DUF3899 - PFAM28P - GREMLIN Contacts

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DUF3899 - Domain of unknown function (DUF3899)

PFAM:	PF13038	Sequences: INALFIVGLLLLIIGLLLFVSNGGFFDGFSYGFRKLFRRFFRKKKKKKESYYEYKEEKKEKKKKSTLPLLIVGLILLLLSIILLF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	85 (84)
Sequences:	1048 (956)
Seq/√Len:	104.3
META:	0.651

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
8_G	77_L	3.456	1.00
49_E	57_E	2.984	1.00
24_G	27_D	2.862	1.00
50_S	53_E	2.579	1.00
20_V	25_F	2.324	1.00
52_Y	56_E	2.257	1.00
15_G	73_G	2.022	1.00
8_G	80_S	1.875	1.00
3_A	7_V	1.870	1.00
13_I	17_L	1.853	1.00
12_L	73_G	1.829	1.00
20_V	23_G	1.816	1.00
16_L	19_F	1.717	1.00
51_Y	55_K	1.709	1.00
5_F	80_S	1.655	1.00
37_F	40_F	1.640	1.00
4_L	79_L	1.638	1.00
51_Y	54_Y	1.631	1.00
31_Y	54_Y	1.573	1.00
1_I	5_F	1.504	1.00
6_I	9_L	1.497	1.00
19_F	23_G	1.431	1.00
11_L	70_L	1.384	1.00
18_L	22_N	1.371	1.00
1_I	4_L	1.356	0.99
50_S	54_Y	1.309	0.99
67_L	70_L	1.308	0.99
1_I	84_L	1.240	0.99
20_V	26_F	1.235	0.99
17_L	27_D	1.221	0.99
46_K	50_S	1.138	0.98
15_G	74_L	1.127	0.98
9_L	13_I	1.100	0.98
1_I	83_L	1.086	0.98
22_N	27_D	1.080	0.97
71_I	74_L	1.077	0.97
48_K	51_Y	1.050	0.97
17_L	30_S	1.041	0.97
27_D	32_G	1.022	0.96
12_L	16_L	0.998	0.96
13_I	80_S	0.997	0.96
75_I	81_I	0.997	0.96
79_L	83_L	0.983	0.96
34_R	43_K	0.976	0.95
1_I	81_I	0.960	0.95
14_I	69_L	0.960	0.95
32_G	36_L	0.955	0.95
35_K	41_F	0.942	0.94
18_L	72_V	0.934	0.94
27_D	55_K	0.929	0.94
75_I	79_L	0.924	0.94
48_K	54_Y	0.920	0.94
70_L	74_L	0.901	0.93
33_F	37_F	0.900	0.93
8_G	73_G	0.868	0.92
4_L	7_V	0.854	0.91
25_F	28_G	0.847	0.91
30_S	58_K	0.840	0.90
11_L	32_G	0.834	0.90
71_I	82_I	0.831	0.90
72_V	75_I	0.825	0.89
69_L	72_V	0.818	0.89
68_P	71_I	0.813	0.89
5_F	26_F	0.806	0.88
23_G	29_F	0.799	0.88
30_S	34_R	0.796	0.88
65_S	74_L	0.793	0.87
35_K	46_K	0.784	0.87
76_L	80_S	0.772	0.86
17_L	24_G	0.770	0.86
22_N	33_F	0.755	0.85
31_Y	35_K	0.743	0.84
56_E	59_K	0.737	0.83
27_D	33_F	0.736	0.83
6_I	10_L	0.733	0.83
54_Y	58_K	0.730	0.83
13_I	16_L	0.730	0.83
54_Y	57_E	0.722	0.82
22_N	66_T	0.715	0.81
49_E	53_E	0.712	0.81
15_G	80_S	0.710	0.81
1_I	30_S	0.703	0.80
52_Y	59_K	0.699	0.80
4_L	72_V	0.694	0.80
9_L	18_L	0.693	0.79
46_K	49_E	0.691	0.79
74_L	78_L	0.684	0.79
10_L	44_K	0.680	0.78
45_K	49_E	0.679	0.78
5_F	77_L	0.674	0.78
23_G	28_G	0.660	0.76
47_K	51_Y	0.660	0.76
28_G	35_K	0.659	0.76
30_S	57_E	0.648	0.75
22_N	32_G	0.627	0.72
46_K	56_E	0.622	0.72
39_R	51_Y	0.618	0.71
24_G	32_G	0.617	0.71
62_K	69_L	0.611	0.70
15_G	70_L	0.609	0.70
1_I	21_S	0.596	0.68
13_I	34_R	0.593	0.68
29_F	33_F	0.592	0.68
48_K	63_K	0.589	0.68
49_E	71_I	0.585	0.67
11_L	73_G	0.581	0.67
72_V	76_L	0.577	0.66
32_G	40_F	0.571	0.65
3_A	8_G	0.567	0.65
5_F	25_F	0.564	0.64
59_K	84_L	0.563	0.64
63_K	66_T	0.559	0.64
46_K	60_E	0.544	0.61
38_R	47_K	0.544	0.61
72_V	79_L	0.541	0.61
16_L	63_K	0.541	0.61
41_F	44_K	0.534	0.60
55_K	59_K	0.529	0.59
13_I	18_L	0.524	0.59
12_L	77_L	0.522	0.58
19_F	68_P	0.517	0.58
4_L	80_S	0.509	0.56
66_T	70_L	0.508	0.56
18_L	74_L	0.504	0.56
2_N	70_L	0.502	0.55
37_F	77_L	0.500	0.55

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
3owqA	1	0	8	0.856	Contact Map
3j9pD	4	0.9412	6.7	0.861	Contact Map
2bg9A	1	0.9412	6.6	0.862	Contact Map
4r1iA	2	0.4353	6.4	0.863	Contact Map
4nv5A	1	0.3059	5.3	0.868	Contact Map
4r0cA	3	0.2941	5.3	0.868	Contact Map
2kncA	1	0.4824	5.2	0.869	Contact Map
2bg9B	1	0.9412	5.1	0.869	Contact Map
2onkC	2	0.2588	5.1	0.869	Contact Map
2bg9E	1	0.9412	4.6	0.872	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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