GREMLIN Database
HFQ - RNA-binding protein Hfq
UniProt: O31796 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 73 (68)
Sequences: 570 (227)
Seq/√Len: 27.5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
43_V59_I5.7901.00
27_N61_T2.4490.99
6_I62_F2.2200.98
12_N38_F2.1680.98
12_N15_R2.1430.97
31_L45_L2.1370.97
13_Q17_E1.9950.96
42_T53_L1.7770.93
17_E38_F1.7310.92
27_N60_S1.7260.92
30_Q46_E1.6090.88
31_L52_Q1.5660.87
22_T60_S1.5650.87
14_I68_V1.5180.85
10_F35_V1.4750.83
8_D38_F1.4400.82
36_K46_E1.4230.81
6_I41_F1.4230.81
32_R50_K1.4060.80
12_N16_K1.3650.78
17_E66_K1.3230.76
24_F63_A1.2720.73
52_Q70_L1.2540.72
6_I9_Q1.2190.70
47_S50_K1.2110.69
21_V35_V1.1640.66
13_Q69_Q1.1200.63
3_P70_L1.1180.63
14_I21_V1.0620.59
4_I13_Q1.0580.59
5_N14_I1.0540.58
65_Q68_V1.0030.55
30_Q50_K0.9880.53
24_F70_L0.9870.53
23_V62_F0.9570.51
46_E49_G0.9490.51
52_Q60_S0.9450.50
35_V45_L0.9380.50
31_L47_S0.9320.49
24_F58_A0.9060.47
65_Q69_Q0.9040.47
36_K66_K0.9030.47
4_I70_L0.9000.47
6_I55_Y0.8860.46
26_L60_S0.8840.46
37_G44_L0.8770.45
15_R37_G0.8720.45
42_T51_Q0.8620.44
59_I66_K0.8480.43
5_N51_Q0.8380.42
20_Y66_K0.8340.42
44_L53_L0.8090.40
13_Q21_V0.8020.39
28_G60_S0.7990.39
19_T67_N0.7960.39
10_F21_V0.7930.39
6_I23_V0.7760.38
3_P41_F0.7690.37
20_Y62_F0.7520.36
35_V47_S0.7460.35
4_I69_Q0.7410.35
26_L61_T0.7400.35
9_Q70_L0.7380.35
7_Q11_L0.7260.34
26_L53_L0.7100.33
48_E64_P0.7080.33
5_N68_V0.6920.32
30_Q63_A0.6690.30
21_V41_F0.6570.30
4_I44_L0.6520.29
16_K36_K0.6480.29
6_I37_G0.6270.28
15_R40_N0.6140.27
47_S52_Q0.6120.27
27_N42_T0.6090.27
21_V70_L0.6020.26
4_I14_I0.5970.26
36_K42_T0.5970.26
42_T55_Y0.5940.26
19_T65_Q0.5840.25
3_P32_R0.5830.25
4_I9_Q0.5810.25
8_D53_L0.5760.25
46_E51_Q0.5710.24
9_Q44_L0.5700.24
24_F43_V0.5630.24
30_Q47_S0.5560.24
21_V62_F0.5530.23
34_Q63_A0.5500.23
29_F51_Q0.5380.23
5_N12_N0.5360.23
14_I37_G0.5350.22
22_T58_A0.5320.22
5_N8_D0.5230.22
12_N37_G0.5180.22
22_T34_Q0.5150.21
34_Q54_I0.5140.21
34_Q65_Q0.5100.21
22_T48_E0.5090.21
18_N42_T0.5080.21
28_G58_A0.5070.21
46_E53_L0.5000.21
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  
3ahuA 3 0.9041 100 0.164 Contact Map
4nl2D 3 1 100 0.19 Contact Map
1kq1A 5 0.8904 100 0.192 Contact Map
3sb2A 3 0.9452 100 0.201 Contact Map
1u1sA 3 0.9178 100 0.202 Contact Map
2y90A 3 0.8767 100 0.204 Contact Map
4pnoA 3 0.8767 99.9 0.239 Contact Map
4x9cA 3 0.7945 99.9 0.341 Contact Map
3hfoA 4 0.8767 99.9 0.343 Contact Map
3hfnA 3 0.8219 99.9 0.351 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.

Page generated in 0.0048 seconds.