YBDD - ECOLI - GREMLIN Contacts

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YBDD - Uncharacterized protein YbdD

UniProt:	P0AAS9	Sequences: MFDSLAKAGKYLGQAAKLMIGMPDYDNYVEHMRVNHPDQTPMTYEEFFRERQDARYGGKGGARCC	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11107
Length:	65 (61)
Sequences:	268 (141)
Seq/√Len:	18.0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
43_T	46_E	4.803	1.00
48_F	52_Q	3.993	1.00
11_Y	14_Q	2.785	0.98
15_A	18_L	2.409	0.95
23_P	56_Y	2.323	0.94
51_R	57_G	2.028	0.89
30_E	34_V	1.907	0.86
14_Q	53_D	1.667	0.77
32_M	39_Q	1.665	0.77
16_A	26_D	1.631	0.75
23_P	51_R	1.574	0.73
44_Y	51_R	1.423	0.65
20_I	49_R	1.336	0.60
46_E	60_G	1.306	0.58
8_A	34_V	1.179	0.50
30_E	40_T	1.160	0.49
12_L	57_G	1.151	0.48
19_M	63_R	1.114	0.46
49_R	57_G	1.103	0.45
54_A	59_K	1.081	0.44
57_G	64_C	1.075	0.44
9_G	12_L	1.063	0.43
48_F	65_C	1.062	0.43
37_P	54_A	1.051	0.42
24_D	63_R	1.024	0.41
24_D	33_R	1.024	0.41
54_A	58_G	1.012	0.40
20_I	38_D	1.006	0.39
15_A	22_M	0.989	0.38
23_P	65_C	0.985	0.38
22_M	62_A	0.974	0.38
30_E	60_G	0.969	0.37
53_D	62_A	0.953	0.36
20_I	53_D	0.945	0.36
12_L	26_D	0.927	0.35
30_E	38_D	0.921	0.35
32_M	38_D	0.915	0.34
26_D	35_N	0.893	0.33
9_G	43_T	0.892	0.33
54_A	62_A	0.854	0.31
18_L	47_F	0.850	0.31
26_D	44_Y	0.847	0.31
11_Y	44_Y	0.841	0.30
29_V	41_P	0.835	0.30
15_A	19_M	0.833	0.30
5_L	16_A	0.819	0.29
35_N	45_E	0.817	0.29
38_D	42_M	0.807	0.29
17_K	24_D	0.782	0.27
10_K	61_G	0.777	0.27
9_G	13_G	0.777	0.27
6_A	60_G	0.774	0.27
22_M	56_Y	0.764	0.26
5_L	20_I	0.754	0.26
23_P	48_F	0.751	0.26
58_G	62_A	0.738	0.25
23_P	55_R	0.737	0.25
46_E	53_D	0.731	0.25
43_T	56_Y	0.729	0.25
16_A	51_R	0.728	0.25
22_M	52_Q	0.727	0.25
10_K	44_Y	0.712	0.24
52_Q	57_G	0.690	0.23
19_M	42_M	0.672	0.22
6_A	30_E	0.664	0.22
42_M	49_R	0.663	0.22
15_A	24_D	0.659	0.22
41_P	56_Y	0.652	0.21
22_M	47_F	0.651	0.21
39_Q	50_E	0.648	0.21
14_Q	24_D	0.639	0.21
41_P	63_R	0.630	0.21
32_M	41_P	0.626	0.20
10_K	39_Q	0.625	0.20
13_G	22_M	0.622	0.20
6_A	34_V	0.595	0.19
16_A	24_D	0.594	0.19
29_V	34_V	0.585	0.19
29_V	39_Q	0.578	0.19
6_A	9_G	0.569	0.18
27_N	40_T	0.568	0.18
33_R	53_D	0.547	0.17
58_G	61_G	0.542	0.17
12_L	42_M	0.537	0.17
42_M	51_R	0.534	0.17
10_K	30_E	0.528	0.17
22_M	35_N	0.524	0.17
57_G	65_C	0.521	0.17
9_G	44_Y	0.517	0.16
32_M	54_A	0.510	0.16
50_E	57_G	0.505	0.16
17_K	51_R	0.500	0.16

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
4s28A	2	0.9385	10.3	0.921	Contact Map
4tpsB	1	1	9.3	0.923	Contact Map
2im9A	1	0.9231	8.3	0.925	Contact Map
2iw0A	1	0.5385	8	0.925	Contact Map
3epoA	2	0.9385	7.7	0.926	Contact Map
4iaoA	1	0.9846	7	0.927	Contact Map
3qtmA	1	0.5077	6.6	0.928	Contact Map
3msvA	2	0.5077	6.5	0.928	Contact Map
3dr3A	4	0.4462	5.6	0.93	Contact Map
3j0aA	1	0.6615	5.6	0.93	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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