GREMLIN Database
YHBY - RNA-binding protein YhbY
UniProt: P0AGK4 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG12794
Length: 97 (89)
Sequences: 726 (244)
Seq/√Len: 25.9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
38_E86_R4.0781.00
24_L62_I3.6341.00
87_P91_R2.9031.00
37_I84_L2.8641.00
10_H14_L2.6770.99
41_L72_A2.5980.99
87_P90_E2.3940.99
55_D62_I2.1250.97
32_G36_E2.0550.96
75_V83_V2.0340.96
72_A90_E1.7190.90
67_V74_N1.6750.89
24_L69_E1.6460.88
41_L90_E1.6070.87
25_G48_K1.5330.84
28_G57_E1.5130.83
66_I84_L1.5000.83
8_K12_K1.4820.82
22_V36_E1.4730.81
22_V70_T1.4280.79
67_V77_V1.4090.78
64_E86_R1.4070.78
6_K14_L1.4050.78
8_K16_H1.3830.77
22_V43_H1.3720.76
71_G87_P1.3010.72
22_V86_R1.2930.72
46_L62_I1.2550.70
39_Q46_L1.2260.68
46_L84_L1.1860.65
29_L34_L1.1810.65
30_T74_N1.1790.65
43_H70_T1.1740.64
50_K81_T1.1640.64
66_I73_C1.1630.64
15_A18_L1.1470.63
47_I66_I1.1220.61
38_E41_L1.0350.55
26_S46_L1.0290.54
51_I62_I1.0280.54
25_G82_L0.9940.52
45_E83_V0.9900.51
37_I68_R0.9890.51
5_T17_P0.9640.49
5_T9_Q0.9640.49
45_E85_Y0.9610.49
27_N43_H0.9490.48
34_L90_E0.9470.48
60_T64_E0.9460.48
58_T76_Q0.9460.48
58_T61_L0.9430.48
33_V42_E0.9370.47
39_Q84_L0.9290.47
35_A39_Q0.9110.45
64_E68_R0.8970.44
27_N33_V0.8960.44
24_L49_V0.8840.43
28_G53_T0.8740.43
49_V77_V0.8650.42
73_C87_P0.8640.42
21_V40_A0.8530.41
44_H79_G0.8460.41
48_K79_G0.8250.39
28_G45_E0.8170.39
21_V50_K0.8150.39
3_L12_K0.7990.37
33_V53_T0.7940.37
25_G49_V0.7920.37
17_P81_T0.7790.36
41_L47_I0.7700.35
13_G16_H0.7600.35
11_L70_T0.7570.35
21_V78_I0.7490.34
60_T80_K0.7450.34
32_G37_I0.7360.33
34_L65_A0.7360.33
73_C83_V0.7320.33
29_L42_E0.7280.33
33_V49_V0.7270.33
38_E66_I0.7080.31
71_G90_E0.7060.31
54_E75_V0.7020.31
10_H76_Q0.6990.31
31_E70_T0.6980.31
25_G84_L0.6940.30
53_T62_I0.6900.30
12_K66_I0.6860.30
38_E77_V0.6810.30
35_A56_R0.6780.29
64_E70_T0.6460.28
24_L56_R0.6400.27
26_S88_T0.6390.27
13_G26_S0.6300.27
3_L16_H0.6270.26
35_A53_T0.6260.26
8_K75_V0.6260.26
8_K71_G0.6260.26
24_L72_A0.6250.26
35_A89_K0.6250.26
63_V77_V0.6200.26
59_K67_V0.6200.26
20_P46_L0.6190.26
38_E87_P0.6160.26
9_Q16_H0.6140.26
19_K56_R0.6100.25
65_A71_G0.6070.25
55_D84_L0.6060.25
6_K15_A0.6000.25
45_E79_G0.5990.25
5_T11_L0.5980.25
12_K74_N0.5970.25
39_Q82_L0.5960.25
34_L71_G0.5950.25
6_K44_H0.5920.24
34_L59_K0.5910.24
66_I82_L0.5830.24
26_S82_L0.5830.24
41_L67_V0.5780.24
36_E46_L0.5680.23
36_E53_T0.5590.23
70_T85_Y0.5580.23
27_N69_E0.5510.22
36_E41_L0.5440.22
21_V37_I0.5390.22
13_G35_A0.5350.22
52_A82_L0.5340.21
3_L28_G0.5330.21
22_V49_V0.5310.21
20_P51_I0.5220.21
48_K78_I0.5160.21
4_S10_H0.5120.20
24_L27_N0.5120.20
61_L64_E0.5040.20
60_T63_V0.5000.20
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  
1jo0A 1 1 100 0.213 Contact Map
1rq8A 1 0.9897 99.9 0.251 Contact Map
3wryA 1 0.7423 18.7 0.915 Contact Map
4c26A 1 0.4845 12.9 0.921 Contact Map
4nx1A 1 0.3918 8.7 0.927 Contact Map
4kix5 1 0.9278 8.5 0.927 Contact Map
3sbxA 2 0.6907 8.5 0.927 Contact Map
2hm2Q 1 0.7113 8.4 0.927 Contact Map
1pn5A 1 0.7423 8.1 0.928 Contact Map
3quaA 2 0.701 7.9 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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