DUF1816 - PFAM28P - GREMLIN Contacts

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DUF1816 - Domain of unknown function (DUF1816)

PFAM:	PF08846	Sequences: NKLGLAWWAEIETEQPRCTYYFGPFLTKREAKEALSGYIEDLEQEGAQGIKHSIKRCKPEPLTI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	64 (64)
Sequences:	936 (570)
Seq/√Len:	71.3
META:	0.785

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
10_E	55_K	4.246	1.00
32_K	35_L	2.442	1.00
41_D	45_E	2.387	1.00
12_E	19_T	1.995	1.00
4_G	26_L	1.990	1.00
33_E	36_S	1.540	0.99
19_T	64_I	1.424	0.99
15_Q	48_Q	1.408	0.98
37_G	59_P	1.394	0.98
25_F	38_Y	1.391	0.98
7_W	61_P	1.372	0.98
46_G	62_L	1.330	0.98
22_F	37_G	1.322	0.98
20_Y	42_L	1.316	0.97
10_E	57_C	1.315	0.97
45_E	63_T	1.314	0.97
36_S	40_E	1.304	0.97
37_G	40_E	1.290	0.97
31_A	59_P	1.276	0.97
29_R	60_E	1.257	0.97
40_E	59_P	1.231	0.96
9_A	54_I	1.200	0.96
9_A	58_K	1.194	0.96
21_Y	31_A	1.163	0.95
1_N	5_L	1.161	0.95
6_A	56_R	1.154	0.95
12_E	61_P	1.136	0.94
42_L	47_A	1.130	0.94
9_A	38_Y	1.107	0.93
3_L	17_R	1.060	0.92
16_P	45_E	1.054	0.91
6_A	26_L	1.044	0.91
2_K	36_S	1.042	0.91
21_Y	38_Y	1.037	0.91
13_T	45_E	1.031	0.91
16_P	22_F	1.030	0.91
9_A	31_A	1.008	0.90
27_T	30_E	1.004	0.89
11_I	18_C	0.999	0.89
1_N	7_W	0.999	0.89
22_F	40_E	0.974	0.88
40_E	44_Q	0.952	0.87
59_P	64_I	0.946	0.86
42_L	50_I	0.946	0.86
22_F	49_G	0.941	0.86
30_E	38_Y	0.935	0.86
58_K	61_P	0.927	0.85
47_A	59_P	0.886	0.83
37_G	47_A	0.880	0.82
43_E	57_C	0.879	0.82
28_K	32_K	0.876	0.82
2_K	44_Q	0.873	0.82
28_K	53_S	0.867	0.81
21_Y	59_P	0.864	0.81
22_F	59_P	0.862	0.81
53_S	56_R	0.843	0.79
14_E	51_K	0.835	0.79
54_I	59_P	0.821	0.77
6_A	58_K	0.816	0.77
39_I	52_H	0.813	0.77
27_T	43_E	0.786	0.74
11_I	60_E	0.779	0.74
17_R	44_Q	0.773	0.73
15_Q	49_G	0.770	0.73
22_F	54_I	0.752	0.71
26_L	29_R	0.744	0.70
18_C	37_G	0.742	0.70
36_S	61_P	0.739	0.70
27_T	51_K	0.716	0.67
15_Q	35_L	0.697	0.65
41_D	59_P	0.687	0.64
2_K	29_R	0.687	0.64
53_S	60_E	0.684	0.64
52_H	56_R	0.679	0.63
25_F	45_E	0.676	0.63
28_K	35_L	0.671	0.62
13_T	37_G	0.664	0.61
7_W	12_E	0.662	0.61
22_F	41_D	0.659	0.61
18_C	31_A	0.646	0.59
39_I	58_K	0.620	0.56
6_A	24_P	0.601	0.54
12_E	51_K	0.601	0.54
30_E	59_P	0.596	0.53
13_T	42_L	0.592	0.53
5_L	26_L	0.590	0.53
7_W	44_Q	0.579	0.51
17_R	49_G	0.573	0.50
5_L	33_E	0.569	0.50
24_P	41_D	0.541	0.47
2_K	51_K	0.538	0.46
2_K	34_A	0.520	0.44
52_H	55_K	0.515	0.43
33_E	46_G	0.512	0.43
3_L	6_A	0.504	0.42
36_S	39_I	0.500	0.42

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
2lfvA	1	0.9062	35.7	0.877	Contact Map
2crhA	1	0.875	18.1	0.893	Contact Map
1x60A	1	0.7656	14.8	0.898	Contact Map
1utaA	1	0.7969	5.8	0.915	Contact Map
3si5X	1	0.2812	5.6	0.916	Contact Map
4knhA	1	0.6562	5.1	0.917	Contact Map
3eazA	1	0.7188	4.7	0.918	Contact Map
3hhmB	1	0.6406	4	0.921	Contact Map
1tdjA	2	0.2812	3.9	0.922	Contact Map
4bgdA	1	0.8438	3.5	0.924	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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