DUF930 - PFAM28P - GREMLIN Contacts

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DUF930 - Domain of Unknown Function (DUF930)

PFAM:	PF06059	Sequences: LKKLDPEERLEQLCDLEAMEQIRRDKPGYRPDRVVAYALADPKVSGNTLEAPGGAFRSKGKWYALSFRCEVTPDHMKVVSFSYKIGDEIPESEWEAYGL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	99 (99)
Sequences:	1314 (897)
Seq/√Len:	90.1
META:	0.818

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
61_K	88_E	4.358	1.00
56_F	85_I	3.398	1.00
17_E	21_Q	2.958	1.00
25_D	83_Y	2.462	1.00
18_A	81_F	2.379	1.00
39_L	97_Y	2.253	1.00
93_E	96_A	2.157	1.00
51_A	54_G	2.146	1.00
22_I	65_L	2.138	1.00
5_D	8_E	2.093	1.00
32_D	57_R	2.043	1.00
39_L	89_I	1.940	1.00
66_S	84_K	1.916	1.00
29_Y	56_F	1.907	1.00
90_P	94_W	1.870	1.00
22_I	56_F	1.813	1.00
50_E	68_R	1.782	1.00
10_L	71_V	1.719	1.00
20_E	24_R	1.703	1.00
72_T	77_K	1.633	1.00
61_K	91_E	1.597	1.00
54_G	65_L	1.569	1.00
48_T	68_R	1.545	1.00
34_V	65_L	1.502	1.00
44_V	49_L	1.453	0.99
35_V	38_A	1.403	0.99
13_L	78_V	1.394	0.99
51_A	65_L	1.354	0.99
47_N	75_H	1.349	0.99
48_T	70_E	1.348	0.99
70_E	80_S	1.347	0.99
89_I	94_W	1.329	0.99
10_L	49_L	1.313	0.99
32_D	58_S	1.307	0.99
39_L	64_A	1.281	0.99
22_I	85_I	1.277	0.99
93_E	97_Y	1.239	0.98
31_P	58_S	1.239	0.98
77_K	81_F	1.239	0.98
36_A	51_A	1.238	0.98
11_E	37_Y	1.163	0.97
22_I	58_S	1.151	0.97
40_A	81_F	1.133	0.97
40_A	53_G	1.123	0.97
4_L	12_Q	1.116	0.97
64_A	97_Y	1.071	0.96
55_A	89_I	1.005	0.94
30_R	59_K	0.970	0.93
12_Q	54_G	0.938	0.92
26_K	29_Y	0.935	0.92
35_V	55_A	0.932	0.91
47_N	70_E	0.922	0.91
3_K	6_P	0.900	0.90
32_D	53_G	0.876	0.89
41_D	70_E	0.870	0.88
15_D	19_M	0.870	0.88
13_L	81_F	0.859	0.88
16_L	20_E	0.857	0.88
64_A	87_D	0.856	0.88
57_R	94_W	0.848	0.87
91_E	94_W	0.848	0.87
23_R	31_P	0.838	0.86
27_P	59_K	0.832	0.86
13_L	21_Q	0.821	0.85
89_I	99_L	0.820	0.85
42_P	49_L	0.818	0.85
34_V	54_G	0.814	0.85
10_L	75_H	0.790	0.83
52_P	66_S	0.790	0.83
43_K	50_E	0.780	0.82
8_E	11_E	0.770	0.81
11_E	15_D	0.763	0.81
25_D	85_I	0.761	0.81
6_P	75_H	0.760	0.80
46_G	49_L	0.758	0.80
11_E	22_I	0.752	0.80
33_R	89_I	0.736	0.78
19_M	44_V	0.730	0.78
1_L	16_L	0.728	0.78
20_E	23_R	0.727	0.77
45_S	60_G	0.725	0.77
13_L	79_V	0.722	0.77
19_M	22_I	0.715	0.76
41_D	97_Y	0.711	0.76
68_R	82_S	0.708	0.76
95_E	99_L	0.700	0.75
16_L	71_V	0.700	0.75
23_R	54_G	0.699	0.75
50_E	72_T	0.694	0.74
11_E	42_P	0.689	0.74
58_S	61_K	0.685	0.73
18_A	78_V	0.684	0.73
91_E	96_A	0.671	0.72
30_R	99_L	0.671	0.72
11_E	36_A	0.666	0.71
79_V	82_S	0.665	0.71
40_A	92_S	0.662	0.71
76_M	83_Y	0.662	0.71
19_M	34_V	0.652	0.69
36_A	49_L	0.648	0.69
37_Y	64_A	0.645	0.69
38_A	54_G	0.634	0.67
94_W	99_L	0.634	0.67
43_K	46_G	0.633	0.67
16_L	72_T	0.632	0.67
4_L	8_E	0.626	0.66
32_D	60_G	0.622	0.66
12_Q	53_G	0.619	0.66
63_Y	88_E	0.619	0.66
13_L	68_R	0.617	0.65
5_D	29_Y	0.617	0.65
17_E	78_V	0.616	0.65
8_E	53_G	0.612	0.65
72_T	81_F	0.608	0.64
36_A	65_L	0.606	0.64
15_D	38_A	0.602	0.63
19_M	33_R	0.599	0.63
14_C	17_E	0.596	0.63
57_R	89_I	0.592	0.62
33_R	98_G	0.589	0.62
8_E	13_L	0.585	0.61
93_E	98_G	0.583	0.61
91_E	97_Y	0.582	0.61
4_L	15_D	0.573	0.60
19_M	30_R	0.572	0.59
17_E	20_E	0.568	0.59
17_E	56_F	0.562	0.58
8_E	12_Q	0.557	0.57
31_P	78_V	0.548	0.56
71_V	75_H	0.541	0.55
46_G	82_S	0.538	0.55
95_E	98_G	0.537	0.55
37_Y	51_A	0.534	0.54
52_P	60_G	0.531	0.54
80_S	91_E	0.521	0.53
43_K	77_K	0.519	0.52
4_L	31_P	0.519	0.52
43_K	74_D	0.516	0.52
59_K	87_D	0.514	0.52
34_V	55_A	0.513	0.51
67_F	90_P	0.507	0.51
37_Y	98_G	0.505	0.50
20_E	26_K	0.505	0.50
11_E	33_R	0.503	0.50
41_D	51_A	0.502	0.50
70_E	77_K	0.502	0.50
58_S	67_F	0.502	0.50
38_A	55_A	0.500	0.50

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
1t1uA	1	1	12.9	0.928	Contact Map
2m6oA	1	0.3232	12.3	0.929	Contact Map
2fkiA	1	0.697	11.1	0.93	Contact Map
1mlwA	1	0.5455	8.8	0.933	Contact Map
2bzrA	4	0.9091	8.8	0.933	Contact Map
1tohA	3	0.4141	6.8	0.937	Contact Map
3pijA	2	0.8687	6.7	0.937	Contact Map
2infA	2	0.9394	6.2	0.938	Contact Map
1z6bA	3	0.8485	5.9	0.938	Contact Map
1nm8A	1	1	5.7	0.939	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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