GREMLIN Database
YMDF - Uncharacterized protein YmdF
UniProt: P56614 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG14358
Length: 57 (49)
Sequences: 189 (93)
Seq/√Len: 13.3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
40_A43_A2.5940.93
10_N13_E2.5190.92
23_K45_K2.3360.88
28_H50_S1.9800.78
51_S54_K1.9030.75
18_A21_A1.8880.74
29_S39_R1.8380.72
13_E21_A1.6400.63
33_F40_A1.6360.63
31_G39_R1.5720.60
50_S54_K1.4980.56
34_K37_P1.4790.55
18_A22_G1.4270.52
42_E47_G1.3920.50
14_D18_A1.3760.50
10_N21_A1.3520.48
13_E22_G1.2800.44
41_S45_K1.2550.43
10_N22_G1.2410.42
13_E17_R1.2060.41
14_D17_R1.2050.41
16_E19_S1.2020.40
24_K27_Q1.1960.40
30_G35_N1.1920.40
11_F19_S1.1390.37
10_N18_A1.1110.36
13_E18_A1.0510.33
18_A24_K1.0310.32
32_N35_N0.9690.29
30_G50_S0.9330.28
29_S35_N0.9300.28
33_F39_R0.9090.27
37_P45_K0.8980.26
43_A46_K0.8930.26
36_D41_S0.8850.26
19_S22_G0.8590.25
37_P41_S0.8220.23
8_S13_E0.7810.22
23_K28_H0.7690.21
15_R54_K0.7580.21
20_E50_S0.7430.20
40_A46_K0.7370.20
11_F21_A0.7370.20
20_E23_K0.7260.20
39_R43_A0.7190.20
45_K52_H0.7180.20
28_H31_G0.7180.20
12_A42_E0.6910.19
38_Q42_E0.6850.19
11_F18_A0.6730.18
33_F43_A0.6730.18
12_A27_Q0.6650.18
33_F36_D0.6630.18
23_K50_S0.6620.18
10_N17_R0.6520.18
34_K41_S0.6470.17
16_E38_Q0.6350.17
33_F46_K0.6320.17
9_G17_R0.6290.17
29_S33_F0.6050.16
19_S23_K0.5970.16
27_Q54_K0.5820.15
14_D41_S0.5640.15
24_K43_A0.5500.15
8_S31_G0.5480.15
16_E20_E0.5360.14
35_N41_S0.5200.14
8_S11_F0.5180.14
27_Q39_R0.5110.14
7_G50_S0.5080.14
7_G42_E0.5050.13
50_S53_G0.5040.13
20_E27_Q0.5030.13
33_F48_G0.5000.13
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  
4he8J 1 0.0877 1.5 0.914 Contact Map
3p0sA 6 0.0526 1.5 0.914 Contact Map
4gb34 3 0.5263 0.8 0.929 Contact Map
3j3wD 1 0.9298 0.7 0.93 Contact Map
2wn4A 1 0.2281 0.5 0.936 Contact Map
1c8m4 3 0.1754 0.5 0.937 Contact Map
2r2iA 1 0.1579 0.5 0.938 Contact Map
4b6hC 1 0 0.5 0.938 Contact Map
1ncqD 3 0.5263 0.5 0.938 Contact Map
4cdqD 2 0.5263 0.5 0.938 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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