DUF4218 - PFAM28P - GREMLIN Contacts

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DUF4218 - Domain of unknown function (DUF4218)

PFAM:	PF13960	Sequences: AITELCNFFRALCSKVIDVEDLEKLEKEIVETLCKLEKIFPPSFFDIMVHLPVHLVDEARLGGPVQYRWMYPFERYMKVLKGYVRNRARPEGSIAEGYLAEECLTFCSRYLEDVETIGNPPSRNE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	125 (122)
Sequences:	961 (626)
Seq/√Len:	56.7
META:	0.496

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
26_E	60_R	4.690	1.00
26_E	57_D	4.084	1.00
62_G	68_R	3.753	1.00
13_C	69_W	3.271	1.00
83_Y	101_E	2.770	1.00
23_E	60_R	2.652	1.00
4_E	35_K	2.564	1.00
76_Y	80_L	2.555	1.00
17_I	59_A	2.526	1.00
73_F	77_M	2.513	1.00
29_I	52_P	2.251	1.00
78_K	82_G	2.159	1.00
117_I	120_P	2.100	1.00
79_V	83_Y	2.055	1.00
3_T	7_N	1.796	0.99
22_L	56_V	1.675	0.99
4_E	28_E	1.648	0.99
114_V	118_G	1.644	0.99
25_L	29_I	1.618	0.99
46_D	49_V	1.509	0.98
58_E	68_R	1.459	0.97
84_V	92_G	1.454	0.97
105_T	109_R	1.433	0.97
40_F	48_M	1.423	0.97
17_I	71_Y	1.389	0.96
116_T	119_N	1.388	0.96
7_N	10_R	1.376	0.96
93_S	97_G	1.365	0.96
92_G	96_E	1.351	0.96
65_V	69_W	1.340	0.95
109_R	113_D	1.331	0.95
105_T	118_G	1.301	0.95
119_N	122_S	1.260	0.94
42_P	45_F	1.257	0.94
114_V	117_I	1.213	0.92
46_D	52_P	1.213	0.92
75_R	91_E	1.205	0.92
2_I	6_C	1.203	0.92
17_I	22_L	1.169	0.91
26_E	56_V	1.135	0.90
44_F	58_E	1.129	0.89
47_I	90_P	1.126	0.89
114_V	122_S	1.121	0.89
56_V	59_A	1.099	0.88
115_E	122_S	1.089	0.88
33_L	49_V	1.089	0.88
14_S	17_I	1.086	0.87
18_D	21_D	1.082	0.87
50_H	63_G	1.077	0.87
113_D	117_I	1.073	0.87
57_D	61_L	1.054	0.86
98_Y	107_C	1.042	0.85
112_E	121_P	1.035	0.85
49_V	52_P	1.023	0.84
20_E	27_K	1.023	0.84
118_G	121_P	1.010	0.83
15_K	22_L	1.008	0.83
101_E	122_S	1.004	0.83
105_T	108_S	0.992	0.82
7_N	11_A	0.982	0.81
2_I	53_V	0.981	0.81
36_L	46_D	0.971	0.81
109_R	118_G	0.971	0.81
85_R	97_G	0.970	0.81
45_F	48_M	0.970	0.81
108_S	111_L	0.967	0.80
118_G	122_S	0.961	0.80
52_P	56_V	0.954	0.80
115_E	121_P	0.953	0.80
4_E	31_E	0.951	0.79
93_S	98_Y	0.944	0.79
2_I	5_L	0.940	0.79
115_E	119_N	0.939	0.78
114_V	119_N	0.925	0.77
9_F	46_D	0.908	0.76
44_F	49_V	0.895	0.75
111_L	114_V	0.894	0.75
115_E	118_G	0.889	0.75
34_C	37_E	0.886	0.74
79_V	101_E	0.872	0.73
27_K	31_E	0.867	0.73
59_A	67_Y	0.850	0.71
17_I	28_E	0.843	0.71
37_E	42_P	0.834	0.70
113_D	119_N	0.826	0.69
29_I	32_T	0.822	0.69
58_E	71_Y	0.814	0.68
84_V	88_A	0.811	0.68
103_C	107_C	0.809	0.67
105_T	112_E	0.809	0.67
115_E	120_P	0.807	0.67
2_I	14_S	0.790	0.66
