DUF4262 - PFAM28P - GREMLIN Contacts

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DUF4262 - Domain of unknown function (DUF4262)

PFAM:	PF14081	Sequences: DIEEHGWHVQGVFGDEEGPPFAYTIGLWETFGHPELIVFGLPPELAHGLLNEVAERVRAGERFEPGERYDGLLEGFPVEFRPVDPPWYREYLGWALWFYGGDDFPALQLVWPDRNGRFPWEPGFD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	125 (123)
Sequences:	4560 (3659)
Seq/√Len:	329.9
META:	0.889

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
92_L	106_A	3.624	1.00
24_T	50_L	3.218	1.00
11_G	22_A	2.966	1.00
28_W	105_P	2.943	1.00
56_R	61_E	2.786	1.00
33_H	57_V	2.735	1.00
22_A	46_A	2.680	1.00
7_W	54_A	2.384	1.00
27_L	54_A	2.200	1.00
15_D	18_G	2.189	1.00
70_D	77_P	2.143	1.00
9_V	22_A	2.105	1.00
10_Q	25_I	2.097	1.00
51_N	54_A	2.090	1.00
110_V	120_W	2.083	1.00
94_W	97_W	1.940	1.00
36_L	109_L	1.799	1.00
7_W	51_N	1.792	1.00
11_G	43_P	1.771	1.00
68_R	77_P	1.763	1.00
79_E	120_W	1.755	1.00
25_I	95_A	1.728	1.00
37_I	92_L	1.704	1.00
53_V	109_L	1.673	1.00
9_V	47_H	1.618	1.00
117_R	123_G	1.614	1.00
113_D	117_R	1.553	1.00
82_P	105_P	1.537	1.00
9_V	51_N	1.490	1.00
47_H	51_N	1.484	1.00
96_L	104_F	1.478	1.00
68_R	79_E	1.420	1.00
31_F	58_R	1.407	1.00
84_D	87_W	1.353	1.00
80_F	109_L	1.339	1.00
64_E	67_E	1.268	1.00
28_W	32_G	1.258	1.00
65_P	81_R	1.233	1.00
11_G	47_H	1.223	1.00
36_L	53_V	1.223	1.00
14_G	20_P	1.216	1.00
39_F	91_Y	1.196	1.00
48_G	52_E	1.182	1.00
12_V	23_Y	1.161	1.00
69_Y	80_F	1.161	1.00
87_W	90_E	1.154	1.00
96_L	102_D	1.139	1.00
81_R	110_V	1.133	1.00
73_L	78_V	1.126	1.00
31_F	54_A	1.088	1.00
65_P	82_P	1.085	1.00
29_E	98_F	1.071	1.00
82_P	107_L	1.043	1.00
113_D	124_F	1.039	1.00
66_G	81_R	1.031	1.00
88_Y	92_L	1.029	1.00
43_P	46_A	1.020	1.00
87_W	91_Y	1.015	1.00
38_V	46_A	0.998	1.00
15_D	19_P	0.987	1.00
41_L	111_W	0.982	1.00
52_E	56_R	0.982	1.00
27_L	36_L	0.979	1.00
54_A	58_R	0.976	1.00
117_R	121_E	0.965	1.00
63_F	80_F	0.963	1.00
37_I	106_A	0.958	1.00
85_P	103_D	0.957	1.00
52_E	55_E	0.941	1.00
2_I	98_F	0.919	1.00
21_F	87_W	0.916	1.00
53_V	56_R	0.911	1.00
73_L	76_F	0.908	1.00
69_Y	72_L	0.908	1.00
77_P	116_G	0.907	1.00
45_L	49_L	0.906	1.00
76_F	112_P	0.903	1.00
76_F	116_G	0.896	1.00
5_H	51_N	0.880	1.00
9_V	54_A	0.862	1.00
36_L	107_L	0.853	1.00
27_L	31_F	0.851	1.00
14_G	18_G	0.850	1.00
85_P	88_Y	0.838	1.00
13_F	16_E	0.832	1.00
88_Y	93_G	0.819	1.00
46_A	49_L	0.816	1.00
83_V	92_L	0.799	1.00
93_G	96_L	0.791	1.00
14_G	19_P	0.791	1.00
55_E	58_R	0.791	1.00
41_L	45_L	0.784	1.00
111_W	124_F	0.768	1.00
