DUF438 - PFAM28P - GREMLIN Contacts

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DUF438 - Family of unknown function (DUF438)

PFAM:	PF04282	Sequences: LKEIIKRLHEGESPEEVKEEFKELLGDVSASEIAEMEQELIAEGLPVEEIQRLCDVHAAVFKGSLEE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	67 (66)
Sequences:	3424 (1925)
Seq/√Len:	236.9
META:	0.908

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
7_R	20_E	5.553	1.00
7_R	12_E	4.049	1.00
12_E	16_E	2.384	1.00
47_V	51_Q	2.083	1.00
13_S	16_E	2.079	1.00
49_E	52_R	2.069	1.00
2_K	43_E	2.002	1.00
3_E	7_R	1.919	1.00
6_K	43_E	1.881	1.00
41_I	50_I	1.829	1.00
30_A	34_A	1.624	1.00
38_Q	42_A	1.620	1.00
54_C	57_H	1.453	1.00
12_E	17_V	1.429	1.00
7_R	10_E	1.388	1.00
6_K	10_E	1.374	1.00
22_K	59_A	1.305	1.00
2_K	6_K	1.283	1.00
22_K	63_G	1.277	1.00
1_L	36_M	1.271	1.00
39_E	42_A	1.258	1.00
18_K	22_K	1.248	1.00
47_V	50_I	1.223	1.00
18_K	63_G	1.175	1.00
19_E	23_E	1.173	1.00
59_A	62_K	1.146	1.00
5_I	36_M	1.138	1.00
31_S	35_E	1.117	1.00
9_H	49_E	1.075	1.00
41_I	47_V	1.003	1.00
37_E	54_C	0.999	1.00
62_K	65_L	0.998	1.00
48_E	51_Q	0.971	1.00
16_E	20_E	0.963	1.00
2_K	39_E	0.949	1.00
14_P	60_V	0.917	1.00
18_K	59_A	0.910	1.00
28_V	32_E	0.909	1.00
37_E	57_H	0.887	0.99
62_K	66_E	0.862	0.99
23_E	26_G	0.859	0.99
21_F	61_F	0.841	0.99
33_I	61_F	0.836	0.99
6_K	36_M	0.833	0.99
5_I	45_L	0.827	0.99
3_E	10_E	0.824	0.99
3_E	20_E	0.823	0.99
11_G	14_P	0.812	0.99
30_A	33_I	0.800	0.99
34_A	51_Q	0.792	0.99
21_F	33_I	0.768	0.98
61_F	64_S	0.754	0.98
6_K	49_E	0.754	0.98
47_V	58_A	0.751	0.98
56_V	61_F	0.748	0.98
8_L	17_V	0.742	0.98
4_I	28_V	0.739	0.98
38_Q	47_V	0.732	0.98
16_E	19_E	0.715	0.98
8_L	52_R	0.708	0.97
25_L	29_S	0.692	0.97
12_E	20_E	0.668	0.96
35_E	39_E	0.668	0.96
39_E	43_E	0.666	0.96
20_E	23_E	0.658	0.96
23_E	27_D	0.649	0.96
34_A	58_A	0.649	0.96
26_G	29_S	0.647	0.96
3_E	24_L	0.646	0.96
20_E	24_L	0.631	0.95
45_L	49_E	0.627	0.95
58_A	62_K	0.620	0.95
46_P	52_R	0.615	0.94
58_A	63_G	0.613	0.94
14_P	59_A	0.612	0.94
21_F	28_V	0.598	0.93
61_F	65_L	0.579	0.92
59_A	63_G	0.574	0.92
9_H	45_L	0.573	0.92
19_E	22_K	0.567	0.91
22_K	26_G	0.567	0.91
26_G	64_S	0.554	0.91
38_Q	41_I	0.549	0.90
19_E	66_E	0.548	0.90
9_H	33_I	0.547	0.90
17_V	20_E	0.547	0.90
25_L	30_A	0.539	0.89
6_K	45_L	0.536	0.89
37_E	53_L	0.522	0.88
15_E	18_K	0.519	0.87
28_V	33_I	0.515	0.87
9_H	43_E	0.514	0.87
42_A	45_L	0.511	0.87
38_Q	58_A	0.511	0.87
31_S	34_A	0.510	0.87
4_I	60_V	0.504	0.86
46_P	49_E	0.503	0.86
6_K	9_H	0.503	0.86
29_S	36_M	0.500	0.86

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
3nufA	2	0.9254	54.2	0.809	Contact Map
4v3iA	2	0.8209	38.2	0.826	Contact Map
4muoA	2	0.9851	35.7	0.829	Contact Map
4gtnA	2	1	30.5	0.835	Contact Map
4giuA	2	1	29.9	0.836	Contact Map
1o17A	2	0.9851	26.6	0.84	Contact Map
1vquA	2	0.9701	26.3	0.84	Contact Map
3u66A	4	0.8806	23.6	0.844	Contact Map
3h5qA	2	1	20.1	0.849	Contact Map
1brwA	2	1	19.8	0.849	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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