42_P	58_E	0.781	0.65
114_V	121_P	0.780	0.65
22_L	90_P	0.778	0.64
70_M	98_Y	0.774	0.64
2_I	92_G	0.771	0.64
33_L	45_F	0.770	0.64
63_G	74_E	0.769	0.63
26_E	30_V	0.760	0.63
109_R	116_T	0.753	0.62
112_E	117_I	0.751	0.62
3_T	12_L	0.736	0.60
112_E	123_R	0.733	0.60
24_K	76_Y	0.724	0.59
108_S	120_P	0.723	0.59
28_E	71_Y	0.719	0.58
104_L	108_S	0.711	0.57
109_R	112_E	0.708	0.57
40_F	72_P	0.707	0.57
35_K	38_K	0.703	0.57
31_E	35_K	0.701	0.56
8_F	29_I	0.700	0.56
107_C	112_E	0.699	0.56
4_E	14_S	0.698	0.56
117_I	122_S	0.695	0.56
15_K	56_V	0.693	0.55
117_I	121_P	0.688	0.55
39_I	119_N	0.687	0.55
84_V	90_P	0.681	0.54
46_D	82_G	0.680	0.54
67_Y	77_M	0.676	0.54
5_L	52_P	0.674	0.53
11_A	25_L	0.669	0.53
97_G	101_E	0.667	0.53
104_L	118_G	0.661	0.52
23_E	56_V	0.660	0.52
112_E	120_P	0.654	0.51
51_L	91_E	0.654	0.51
8_F	36_L	0.649	0.51
10_R	79_V	0.647	0.50
104_L	111_L	0.643	0.50
21_D	93_S	0.635	0.49
116_T	120_P	0.623	0.48
25_L	45_F	0.618	0.47
49_V	56_V	0.615	0.47
83_Y	107_C	0.612	0.47
119_N	123_R	0.609	0.46
52_P	117_I	0.607	0.46
10_R	13_C	0.605	0.46
78_K	87_R	0.605	0.46
64_P	71_Y	0.601	0.45
34_C	38_K	0.597	0.45
33_L	40_F	0.597	0.45
12_L	66_Q	0.597	0.45
28_E	62_G	0.593	0.45
109_R	115_E	0.593	0.45
79_V	97_G	0.582	0.43
3_T	97_G	0.577	0.43
29_I	114_V	0.575	0.43
16_V	59_A	0.575	0.43
104_L	107_C	0.575	0.43
36_L	45_F	0.574	0.43
78_K	103_C	0.574	0.43
87_R	90_P	0.573	0.42
3_T	21_D	0.573	0.42
10_R	18_D	0.568	0.42
72_P	94_I	0.566	0.42
33_L	43_S	0.566	0.42
71_Y	74_E	0.565	0.42
105_T	116_T	0.563	0.41
63_G	123_R	0.562	0.41
69_W	73_F	0.562	0.41
22_L	26_E	0.559	0.41
86_N	93_S	0.548	0.40
70_M	90_P	0.546	0.40
104_L	121_P	0.544	0.39
70_M	75_R	0.542	0.39
12_L	59_A	0.542	0.39
71_Y	96_E	0.542	0.39
42_P	86_N	0.539	0.39
64_P	78_K	0.539	0.39
101_E	118_G	0.533	0.38
83_Y	90_P	0.529	0.38
111_L	115_E	0.526	0.38
28_E	32_T	0.523	0.37
36_L	43_S	0.517	0.37
72_P	79_V	0.517	0.37
105_T	120_P	0.512	0.36
38_K	88_A	0.508	0.36
53_V	61_L	0.505	0.35
31_E	82_G	0.503	0.35
54_H	63_G	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
4i77Z	1	0.36	6.9	0.936	Contact Map
3s51A	4	0.928	6.8	0.936	Contact Map
4pjwA	1	0.832	5.8	0.938	Contact Map
4ne3B	2	0.376	5.3	0.939	Contact Map
4aikA	2	0.328	5	0.94	Contact Map
1vsy4	1	0.376	4.9	0.94	Contact Map
4e45B	2	0.376	4.4	0.942	Contact Map
4amsA	1	0.536	4.1	0.942	Contact Map
1w53A	2	0.472	4.1	0.942	Contact Map
1hy5A	1	0.352	4	0.943	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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