DUF4288 - PFAM28P - GREMLIN Contacts

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DUF4288 - Domain of unknown function (DUF4288)

PFAM:	PF14119	Sequences: WYLAKLVFRIIVGDDGDHRPQFEEQLRLIRADSEEEAFEKAEALGKEEEDSYLNPDGQLVRWKFIGVRELYELDDELEDGAEVYS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	85 (84)
Sequences:	3829 (3092)
Seq/√Len:	337.3
META:	0.956

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
3_L	26_L	3.083	1.00
40_K	79_D	2.939	1.00
9_R	65_I	2.847	1.00
10_I	62_W	2.601	1.00
32_D	36_E	2.461	1.00
4_A	41_A	2.398	1.00
4_A	70_L	2.384	1.00
5_K	24_E	2.359	1.00
54_N	58_Q	1.951	1.00
38_F	42_E	1.827	1.00
38_F	70_L	1.825	1.00
40_K	43_A	1.732	1.00
45_G	64_F	1.710	1.00
25_Q	48_E	1.698	1.00
6_L	45_G	1.692	1.00
51_S	59_L	1.670	1.00
6_L	27_R	1.628	1.00
11_I	63_K	1.610	1.00
53_L	59_L	1.570	1.00
54_N	60_V	1.489	1.00
46_K	49_E	1.473	1.00
9_R	63_K	1.423	1.00
11_I	61_R	1.407	1.00
22_F	68_R	1.388	1.00
52_Y	60_V	1.384	1.00
42_E	64_F	1.376	1.00
10_I	21_Q	1.285	1.00
33_S	36_E	1.272	1.00
74_D	81_A	1.258	1.00
67_V	70_L	1.212	1.00
71_Y	85_S	1.202	1.00
31_A	37_A	1.189	1.00
14_D	58_Q	1.127	1.00
53_L	57_G	1.122	1.00
36_E	40_K	1.098	1.00
27_R	48_E	1.097	1.00
42_E	46_K	1.096	1.00
5_K	26_L	1.091	1.00
9_R	20_P	1.061	1.00
27_R	44_L	1.047	1.00
64_F	67_V	1.003	1.00
3_L	83_V	0.990	1.00
7_V	68_R	0.986	1.00
5_K	69_E	0.985	1.00
31_A	36_E	0.982	1.00
50_D	53_L	0.981	1.00
8_F	25_Q	0.960	1.00
29_I	41_A	0.956	1.00
12_V	54_N	0.955	1.00
5_K	68_R	0.948	1.00
2_Y	34_E	0.947	1.00
39_E	42_E	0.945	1.00
12_V	60_V	0.933	1.00
36_E	39_E	0.930	1.00
78_E	81_A	0.918	1.00
7_V	24_E	0.904	1.00
24_E	68_R	0.885	1.00
51_S	61_R	0.881	1.00
38_F	67_V	0.863	1.00
16_G	40_K	0.857	1.00
8_F	48_E	0.856	1.00
69_E	73_L	0.834	1.00
43_A	47_E	0.821	1.00
13_G	59_L	0.811	1.00
20_P	65_I	0.788	1.00
50_D	62_W	0.784	1.00
42_E	66_G	0.780	1.00
12_V	16_G	0.759	1.00
34_E	70_L	0.754	1.00
12_V	58_Q	0.746	0.99
21_Q	52_Y	0.745	0.99
35_E	39_E	0.725	0.99
32_D	39_E	0.718	0.99
49_E	53_L	0.718	0.99
47_E	72_E	0.705	0.99
29_I	40_K	0.702	0.99
13_G	18_H	0.701	0.99
41_A	45_G	0.699	0.99
6_L	44_L	0.682	0.99
11_I	18_H	0.680	0.99
13_G	58_Q	0.662	0.99
8_F	27_R	0.660	0.99
45_G	49_E	0.660	0.99
35_E	42_E	0.651	0.99
39_E	43_A	0.646	0.99
34_E	72_E	0.632	0.98
45_G	48_E	0.632	0.98
21_Q	62_W	0.630	0.98
28_L	83_V	0.628	0.98
7_V	10_I	0.627	0.98
75_D	78_E	0.612	0.98
44_L	79_D	0.604	0.98
72_E	75_D	0.599	0.98
29_I	44_L	0.593	0.97
26_L	73_L	0.588	0.97
73_L	77_L	0.571	0.97
13_G	16_G	0.568	0.97
50_D	56_D	0.565	0.97
11_I	20_P	0.565	0.97
74_D	78_E	0.564	0.97
35_E	38_F	0.563	0.97
5_K	22_F	0.561	0.96
45_G	67_V	0.561	0.96
74_D	77_L	0.560	0.96
8_F	49_E	0.554	0.96
44_L	48_E	0.554	0.96
28_L	73_L	0.552	0.96
20_P	23_E	0.549	0.96
77_L	81_A	0.543	0.96
32_D	43_A	0.543	0.96
69_E	84_Y	0.534	0.95
52_Y	55_P	0.531	0.95
8_F	23_E	0.531	0.95
5_K	84_Y	0.531	0.95
12_V	52_Y	0.528	0.95
78_E	84_Y	0.525	0.95
19_R	22_F	0.522	0.95
49_E	52_Y	0.521	0.95
27_R	45_G	0.519	0.95
6_L	67_V	0.515	0.94
1_W	77_L	0.514	0.94
72_E	78_E	0.508	0.94
5_K	65_I	0.507	0.94
30_R	34_E	0.507	0.94
3_L	9_R	0.504	0.94
34_E	69_E	0.500	0.94

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
1zrtD	1	0.3529	8.7	0.888	Contact Map
1pp9D	2	0.4	7.9	0.89	Contact Map
1tdjA	2	0.9647	3.9	0.905	Contact Map
3cx5D	2	0.4353	3.9	0.905	Contact Map
2yiuB	1	0.3059	3.9	0.905	Contact Map
2qsdA	2	0.6941	3.4	0.907	Contact Map
2z0lA	3	0.3882	3.3	0.909	Contact Map
3iauA	1	0.9765	2.7	0.913	Contact Map
2qjyB	1	0.3882	2.5	0.914	Contact Map
3vk8A	1	0.9529	2.5	0.914	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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