DUF4064 - PFAM28P - GREMLIN Contacts

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DUF4064 - Protein of unknown function (DUF4064)

PFAM:	PF13273	Sequences: KRTAEFVLGIIGGILGILGGLFALFIGGLGSDAFKEELQEQMQEEPAEQILDSLGGLIIGLGIVAIILSILGIVGAILIKKKPKLAGILLLIAGILSLIS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	100 (99)
Sequences:	1222 (1016)
Seq/√Len:	102.1
META:	0.597

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
6_F	10_I	4.566	1.00
2_R	5_E	3.215	1.00
13_G	76_A	3.144	1.00
10_I	14_I	3.076	1.00
3_T	7_V	2.964	1.00
73_I	77_I	2.795	1.00
75_G	86_A	2.650	1.00
9_G	90_L	2.361	1.00
89_L	93_A	2.345	1.00
86_A	90_L	2.037	1.00
76_A	79_I	2.015	1.00
88_I	92_I	1.915	1.00
72_G	90_L	1.759	1.00
16_G	97_S	1.756	1.00
68_L	96_L	1.713	1.00
85_L	89_L	1.711	1.00
16_G	69_S	1.548	1.00
71_L	75_G	1.543	1.00
65_A	97_S	1.525	1.00
16_G	72_G	1.522	1.00
86_A	93_A	1.501	1.00
15_L	19_G	1.492	1.00
58_I	62_G	1.443	1.00
75_G	90_L	1.420	1.00
10_I	13_G	1.394	1.00
7_V	11_I	1.386	1.00
86_A	89_L	1.380	1.00
5_E	80_K	1.368	0.99
5_E	79_I	1.347	0.99
93_A	97_S	1.268	0.99
7_V	14_I	1.255	0.99
41_Q	45_E	1.250	0.99
23_A	28_G	1.219	0.99
41_Q	44_E	1.188	0.99
5_E	81_K	1.175	0.98
72_G	93_A	1.166	0.98
70_I	74_V	1.158	0.98
37_E	40_E	1.086	0.97
85_L	88_I	1.081	0.97
22_F	27_G	1.065	0.97
59_I	63_I	1.048	0.97
83_P	86_A	1.040	0.97
1_K	5_E	1.037	0.97
89_L	98_L	1.019	0.96
75_G	79_I	1.005	0.96
20_G	24_L	1.005	0.96
13_G	16_G	1.001	0.96
39_Q	46_P	0.990	0.95
1_K	6_F	0.987	0.95
9_G	13_G	0.948	0.94
20_G	69_S	0.948	0.94
9_G	77_I	0.932	0.94
36_E	39_Q	0.923	0.93
40_E	44_E	0.888	0.92
79_I	94_G	0.880	0.92
55_G	59_I	0.876	0.92
13_G	73_I	0.875	0.91
87_G	91_L	0.873	0.91
53_S	63_I	0.872	0.91
10_I	76_A	0.861	0.91
4_A	81_K	0.849	0.90
83_P	87_G	0.847	0.90
37_E	41_Q	0.845	0.90
15_L	18_L	0.840	0.90
39_Q	44_E	0.837	0.90
39_Q	42_M	0.835	0.89
42_M	45_E	0.830	0.89
57_L	67_I	0.828	0.89
38_L	43_Q	0.820	0.89
47_A	50_I	0.818	0.88
79_I	86_A	0.816	0.88
72_G	94_G	0.803	0.88
35_K	39_Q	0.789	0.87
6_F	86_A	0.783	0.86
94_G	98_L	0.782	0.86
21_L	25_F	0.762	0.85
28_G	31_S	0.756	0.84
9_G	94_G	0.752	0.84
35_K	38_L	0.746	0.83
26_I	30_G	0.734	0.82
5_E	76_A	0.734	0.82
75_G	80_K	0.734	0.82
79_I	90_L	0.728	0.82
10_I	72_G	0.726	0.82
67_I	70_I	0.718	0.81
72_G	75_G	0.710	0.80
78_L	81_K	0.706	0.80
39_Q	43_Q	0.706	0.80
10_I	86_A	0.700	0.79
19_G	23_A	0.698	0.79
90_L	94_G	0.676	0.77
62_G	68_L	0.674	0.77
69_S	76_A	0.669	0.76
4_A	11_I	0.660	0.75
21_L	86_A	0.656	0.75
68_L	71_L	0.656	0.75
4_A	10_I	0.652	0.74
55_G	58_I	0.651	0.74
56_G	92_I	0.645	0.74
63_I	70_I	0.643	0.73
54_L	58_I	0.640	0.73
18_L	21_L	0.639	0.73
12_G	72_G	0.635	0.72
78_L	89_L	0.634	0.72
16_G	90_L	0.627	0.71
30_G	52_D	0.625	0.71
32_D	69_S	0.624	0.71
59_I	62_G	0.619	0.70
24_L	62_G	0.616	0.70
81_K	94_G	0.616	0.70
20_G	66_I	0.611	0.70
13_G	90_L	0.610	0.69
2_R	72_G	0.609	0.69
30_G	56_G	0.608	0.69
43_Q	46_P	0.608	0.69
4_A	64_V	0.605	0.69
68_L	75_G	0.605	0.69
20_G	27_G	0.602	0.68
25_F	28_G	0.597	0.68
1_K	82_K	0.592	0.67
18_L	31_S	0.590	0.67
4_A	83_P	0.584	0.66
2_R	93_A	0.575	0.65
8_L	17_I	0.570	0.64
89_L	96_L	0.567	0.64
32_D	56_G	0.564	0.63
33_A	51_L	0.560	0.63
12_G	16_G	0.554	0.62
18_L	30_G	0.549	0.61
14_I	18_L	0.547	0.61
92_I	95_I	0.546	0.61
9_G	76_A	0.544	0.61
21_L	31_S	0.539	0.60
40_E	43_Q	0.532	0.59
33_A	60_G	0.530	0.59
90_L	97_S	0.526	0.58
62_G	77_I	0.526	0.58
13_G	78_L	0.523	0.58
22_F	25_F	0.521	0.57
54_L	61_L	0.521	0.57
19_G	24_L	0.519	0.57
91_L	95_I	0.518	0.57
3_T	73_I	0.517	0.57
72_G	77_I	0.516	0.57
75_G	97_S	0.510	0.56
27_G	55_G	0.503	0.55
68_L	72_G	0.501	0.54
6_F	83_P	0.500	0.54

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
3d31C	2	0.93	19.3	0.844	Contact Map
4p79A	1	0.78	18.8	0.845	Contact Map
3x29A	1	0.74	10.7	0.861	Contact Map
4pypA	1	0.97	8	0.869	Contact Map
2onkC	2	0.92	7.7	0.87	Contact Map
4i0uA	4	0.62	7.5	0.871	Contact Map
4ib4A	1	0.49	7.4	0.871	Contact Map
3ddlA	2	0.56	7	0.873	Contact Map
4tquN	1	1	7	0.873	Contact Map
4httA	1	0.97	6.5	0.875	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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