DUF4216 - PFAM28P - GREMLIN Contacts

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DUF4216 - Domain of unknown function (DUF4216)

PFAM:	PF13952	Sequences: IELDYGGEFKVVLFKCDWFDKNRGVKVDKYGFTLVNLNRLGYKDDPFILASQATQVFYVPDPSDKNWHVV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	70 (69)
Sequences:	1777 (1138)
Seq/√Len:	137.0
META:	0.701

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
48_I	53_A	4.886	1.00
19_F	37_L	3.727	1.00
17_D	40_L	2.655	1.00
37_L	68_H	2.138	1.00
2_E	10_K	1.991	1.00
4_D	9_F	1.989	1.00
25_V	33_T	1.943	1.00
60_P	66_N	1.877	1.00
15_K	46_P	1.751	1.00
41_G	45_D	1.677	1.00
19_F	40_L	1.615	1.00
65_K	68_H	1.599	1.00
36_N	66_N	1.460	1.00
60_P	65_K	1.450	1.00
3_L	11_V	1.431	1.00
6_G	10_K	1.418	1.00
13_L	46_P	1.415	1.00
28_D	31_G	1.393	1.00
1_I	47_F	1.374	1.00
34_L	41_G	1.373	1.00
60_P	68_H	1.347	1.00
16_C	20_D	1.323	1.00
59_V	64_D	1.294	1.00
19_F	35_V	1.275	1.00
6_G	17_D	1.235	1.00
49_L	52_Q	1.229	1.00
60_P	63_S	1.201	1.00
32_F	36_N	1.133	0.99
26_K	34_L	1.119	0.99
45_D	48_I	1.117	0.99
40_L	44_D	1.115	0.99
24_G	50_A	1.114	0.99
1_I	36_N	1.073	0.99
16_C	24_G	1.060	0.99
36_N	41_G	1.028	0.99
21_K	27_V	1.000	0.98
47_F	68_H	0.988	0.98
50_A	55_Q	0.981	0.98
4_D	10_K	0.975	0.98
29_K	32_F	0.964	0.98
6_G	9_F	0.947	0.98
4_D	8_E	0.939	0.97
21_K	29_K	0.909	0.97
61_D	65_K	0.901	0.97
57_F	61_D	0.886	0.96
32_F	59_V	0.880	0.96
42_Y	45_D	0.859	0.96
26_K	64_D	0.840	0.95
12_V	19_F	0.836	0.95
38_N	50_A	0.807	0.94
66_N	69_V	0.774	0.93
34_L	57_F	0.763	0.92
20_D	39_R	0.749	0.91
48_I	69_V	0.749	0.91
25_V	44_D	0.746	0.91
10_K	41_G	0.738	0.91
34_L	61_D	0.736	0.91
1_I	41_G	0.735	0.91
2_E	9_F	0.722	0.90
27_V	30_Y	0.716	0.89
17_D	45_D	0.716	0.89
9_F	39_R	0.714	0.89
5_Y	44_D	0.695	0.88
42_Y	49_L	0.694	0.88
54_T	58_Y	0.678	0.87
8_E	30_Y	0.668	0.86
1_I	33_T	0.668	0.86
39_R	51_S	0.665	0.86
51_S	54_T	0.665	0.86
24_G	58_Y	0.660	0.85
9_F	12_V	0.655	0.85
31_G	64_D	0.649	0.84
33_T	37_L	0.647	0.84
14_F	58_Y	0.645	0.84
34_L	69_V	0.633	0.83
4_D	7_G	0.629	0.82
7_G	54_T	0.629	0.82
16_C	56_V	0.618	0.81
19_F	69_V	0.615	0.81
7_G	12_V	0.610	0.80
26_K	38_N	0.579	0.77
13_L	16_C	0.575	0.76
21_K	48_I	0.575	0.76
50_A	53_A	0.571	0.76
30_Y	42_Y	0.570	0.76
61_D	64_D	0.566	0.75
3_L	40_L	0.563	0.75
23_R	38_N	0.555	0.74
12_V	37_L	0.550	0.73
1_I	12_V	0.549	0.73
35_V	62_P	0.542	0.72
12_V	26_K	0.541	0.72
28_D	50_A	0.527	0.70
7_G	62_P	0.525	0.70
37_L	41_G	0.522	0.69
24_G	66_N	0.521	0.69
34_L	67_W	0.513	0.68
38_N	43_K	0.512	0.68
31_G	37_L	0.510	0.67
45_D	56_V	0.510	0.67
49_L	63_S	0.509	0.67
1_I	7_G	0.501	0.66
4_D	12_V	0.501	0.66
20_D	46_P	0.500	0.66

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
2mwiA	1	0.6	13.8	0.893	Contact Map
4mhlA	1	0.4143	3	0.922	Contact Map
4qfuA	5	0.7286	2.7	0.923	Contact Map
4bgdA	1	0.7429	2.4	0.925	Contact Map
4my6A	1	0.3857	2	0.928	Contact Map
2e1bA	1	0.4429	2	0.929	Contact Map
2kcmA	1	0.7	1.9	0.929	Contact Map
2fgtA	1	0.9	1.6	0.932	Contact Map
4f92B	1	0.7	1.6	0.933	Contact Map
3winC	1	0.9857	1.5	0.933	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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