GREMLIN Database
YRDB - Uncharacterized protein YrdB
UniProt: P45795 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG12839
Length: 85 (84)
Sequences: 187 (136)
Seq/√Len: 14.8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
34_A81_W3.4870.99
8_P23_P2.9070.97
77_D81_W2.6540.95
24_A31_L2.4640.93
46_G52_W2.3570.91
6_Q65_E2.3550.91
63_L67_A2.2770.90
11_E61_W2.1030.86
77_D83_W1.7750.74
70_L75_S1.7110.71
44_F76_E1.6950.70
41_A57_R1.6280.67
55_S82_V1.6260.67
49_P52_W1.5750.65
11_E29_M1.5450.63
26_V66_E1.4910.60
13_W23_P1.4360.57
67_A82_V1.4250.57
30_Q76_E1.4240.56
31_L82_V1.4000.55
9_D70_L1.3790.54
21_C41_A1.3630.53
8_P32_T1.3440.52
79_Q83_W1.3130.50
15_E50_E1.2900.49
34_A83_W1.2740.48
6_Q61_W1.2510.47
25_L66_E1.2230.45
69_N79_Q1.2030.44
32_T81_W1.1860.43
26_V31_L1.1700.42
16_N69_N1.1690.42
12_E42_Y1.1540.42
6_Q11_E1.1460.41
19_C63_L1.1390.41
5_I27_N1.1040.39
44_F59_H1.0860.38
68_E74_Q1.0840.38
4_A50_E1.0800.38
35_I73_E1.0640.37
47_D51_Q1.0370.35
43_R59_H1.0260.35
6_Q76_E1.0010.34
11_E23_P0.9910.33
42_Y69_N0.9790.32
20_V75_S0.9780.32
25_L61_W0.9620.32
59_H84_L0.9620.32
24_A74_Q0.9530.31
10_R23_P0.9480.31
32_T40_L0.9440.31
15_E75_S0.9430.31
9_D18_K0.9330.30
19_C62_D0.9290.30
36_S72_Q0.9290.30
67_A83_W0.9280.30
57_R61_W0.9050.29
57_R66_E0.8870.28
55_S59_H0.8840.28
65_E70_L0.8830.28
20_V70_L0.8720.27
14_D17_K0.8510.27
24_A58_Q0.8470.26
6_Q29_M0.8450.26
61_W72_Q0.8250.25
36_S42_Y0.8140.25
31_L67_A0.8100.25
29_M72_Q0.8050.25
9_D14_D0.8050.25
11_E57_R0.7980.24
4_A52_W0.7980.24
4_A72_Q0.7980.24
51_Q84_L0.7930.24
4_A11_E0.7620.23
73_E82_V0.7560.23
40_L54_A0.7560.23
46_G75_S0.7520.22
14_D38_E0.7510.22
4_A81_W0.7440.22
30_Q73_E0.7410.22
8_P43_R0.7370.22
63_L80_G0.7310.22
32_T67_A0.7290.22
16_N42_Y0.7190.21
23_P34_A0.7150.21
32_T77_D0.6970.20
27_N63_L0.6970.20
44_F55_S0.6790.20
23_P32_T0.6720.19
38_E78_D0.6690.19
24_A67_A0.6630.19
17_K35_I0.6540.19
73_E84_L0.6390.18
17_K20_V0.6370.18
47_D55_S0.6290.18
40_L50_E0.6170.18
12_E38_E0.6160.18
21_C69_N0.6140.18
21_C32_T0.6100.17
6_Q25_L0.6080.17
19_C34_A0.6060.17
49_P54_A0.6060.17
29_M61_W0.6010.17
69_N78_D0.6000.17
51_Q58_Q0.5910.17
62_D69_N0.5780.16
59_H65_E0.5750.16
21_C83_W0.5740.16
30_Q82_V0.5730.16
23_P45_T0.5730.16
8_P22_F0.5700.16
51_Q82_V0.5700.16
12_E74_Q0.5680.16
21_C34_A0.5600.16
31_L74_Q0.5530.16
36_S53_L0.5400.15
13_W65_E0.5300.15
46_G58_Q0.5290.15
8_P34_A0.5280.15
20_V40_L0.5160.15
50_E72_Q0.5160.15
19_C83_W0.5120.14
9_D62_D0.5080.14
14_D21_C0.5070.14
18_K42_Y0.5040.14
41_A75_S0.5000.14
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  
2gpiA 1 1 100 0.246 Contact Map
3f2gA 1 0.8235 15.8 0.924 Contact Map
3j21E 1 0.6824 11.6 0.928 Contact Map
1oo2A 4 0.5882 11.5 0.929 Contact Map
1vq8D 1 0.4118 11.3 0.929 Contact Map
1f86A 4 0.5765 10.8 0.93 Contact Map
2g2nA 5 0.5765 8.3 0.933 Contact Map
1v92A 1 0.5412 6.1 0.937 Contact Map
3qvaA 4 0.6118 5.5 0.939 Contact Map
1n0eA 5 0.8824 5.1 0.939 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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