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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