GREMLIN Database
YGDI - Uncharacterized lipoprotein YgdI
UniProt: P65292 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG13081
Length: 75 (70)
Sequences: 212 (126)
Seq/√Len: 15.0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
44_D47_T3.2990.99
51_S59_K2.2340.89
43_T50_I2.1880.88
26_V34_T2.0160.83
28_H34_T1.9230.80
23_S72_E1.8630.78
26_V58_N1.8470.77
5_A8_I1.7670.74
36_V70_M1.6550.69
38_D60_Q1.6410.68
27_M54_D1.6240.68
50_I70_M1.5830.65
53_K64_R1.5790.65
58_N66_D1.5650.65
38_D42_Q1.5220.62
12_M49_M1.5180.62
29_T61_Q1.5160.62
31_D49_M1.3830.55
37_S44_D1.3730.54
5_A18_S1.2970.50
34_T71_V1.2840.49
37_S56_N1.2240.46
8_I13_L1.2190.46
52_Y63_N1.2180.45
26_V39_G1.2070.45
33_R60_Q1.1990.44
28_H60_Q1.1990.44
24_N55_A1.1710.43
39_G46_D1.1380.41
27_M43_T1.1370.41
29_T47_T1.1230.40
16_A19_A1.1220.40
43_T64_R1.1020.39
21_S37_S1.0850.38
31_D68_K1.0660.37
4_T10_A1.0550.37
9_S13_L1.0420.36
12_M15_F1.0140.35
19_A55_A0.9720.32
31_D60_Q0.9670.32
62_I65_T0.9660.32
19_A38_D0.9560.32
45_N64_R0.9560.32
8_I38_D0.9240.30
61_Q67_V0.9180.30
24_N59_K0.9030.29
33_R54_D0.8910.29
5_A14_T0.8870.28
37_S49_M0.8830.28
5_A10_A0.8540.27
4_T17_L0.8530.27
36_V43_T0.8520.27
6_A18_S0.8510.27
31_D61_Q0.8480.27
8_I16_A0.8440.26
26_V63_N0.8400.26
35_I50_I0.8390.26
17_L33_R0.8330.26
24_N34_T0.7970.24
21_S64_R0.7930.24
27_M59_K0.7850.24
7_I31_D0.7790.24
35_I55_A0.7660.23
7_I11_C0.7630.23
59_K65_T0.7620.23
34_T70_M0.7620.23
13_L17_L0.7580.23
21_S24_N0.7550.23
65_T68_K0.7460.22
4_T7_I0.7360.22
14_T67_V0.7340.22
39_G68_K0.7310.22
25_Y69_E0.7260.22
36_V64_R0.7210.21
14_T18_S0.7210.21
31_D50_I0.7070.21
28_H50_I0.7010.21
21_S53_K0.6950.20
25_Y60_Q0.6920.20
27_M36_V0.6890.20
34_T60_Q0.6890.20
56_N67_V0.6860.20
25_Y28_H0.6760.20
28_H70_M0.6720.20
12_M50_I0.6600.19
9_S58_N0.6440.19
11_C53_K0.6350.18
24_N36_V0.6340.18
7_I16_A0.6110.18
25_Y54_D0.6090.18
44_D51_S0.6020.17
54_D67_V0.6000.17
25_Y71_V0.6000.17
28_H36_V0.5850.17
14_T17_L0.5780.17
10_A16_A0.5750.16
24_N51_S0.5670.16
4_T16_A0.5590.16
9_S35_I0.5530.16
5_A9_S0.5510.16
55_A68_K0.5230.15
33_R62_I0.5160.15
14_T38_D0.5150.15
12_M17_L0.5050.14
14_T19_A0.5000.14
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

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  
3bduA 3 0.7067 99.9 0.327 Contact Map
2jn0A 1 0.6667 99.9 0.328 Contact Map
2k57A 1 0.7333 99.9 0.336 Contact Map
2rd1A 2 0.72 99.9 0.34 Contact Map
2ra2A 3 0.7467 99.9 0.347 Contact Map
2rb6A 2 0.72 99.9 0.354 Contact Map
3tlkA 1 0.3733 94.5 0.825 Contact Map
4n01A 1 0.4133 91.6 0.843 Contact Map
4utoA 1 0.56 86.8 0.857 Contact Map
3ombA 1 0.56 82.2 0.865 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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