DUF4387 - PFAM28P - GREMLIN Contacts

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DUF4387 - Domain of unknown function (DUF4387)

PFAM:	PF14330	Sequences: LGDLAKVIRSKNAGPFELTFDIIFDDRETYERVKASGVLTRELIARLYGVPPERIVKFFEFDPALAIKITIPRPVPSGSPGDRDVYGAQQHAPLLDLE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	98 (96)
Sequences:	4695 (2919)
Seq/√Len:	297.9
META:	0.915

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
27_R	31_E	4.194	1.00
26_D	29_T	3.890	1.00
27_R	65_L	3.416	1.00
42_E	52_P	3.058	1.00
31_E	35_A	2.484	1.00
34_K	62_D	2.482	1.00
30_Y	62_D	2.473	1.00
34_K	60_E	2.320	1.00
24_F	33_V	2.127	1.00
77_S	85_V	1.997	1.00
17_E	70_T	1.989	1.00
25_D	29_T	1.986	1.00
60_E	67_I	1.953	1.00
43_L	46_R	1.862	1.00
20_F	71_I	1.705	1.00
5_A	22_I	1.679	1.00
56_V	72_P	1.669	1.00
42_E	46_R	1.620	1.00
92_A	95_L	1.545	1.00
32_R	36_S	1.491	1.00
37_G	60_E	1.481	1.00
58_F	69_I	1.468	1.00
45_A	52_P	1.466	1.00
16_F	76_P	1.448	1.00
30_Y	60_E	1.444	1.00
6_K	25_D	1.441	1.00
61_F	64_A	1.434	1.00
41_R	52_P	1.426	1.00
4_L	29_T	1.351	1.00
73_R	82_D	1.349	1.00
82_D	85_V	1.348	1.00
31_E	62_D	1.347	1.00
31_E	34_K	1.322	1.00
75_V	81_G	1.224	1.00
27_R	62_D	1.210	1.00
45_A	55_I	1.206	1.00
76_P	79_S	1.199	1.00
88_A	91_H	1.135	1.00
23_I	66_A	1.057	1.00
43_L	97_L	1.056	1.00
55_I	72_P	1.049	1.00
39_L	58_F	1.046	1.00
20_F	94_L	1.043	1.00
18_L	87_G	1.037	1.00
18_L	71_I	1.024	1.00
50_V	71_I	1.023	1.00
43_L	47_L	1.018	1.00
51_P	55_I	1.004	1.00
75_V	79_S	0.986	1.00
44_I	69_I	0.984	1.00
4_L	33_V	0.961	1.00
40_T	43_L	0.958	1.00
86_Y	91_H	0.950	1.00
75_V	82_D	0.892	1.00
29_T	32_R	0.837	1.00
30_Y	34_K	0.835	1.00
41_R	58_F	0.833	1.00
23_I	64_A	0.830	1.00
74_P	83_R	0.817	1.00
33_V	36_S	0.804	1.00
79_S	82_D	0.801	1.00
45_A	72_P	0.794	0.99
20_F	69_I	0.787	0.99
4_L	32_R	0.785	0.99
83_R	88_A	0.782	0.99
17_E	56_V	0.773	0.99
5_A	8_I	0.770	0.99
28_E	31_E	0.762	0.99
58_F	67_I	0.762	0.99
11_K	15_P	0.761	0.99
17_E	72_P	0.761	0.99
28_E	32_R	0.759	0.99
19_T	70_T	0.759	0.99
48_Y	93_P	0.758	0.99
40_T	58_F	0.753	0.99
34_K	67_I	0.750	0.99
57_K	72_P	0.739	0.99
1_L	8_I	0.739	0.99
20_F	44_I	0.735	0.99
91_H	95_L	0.735	0.99
50_V	55_I	0.725	0.99
20_F	48_Y	0.722	0.99
7_V	88_A	0.714	0.99
18_L	74_P	0.689	0.99
78_G	82_D	0.686	0.99
40_T	46_R	0.683	0.98
77_S	86_Y	0.673	0.98
9_R	23_I	0.666	0.98
73_R	78_G	0.663	0.98
44_I	48_Y	0.663	0.98
41_R	45_A	0.653	0.98
38_V	43_L	0.650	0.98
25_D	65_L	0.644	0.98
18_L	73_R	0.638	0.98
5_A	33_V	0.637	0.98
18_L	90_Q	0.632	0.97
59_F	70_T	0.625	0.97
39_L	44_I	0.620	0.97
61_F	70_T	0.620	0.97
17_E	64_A	0.618	0.97
22_I	69_I	0.611	0.97
7_V	23_I	0.605	0.97
38_V	97_L	0.601	0.97
7_V	91_H	0.592	0.96
17_E	76_P	0.590	0.96
3_D	6_K	0.590	0.96
41_R	56_V	0.589	0.96
88_A	92_A	0.586	0.96
48_Y	71_I	0.582	0.96
59_F	86_Y	0.581	0.96
35_A	60_E	0.576	0.96
86_Y	92_A	0.575	0.96
88_A	95_L	0.574	0.96
77_S	80_P	0.572	0.96
5_A	25_D	0.569	0.95
14_G	73_R	0.569	0.95
7_V	18_L	0.564	0.95
10_S	20_F	0.558	0.95
42_E	53_E	0.557	0.95
76_P	82_D	0.555	0.95
37_G	40_T	0.553	0.95
41_R	55_I	0.551	0.95
85_V	91_H	0.551	0.95
22_I	67_I	0.551	0.95
92_A	96_D	0.546	0.94
2_G	96_D	0.541	0.94
78_G	85_V	0.540	0.94
25_D	64_A	0.536	0.94
29_T	65_L	0.530	0.93
1_L	4_L	0.528	0.93
39_L	43_L	0.528	0.93
11_K	86_Y	0.523	0.93
11_K	16_F	0.522	0.93
48_Y	91_H	0.522	0.93
41_R	60_E	0.522	0.93
78_G	83_R	0.520	0.93
33_V	67_I	0.517	0.92
29_T	38_V	0.516	0.92
45_A	51_P	0.512	0.92
2_G	8_I	0.510	0.92
33_V	37_G	0.508	0.92
5_A	24_F	0.504	0.91
25_D	33_V	0.504	0.91
13_A	17_E	0.500	0.91

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
3uowA	2	0.3367	12.4	0.933	Contact Map
3tqiA	3	0.3265	8.3	0.938	Contact Map
4ecqA	1	0.7755	8.1	0.938	Contact Map
2dplA	2	0.3367	7.7	0.939	Contact Map
4j2nA	4	0.5102	7.4	0.94	Contact Map
2ywbA	4	0.3367	7.2	0.94	Contact Map
1gpmA	3	0.3367	6	0.942	Contact Map
5a0dA	1	0.3776	5.2	0.944	Contact Map
3hhwA	3	0.6531	4.7	0.945	Contact Map
1dgwA	3	0.7143	4.4	0.946	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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