DUF1828 - PFAM28P - GREMLIN Contacts

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DUF1828 - Domain of unknown function DUF1828

PFAM:	PF08861	Sequences: TPFLDRDGDHIQIYLKKRENGGWRLTDDGYTLMDLEYSGCDLDLSPKRQKLLENILNGFGVELDDGELVVEATPENFPQAKHNLIQALLAV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	91 (90)
Sequences:	3713 (2983)
Seq/√Len:	314.4
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
61_V	87_A	3.431	1.00
72_A	80_A	2.667	1.00
61_V	68_L	2.558	1.00
64_D	69_V	2.330	1.00
49_Q	53_E	2.232	1.00
7_D	34_D	2.078	1.00
24_R	69_V	2.061	1.00
11_I	88_L	2.057	1.00
11_I	89_L	1.938	1.00
24_R	71_E	1.755	1.00
22_G	71_E	1.718	1.00
76_N	79_Q	1.672	1.00
62_E	69_V	1.645	1.00
16_K	24_R	1.629	1.00
70_V	84_L	1.612	1.00
32_L	63_L	1.566	1.00
15_L	23_W	1.526	1.00
31_T	88_L	1.499	1.00
63_L	66_G	1.473	1.00
25_L	84_L	1.472	1.00
52_L	63_L	1.468	1.00
18_R	24_R	1.449	1.00
62_E	71_E	1.406	1.00
4_L	10_H	1.370	1.00
77_F	81_K	1.332	1.00
36_E	41_D	1.324	1.00
56_L	63_L	1.296	1.00
58_G	90_A	1.293	1.00
26_T	67_E	1.280	1.00
36_E	66_G	1.276	1.00
53_E	57_N	1.263	1.00
80_A	83_N	1.247	1.00
73_T	76_N	1.235	1.00
12_Q	30_Y	1.209	1.00
76_N	80_A	1.198	1.00
15_L	25_L	1.184	1.00
84_L	88_L	1.176	1.00
23_W	74_P	1.165	1.00
79_Q	83_N	1.136	1.00
39_G	42_L	1.115	1.00
33_M	66_G	1.112	1.00
24_R	64_D	1.104	1.00
70_V	80_A	1.084	1.00
72_A	76_N	1.079	1.00
18_R	22_G	1.077	1.00
86_Q	89_L	1.055	1.00
5_D	34_D	1.022	1.00
33_M	36_E	1.021	1.00
32_L	52_L	1.000	1.00
53_E	63_L	0.994	1.00
5_D	30_Y	0.987	1.00
68_L	84_L	0.969	1.00
59_F	86_Q	0.955	1.00
50_K	54_N	0.955	1.00
16_K	20_N	0.935	1.00
13_I	81_K	0.922	1.00
56_L	91_V	0.903	1.00
16_K	26_T	0.901	1.00
47_K	50_K	0.896	1.00
1_T	4_L	0.886	1.00
29_G	67_E	0.883	1.00
17_K	20_N	0.874	1.00
81_K	85_I	0.869	1.00
25_L	81_K	0.860	1.00
52_L	56_L	0.857	1.00
14_Y	28_D	0.850	1.00
45_S	49_Q	0.850	1.00
6_R	34_D	0.830	1.00
70_V	83_N	0.825	1.00
17_K	23_W	0.825	1.00
6_R	38_S	0.815	1.00
37_Y	66_G	0.815	1.00
59_F	90_A	0.811	1.00
33_M	37_Y	0.807	1.00
55_I	59_F	0.799	1.00
11_I	31_T	0.788	1.00
47_K	51_L	0.785	1.00
23_W	77_F	0.783	1.00
61_V	70_V	0.783	1.00
82_H	85_I	0.776	1.00
5_D	11_I	0.774	1.00
51_L	54_N	0.760	0.99
4_L	8_G	0.744	0.99
30_Y	34_D	0.741	0.99
63_L	68_L	0.737	0.99
13_I	25_L	0.721	0.99
13_I	84_L	0.719	0.99
3_F	86_Q	0.716	0.99
73_T	80_A	0.708	0.99
72_A	77_F	0.707	0.99
78_P	81_K	0.707	0.99
25_L	80_A	0.700	0.99
30_Y	33_M	0.699	0.99
56_L	59_F	0.693	0.99
48_R	51_L	0.686	0.99
66_G	75_E	0.679	0.99
78_P	82_H	0.673	0.99
85_I	89_L	0.673	0.99
46_P	50_K	0.665	0.98
55_I	58_G	0.663	0.98
5_D	12_Q	0.663	0.98
79_Q	82_H	0.661	0.98
22_G	73_T	0.658	0.98
86_Q	91_V	0.643	0.98
46_P	49_Q	0.636	0.98
3_F	85_I	0.635	0.98
19_E	24_R	0.634	0.98
63_L	69_V	0.631	0.98
51_L	55_I	0.631	0.98
55_I	87_A	0.629	0.98
53_E	62_E	0.609	0.97
77_F	85_I	0.607	0.97
19_E	62_E	0.599	0.97
25_L	88_L	0.590	0.97
7_D	37_Y	0.588	0.97
1_T	5_D	0.584	0.97
61_V	84_L	0.577	0.96
16_K	28_D	0.570	0.96
13_I	88_L	0.560	0.96
21_G	73_T	0.559	0.96
52_L	55_I	0.556	0.95
16_K	19_E	0.545	0.95
1_T	10_H	0.541	0.95
15_L	72_A	0.535	0.94
71_E	74_P	0.532	0.94
21_G	74_P	0.531	0.94
30_Y	37_Y	0.531	0.94
50_K	53_E	0.530	0.94
58_G	91_V	0.529	0.94
2_P	13_I	0.525	0.94
2_P	35_L	0.520	0.94
59_F	83_N	0.505	0.93
8_G	12_Q	0.503	0.92
9_D	29_G	0.503	0.92
29_G	35_L	0.500	0.92

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
4es1A	2	0.6813	11.1	0.874	Contact Map
4qr2A	2	0.6264	9.9	0.877	Contact Map
2ivyA	2	0.6374	8.4	0.881	Contact Map
3excX	2	0.6044	7.7	0.883	Contact Map
4tnoA	2	0.6154	6.9	0.885	Contact Map
1zpwX	2	0.6484	6.9	0.885	Contact Map
3tewA	1	0.4725	6.1	0.888	Contact Map
3oq2A	3	0.6923	5.7	0.89	Contact Map
2ypvA	1	0.9231	5.5	0.891	Contact Map
3uf8A	1	0.9341	4.6	0.895	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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