DUF3039 - PFAM28P - GREMLIN Contacts

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DUF3039 - Protein of unknown function (DUF3039)

PFAM:	PF11238	Sequences: DGDHERFAHYVRKDKITESAVTGTPVVALCGKVWVPSRDPKKFPVCPECKEIYESL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	56 (55)
Sequences:	2078 (745)
Seq/√Len:	100.5
META:	0.886

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_E	51_E	3.977	1.00
17_T	21_V	2.527	1.00
18_E	22_T	2.454	1.00
27_V	33_V	2.371	1.00
50_K	54_E	2.175	1.00
39_D	42_K	2.141	1.00
25_P	33_V	2.015	1.00
16_I	20_A	1.948	1.00
18_E	24_T	1.940	1.00
15_K	18_E	1.832	1.00
11_V	16_I	1.820	1.00
11_V	26_V	1.776	1.00
20_A	37_S	1.738	1.00
2_G	5_E	1.663	1.00
7_F	47_P	1.503	1.00
25_P	35_V	1.495	1.00
12_R	15_K	1.322	0.99
51_E	55_S	1.174	0.98
19_S	38_R	1.169	0.98
17_T	20_A	1.149	0.98
10_Y	50_K	1.110	0.98
19_S	22_T	1.090	0.97
46_C	49_C	1.038	0.96
4_H	7_F	1.032	0.96
2_G	6_R	1.031	0.96
11_V	34_W	0.984	0.95
53_Y	56_L	0.984	0.95
8_A	36_P	0.966	0.95
45_V	50_K	0.964	0.95
10_Y	45_V	0.942	0.94
10_Y	47_P	0.919	0.93
38_R	43_F	0.916	0.93
30_C	46_C	0.896	0.92
25_P	34_W	0.885	0.92
7_F	10_Y	0.861	0.90
12_R	17_T	0.831	0.89
45_V	53_Y	0.814	0.88
28_A	34_W	0.801	0.87
3_D	6_R	0.793	0.86
2_G	34_W	0.789	0.86
24_T	35_V	0.784	0.86
47_P	50_K	0.773	0.85
25_P	32_K	0.748	0.83
39_D	43_F	0.747	0.83
16_I	19_S	0.733	0.82
6_R	38_R	0.724	0.81
16_I	53_Y	0.717	0.80
36_P	39_D	0.712	0.80
12_R	56_L	0.701	0.79
14_D	27_V	0.671	0.76
29_L	33_V	0.668	0.76
13_K	16_I	0.666	0.75
32_K	48_E	0.629	0.71
32_K	47_P	0.586	0.66
13_K	20_A	0.586	0.66
52_I	55_S	0.579	0.65
32_K	43_F	0.578	0.65
35_V	38_R	0.577	0.64
8_A	40_P	0.575	0.64
15_K	22_T	0.569	0.63
25_P	28_A	0.566	0.63
21_V	24_T	0.564	0.63
8_A	41_K	0.564	0.63
10_Y	20_A	0.563	0.63
41_K	52_I	0.562	0.62
41_K	55_S	0.558	0.62
26_V	40_P	0.555	0.62
19_S	36_P	0.554	0.61
29_L	34_W	0.546	0.60
28_A	40_P	0.545	0.60
12_R	16_I	0.544	0.60
16_I	22_T	0.541	0.60
4_H	48_E	0.540	0.59
14_D	17_T	0.538	0.59
6_R	43_F	0.526	0.57
7_F	32_K	0.526	0.57
14_D	18_E	0.520	0.57
9_H	30_C	0.513	0.56
30_C	49_C	0.511	0.55
15_K	19_S	0.504	0.54
16_I	40_P	0.502	0.54
5_E	43_F	0.500	0.54

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
3rmqA	1	0.8929	76.6	0.8	Contact Map
2gmgA	1	0.9464	26.2	0.857	Contact Map
4lqxA	2	0.3571	14.3	0.873	Contact Map
3vthA	1	0.7857	11.1	0.879	Contact Map
4g9iA	1	0.7857	11	0.879	Contact Map
1wqaA	3	0.9286	8.8	0.884	Contact Map
4pqdA	1	0.7321	8.2	0.886	Contact Map
3ttcA	1	0.7857	7.8	0.887	Contact Map
4nqaB	1	0.7321	7.4	0.888	Contact Map
2f7lA	4	0.9286	5.9	0.893	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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