YEED - ECOLI - GREMLIN Contacts

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YEED - UPF0033 protein YeeD

UniProt:	P33014	Sequences: MVIKKLDVVTQVCPFPLIEAKAALAEMVSGDELVIEFDCTQATEAIPQWAAEEGHAITDYQQIGDAAWSITVQKA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11894
Length:	75 (71)
Sequences:	108 (65)
Seq/√Len:	7.7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
17_L	42_A	3.101	0.88
56_A	73_Q	2.933	0.85
12_V	40_T	2.883	0.84
24_L	27_M	2.112	0.61
12_V	37_F	2.039	0.58
21_K	46_I	2.008	0.56
58_T	73_Q	1.971	0.55
8_V	60_Y	1.942	0.54
37_F	40_T	1.927	0.53
12_V	45_A	1.903	0.52
5_K	36_E	1.838	0.50
7_D	36_E	1.823	0.49
24_L	46_I	1.578	0.39
40_T	45_A	1.543	0.38
7_D	11_Q	1.502	0.36
59_D	69_S	1.389	0.32
44_E	67_A	1.339	0.31
10_T	60_Y	1.331	0.30
55_H	73_Q	1.283	0.29
17_L	21_K	1.265	0.28
32_E	73_Q	1.258	0.28
20_A	33_L	1.249	0.28
38_D	41_Q	1.240	0.27
9_V	36_E	1.237	0.27
4_K	28_V	1.213	0.26
5_K	8_V	1.160	0.25
52_E	61_Q	1.126	0.24
25_A	32_E	1.121	0.24
11_Q	69_S	1.112	0.23
48_Q	67_A	1.107	0.23
4_K	8_V	1.099	0.23
32_E	69_S	1.056	0.22
40_T	72_V	1.050	0.22
21_K	48_Q	1.036	0.21
52_E	73_Q	1.031	0.21
11_Q	25_A	1.030	0.21
48_Q	52_E	1.019	0.21
5_K	46_I	1.004	0.20
48_Q	73_Q	0.993	0.20
24_L	53_E	0.979	0.20
37_F	70_I	0.974	0.20
22_A	45_A	0.963	0.19
61_Q	69_S	0.962	0.19
44_E	48_Q	0.938	0.19
11_Q	23_A	0.938	0.19
9_V	67_A	0.918	0.18
11_Q	44_E	0.904	0.18
34_V	58_T	0.887	0.18
55_H	69_S	0.879	0.17
36_E	63_I	0.877	0.17
11_Q	34_V	0.871	0.17
23_A	26_E	0.859	0.17
20_A	35_I	0.850	0.17
26_E	72_V	0.845	0.17
18_I	67_A	0.842	0.17
62_Q	65_D	0.832	0.16
63_I	67_A	0.827	0.16
12_V	72_V	0.827	0.16
53_E	56_A	0.820	0.16
29_S	45_A	0.808	0.16
11_Q	31_D	0.796	0.16
23_A	54_G	0.763	0.15
46_I	57_I	0.736	0.14
5_K	28_V	0.722	0.14
25_A	29_S	0.720	0.14
37_F	45_A	0.706	0.14
9_V	29_S	0.706	0.14
53_E	65_D	0.695	0.13
11_Q	67_A	0.689	0.13
15_F	19_E	0.688	0.13
17_L	51_A	0.682	0.13
26_E	44_E	0.677	0.13
19_E	22_A	0.674	0.13
17_L	53_E	0.663	0.13
25_A	53_E	0.660	0.13
5_K	52_E	0.653	0.13
31_D	69_S	0.649	0.13
56_A	72_V	0.648	0.13
44_E	74_K	0.643	0.13
17_L	66_A	0.642	0.13
34_V	48_Q	0.642	0.13
45_A	74_K	0.628	0.12
34_V	56_A	0.620	0.12
36_E	42_A	0.615	0.12
45_A	62_Q	0.613	0.12
5_K	64_G	0.612	0.12
7_D	42_A	0.602	0.12
51_A	66_A	0.593	0.12
27_M	59_D	0.592	0.12
40_T	46_I	0.589	0.12
35_I	72_V	0.587	0.12
31_D	71_T	0.558	0.11
12_V	15_F	0.557	0.11
18_I	72_V	0.555	0.11
22_A	59_D	0.555	0.11
48_Q	72_V	0.552	0.11
23_A	34_V	0.547	0.11
34_V	72_V	0.545	0.11
57_I	65_D	0.538	0.11
28_V	63_I	0.535	0.11
4_K	64_G	0.531	0.11
4_K	21_K	0.530	0.11
34_V	55_H	0.522	0.11
25_A	52_E	0.519	0.11
52_E	63_I	0.500	0.10
35_I	42_A	0.500	0.10

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
1jdqA	1	1	99.6	0.589	Contact Map
1je3A	1	0.9733	99.5	0.611	Contact Map
3lvjC	1	0.9867	99.5	0.615	Contact Map
1pavA	1	0.9867	99.5	0.619	Contact Map
3hz7A	1	0.96	99.5	0.619	Contact Map
2lxrA	1	0.9333	99.3	0.654	Contact Map
1okgA	1	0.72	96.6	0.828	Contact Map
3fryA	2	0.8	21.1	0.926	Contact Map
2l3mA	1	0.7733	18.3	0.928	Contact Map
3qq5A	3	0.92	17.4	0.928	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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