DUF1825 - PFAM28P - GREMLIN Contacts

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DUF1825 - Domain of unknown function (DUF1825)

PFAM:	PF08855	Sequences: MSFFDSEIVREELKEINELQEEIYGNVFKFPSMDREEKLEHIEKLEELLEKQKIFYTRLSLSDDPEAKEMKEQIKKSAGMMGVDMNQMFDNMSKTLERMKKQI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	103 (101)
Sequences:	1405 (761)
Seq/√Len:	75.7
META:	0.944

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
46_E	100_K	2.790	1.00
71_K	74_I	2.751	1.00
77_S	80_M	2.541	1.00
2_S	5_D	2.525	1.00
69_E	73_Q	2.411	1.00
10_R	14_K	2.313	1.00
11_E	14_K	2.197	1.00
74_I	78_A	2.170	1.00
53_K	90_D	2.090	1.00
34_D	37_E	2.013	1.00
12_E	54_I	1.955	1.00
22_E	44_K	1.917	1.00
88_M	92_M	1.909	1.00
72_E	75_K	1.877	1.00
73_Q	76_K	1.777	1.00
75_K	78_A	1.769	1.00
37_E	40_E	1.724	1.00
29_K	32_S	1.712	1.00
78_A	81_M	1.685	1.00
77_S	81_M	1.658	1.00
53_K	93_S	1.583	0.99
35_R	39_L	1.579	0.99
89_F	96_L	1.559	0.99
50_E	53_K	1.545	0.99
6_S	61_L	1.536	0.99
75_K	79_G	1.481	0.99
95_T	98_R	1.478	0.99
63_D	67_A	1.454	0.99
72_E	76_K	1.452	0.99
48_L	52_Q	1.441	0.99
47_E	51_K	1.416	0.99
15_E	47_E	1.412	0.99
68_K	72_E	1.383	0.99
74_I	77_S	1.371	0.98
54_I	57_T	1.361	0.98
66_E	69_E	1.327	0.98
71_K	75_K	1.292	0.98
76_K	80_M	1.275	0.97
46_E	97_E	1.272	0.97
76_K	79_G	1.267	0.97
91_N	94_K	1.260	0.97
62_S	67_A	1.258	0.97
79_G	82_G	1.233	0.97
35_R	38_K	1.189	0.96
95_T	99_M	1.123	0.95
98_R	102_Q	1.084	0.94
50_E	54_I	1.082	0.94
8_I	12_E	1.058	0.93
98_R	101_K	1.056	0.93
22_E	40_E	1.013	0.91
14_K	21_E	1.011	0.91
20_Q	24_Y	0.990	0.90
90_D	93_S	0.963	0.89
66_E	73_Q	0.959	0.89
11_E	18_E	0.950	0.88
75_K	83_V	0.939	0.88
40_E	43_E	0.931	0.87
90_D	94_K	0.919	0.86
68_K	71_K	0.916	0.86
97_E	101_K	0.913	0.86
32_S	35_R	0.911	0.86
63_D	68_K	0.893	0.85
43_E	100_K	0.888	0.85
30_F	33_M	0.888	0.85
70_M	74_I	0.885	0.84
94_K	98_R	0.883	0.84
59_L	71_K	0.881	0.84
6_S	9_V	0.868	0.83
16_I	48_L	0.865	0.83
87_Q	101_K	0.859	0.83
10_R	47_E	0.846	0.82
70_M	73_Q	0.832	0.80
88_M	95_T	0.829	0.80
38_K	99_M	0.821	0.80
92_M	96_L	0.817	0.79
13_L	27_V	0.799	0.78
15_E	51_K	0.796	0.77
94_K	97_E	0.768	0.75
37_E	43_E	0.768	0.75
11_E	15_E	0.763	0.74
23_I	93_S	0.761	0.74
96_L	99_M	0.754	0.74
78_A	82_G	0.752	0.73
2_S	9_V	0.744	0.73
63_D	69_E	0.742	0.72
67_A	70_M	0.734	0.72
60_S	71_K	0.733	0.71
73_Q	78_A	0.720	0.70
55_F	83_V	0.707	0.69
17_N	21_E	0.706	0.69
49_L	96_L	0.704	0.68
2_S	46_E	0.701	0.68
20_Q	52_Q	0.700	0.68
45_L	96_L	0.698	0.68
75_K	81_M	0.691	0.67
85_M	88_M	0.690	0.67
13_L	41_H	0.687	0.66
74_I	79_G	0.684	0.66
17_N	55_F	0.683	0.66
57_T	61_L	0.681	0.66
8_I	17_N	0.678	0.65
57_T	91_N	0.676	0.65
59_L	70_M	0.664	0.64
88_M	91_N	0.664	0.64
5_D	69_E	0.664	0.64
16_I	20_Q	0.657	0.63
69_E	72_E	0.655	0.63
75_K	80_M	0.648	0.62
3_F	67_A	0.648	0.62
12_E	15_E	0.647	0.62
57_T	60_S	0.633	0.60
15_E	19_L	0.624	0.59
37_E	55_F	0.616	0.58
20_Q	49_L	0.615	0.58
19_L	24_Y	0.612	0.58
77_S	85_M	0.598	0.56
89_F	95_T	0.598	0.56
48_L	56_Y	0.597	0.56
16_I	19_L	0.593	0.55
24_Y	41_H	0.592	0.55
92_M	100_K	0.591	0.55
37_E	91_N	0.583	0.54
10_R	70_M	0.582	0.54
22_E	25_G	0.575	0.53
31_P	44_K	0.569	0.52
9_V	31_P	0.564	0.52
39_L	53_K	0.550	0.50
30_F	56_Y	0.547	0.49
34_D	39_L	0.545	0.49
9_V	55_F	0.545	0.49
83_V	91_N	0.545	0.49
35_R	62_S	0.541	0.49
7_E	10_R	0.539	0.48
29_K	33_M	0.537	0.48
5_D	45_L	0.534	0.48
55_F	73_Q	0.528	0.47
33_M	41_H	0.527	0.47
89_F	99_M	0.522	0.46
42_I	92_M	0.521	0.46
30_F	100_K	0.520	0.46
13_L	93_S	0.520	0.46
41_H	60_S	0.519	0.46
45_L	89_F	0.517	0.46
24_Y	27_V	0.512	0.45
76_K	81_M	0.510	0.45
20_Q	45_L	0.510	0.45
3_F	51_K	0.510	0.45
31_P	34_D	0.504	0.44
13_L	55_F	0.504	0.44
20_Q	63_D	0.504	0.44
95_T	102_Q	0.502	0.44
88_M	99_M	0.500	0.44

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
3onjA	1	0.7864	27.3	0.899	Contact Map
1vcsA	1	0.7864	18.7	0.907	Contact Map
2qywA	1	0.8252	14.1	0.912	Contact Map
1v2zA	2	0.699	13.8	0.912	Contact Map
1r5qA	2	0.5825	12.1	0.914	Contact Map
3zg1A	2	0.5243	11.1	0.916	Contact Map
2xxaA	1	0.8155	7.9	0.921	Contact Map
2p4fA	1	0	6.4	0.925	Contact Map
4kikA	2	0.8641	6.3	0.925	Contact Map
1tlqA	4	0.3786	6.3	0.925	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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