95_A	104_F	0.760	1.00
45_L	48_G	0.758	1.00
10_Q	13_F	0.754	0.99
74_E	77_P	0.748	0.99
23_Y	94_W	0.741	0.99
96_L	101_G	0.739	0.99
42_P	45_L	0.729	0.99
11_G	46_A	0.727	0.99
118_F	124_F	0.725	0.99
118_F	121_E	0.723	0.99
27_L	33_H	0.713	0.99
37_I	91_Y	0.709	0.99
93_G	97_W	0.705	0.99
24_T	27_L	0.702	0.99
21_F	37_I	0.700	0.99
65_P	68_R	0.694	0.99
36_L	50_L	0.689	0.99
10_Q	94_W	0.689	0.99
37_I	83_V	0.688	0.99
25_I	94_W	0.688	0.99
65_P	107_L	0.687	0.99
36_L	57_V	0.684	0.99
21_F	91_Y	0.674	0.99
9_V	50_L	0.667	0.99
63_F	67_E	0.666	0.99
35_E	106_A	0.663	0.99
78_V	109_L	0.657	0.99
3_E	29_E	0.657	0.99
79_E	118_F	0.654	0.99
53_V	80_F	0.653	0.99
53_V	72_L	0.652	0.99
33_H	63_F	0.651	0.99
27_L	50_L	0.647	0.98
38_V	49_L	0.643	0.98
83_V	106_A	0.639	0.98
41_L	49_L	0.635	0.98
41_L	46_A	0.627	0.98
83_V	87_W	0.621	0.98
51_N	55_E	0.616	0.98
88_Y	105_P	0.615	0.98
42_P	46_A	0.615	0.98
88_Y	104_F	0.613	0.98
29_E	99_Y	0.612	0.98
30_T	58_R	0.611	0.98
92_L	96_L	0.606	0.98
24_T	36_L	0.605	0.98
40_G	111_W	0.605	0.98
112_P	116_G	0.604	0.98
50_L	53_V	0.601	0.98
95_A	99_Y	0.600	0.97
7_W	24_T	0.600	0.97
60_G	63_F	0.599	0.97
63_F	69_Y	0.595	0.97
43_P	47_H	0.594	0.97
53_V	69_Y	0.593	0.97
55_E	59_A	0.592	0.97
68_R	121_E	0.591	0.97
54_A	57_V	0.587	0.97
67_E	107_L	0.586	0.97
56_R	59_A	0.584	0.97
35_E	95_A	0.582	0.97
39_F	111_W	0.580	0.97
96_L	103_D	0.579	0.97
13_F	17_E	0.575	0.97
99_Y	104_F	0.573	0.97
117_R	122_P	0.569	0.97
14_G	17_E	0.568	0.97
10_Q	23_Y	0.567	0.96
7_W	27_L	0.561	0.96
6_G	58_R	0.558	0.96
36_L	80_F	0.558	0.96
85_P	89_R	0.558	0.96
81_R	84_D	0.555	0.96
33_H	62_R	0.554	0.96
101_G	104_F	0.551	0.96
65_P	69_Y	0.551	0.96
72_L	78_V	0.549	0.96
8_H	25_I	0.546	0.96
49_L	73_L	0.543	0.96
92_L	95_A	0.537	0.95
56_R	63_F	0.537	0.95
27_L	35_E	0.522	0.94
33_H	53_V	0.522	0.94
111_W	118_F	0.518	0.94
45_L	76_F	0.515	0.94
61_E	67_E	0.513	0.94
89_R	96_L	0.512	0.94
36_L	63_F	0.512	0.94
46_A	50_L	0.509	0.94
66_G	82_P	0.500	0.93
83_V	93_G	0.500	0.93

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
2o8bB	1	0.24	20.7	0.907	Contact Map
3k5jA	1	0.92	9.3	0.921	Contact Map
1vcoA	4	0.432	5.2	0.93	Contact Map
4l4vA	1	0.864	5	0.93	Contact Map
1j0wA	1	0.424	4.8	0.931	Contact Map
1uvjA	1	0.44	3.7	0.934	Contact Map
1s7qA	1	0.856	3.4	0.935	Contact Map
2v76A	1	0.4	3.4	0.936	Contact Map
1s1mA	4	0.496	3.1	0.936	Contact Map
3ff4A	1	0.744	3	0.937	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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