GREMLIN Database
YGGU - UPF0235 protein YggU
UniProt: P52060 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG12981
Length: 96 (81)
Sequences: 594 (435)
Seq/√Len: 48.3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
25_S37_A2.9201.00
24_D39_T2.8191.00
61_V81_I2.7651.00
16_Y76_H2.6811.00
43_V46_Q2.6101.00
55_L79_I2.3071.00
24_D50_H2.0521.00
7_N10_G1.9640.99
33_E76_H1.9200.99
20_K39_T1.8320.99
42_P45_G1.7320.98
70_K78_Q1.6900.98
52_V68_I1.6640.98
36_V51_L1.6260.98
29_L32_D1.5930.97
18_Q35_K1.5190.96
30_H35_K1.4510.95
16_Y30_H1.4340.95
27_V37_A1.4180.95
20_K51_L1.3900.94
10_G80_K1.3900.94
56_G66_V1.3300.93
44_D73_L1.2820.91
7_N80_K1.2820.91
21_A37_A1.2720.91
53_K63_K1.2650.91
52_V66_V1.2510.90
28_G35_K1.2430.90
40_A51_L1.1970.88
62_A65_Q1.1900.88
67_V82_I1.1880.88
56_G65_Q1.1820.87
12_V78_Q1.1490.86
67_V80_K1.1450.86
69_E72_E1.1430.86
14_R32_D1.1340.85
36_V54_F1.1140.84
38_I51_L1.0870.83
55_L66_V1.0810.82
15_L36_V1.0670.81
18_Q30_H1.0490.80
28_G34_V1.0450.80
69_E78_Q1.0430.80
12_V80_K1.0300.79
54_F58_Q1.0040.77
62_A84_P0.9970.77
26_I34_V0.9410.73
24_D51_L0.9040.70
36_V70_K0.9020.69
53_K64_S0.8830.68
15_L68_I0.8820.68
59_F84_P0.8820.68
68_I79_I0.8790.67
46_Q51_L0.8640.66
60_R66_V0.8630.66
14_R76_H0.8560.65
38_I54_F0.8540.65
39_T49_S0.8350.63
59_F86_Q0.8340.63
11_L84_P0.8330.63
38_I50_H0.8290.63
59_F81_I0.8110.61
24_D38_I0.8090.61
23_R37_A0.8000.60
51_L54_F0.7940.59
39_T50_H0.7880.59
54_F64_S0.7880.59
46_Q72_E0.7820.58
20_K43_V0.7790.58
42_P68_I0.7580.56
21_A86_Q0.7540.55
21_A51_L0.7500.55
6_V11_L0.7440.54
17_I36_V0.7380.54
68_I72_E0.7310.53
16_Y45_G0.7290.53
12_V69_E0.7280.53
10_G52_V0.7260.53
26_I54_F0.7250.53
13_L68_I0.7140.51
14_R69_E0.7060.51
36_V55_L0.7050.51
31_G76_H0.7040.50
12_V29_L0.7020.50
19_P75_R0.7000.50
24_D44_D0.6900.49
56_G61_V0.6790.48
22_S39_T0.6690.47
13_L81_I0.6610.46
19_P44_D0.6540.45
36_V58_Q0.6500.45
18_Q37_A0.6370.44
42_P60_R0.6360.44
10_G82_I0.6360.44
30_H42_P0.6350.44
14_R78_Q0.6320.43
22_S57_K0.6210.42
16_Y70_K0.6140.41
25_S54_F0.5930.39
11_L45_G0.5820.38
18_Q75_R0.5810.38
46_Q73_L0.5800.38
15_L79_I0.5780.38
10_G59_F0.5650.37
17_I38_I0.5590.36
51_L55_L0.5550.36
9_D78_Q0.5520.36
9_D27_V0.5520.36
41_P66_V0.5470.35
22_S74_G0.5460.35
67_V86_Q0.5440.35
50_H53_K0.5410.35
24_D54_F0.5360.34
6_V10_G0.5310.34
12_V46_Q0.5270.33
14_R70_K0.5190.33
12_V52_V0.5150.32
6_V86_Q0.5130.32
49_S64_S0.5090.32
49_S57_K0.5040.31
16_Y21_A0.5040.31
49_S80_K0.5000.31
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  
1n91A 1 1 100 0.167 Contact Map
1jrmA 1 0.9479 100 0.243 Contact Map
3nvzC 2 1 29.6 0.911 Contact Map
2w3sB 2 1 26.2 0.914 Contact Map
2xcmC 1 0.875 20.7 0.917 Contact Map
1rm6A 2 1 20.5 0.918 Contact Map
3zyvA 3 0.9896 19 0.919 Contact Map
1ffvB 2 1 19 0.919 Contact Map
3uncA 2 1 17.5 0.92 Contact Map
1t3qB 2 1 17.2 0.921 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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