GREMLIN Database
HFQ - RNA-binding protein Hfq
UniProt: P0A6X3 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG10438
Length: 102 (79)
Sequences: 273 (114)
Seq/√Len: 12.8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
44_I59_I3.7510.99
42_F51_S3.6600.99
7_L62_V3.2500.98
44_I72_S2.2740.86
20_V68_V2.1890.83
41_Q50_V1.9460.75
28_N61_T1.9280.75
32_L46_L1.9140.74
6_S42_F1.9010.73
66_R78_G1.7260.66
69_S76_G1.7200.65
3_K22_V1.7080.65
43_V53_M1.6010.60
37_E47_K1.5860.59
31_K47_K1.5580.58
9_D36_I1.5280.56
73_N77_G1.3700.48
36_I75_A1.3690.48
30_I43_V1.3570.47
38_S63_V1.3510.47
54_V77_G1.3010.44
73_N76_G1.2970.44
21_P67_P1.2440.41
55_Y64_P1.2400.41
76_G79_T1.2060.39
32_L52_Q1.1690.38
33_Q51_S1.1160.35
70_H75_A1.1080.35
1_M6_S1.0760.33
5_Q47_K1.0730.33
31_K37_E1.0480.32
17_R78_G1.0240.31
31_K51_S1.0130.30
11_F46_L1.0080.30
7_L38_S1.0080.30
41_Q63_V1.0010.30
38_S45_L0.9990.30
30_I51_S0.9940.30
35_Q78_G0.9910.29
37_E51_S0.9780.29
37_E43_V0.9710.29
31_K38_S0.9710.29
9_D54_V0.9710.29
3_K10_P0.9590.28
49_T54_V0.9440.27
68_V76_G0.9370.27
6_S51_S0.9350.27
25_Y77_G0.9340.27
37_E53_M0.9300.27
47_K51_S0.9260.27
9_D14_A0.9220.27
13_N17_R0.8960.26
6_S36_I0.8750.25
33_Q47_K0.8750.25
3_K47_K0.8720.25
67_P70_H0.8700.25
23_S48_N0.8640.24
43_V51_S0.8580.24
24_I38_S0.8550.24
33_Q37_E0.8410.23
30_I37_E0.8350.23
2_A11_F0.8330.23
9_D35_Q0.8270.23
45_L50_V0.8240.23
30_I63_V0.8220.23
27_V61_T0.8100.22
5_Q24_I0.8070.22
73_N78_G0.7990.22
35_Q77_G0.7940.22
65_S79_T0.7860.21
6_S44_I0.7750.21
23_S53_M0.7530.20
70_H73_N0.7450.20
7_L10_P0.7430.20
33_Q43_V0.7390.20
13_N16_R0.7330.20
5_Q31_K0.7310.20
74_N78_G0.7280.19
14_A18_E0.7240.19
5_Q14_A0.7150.19
68_V78_G0.7140.19
52_Q60_S0.7100.19
7_L55_Y0.7090.19
21_P48_N0.7050.19
33_Q54_V0.7020.19
66_R74_N0.7020.19
48_N52_Q0.6850.18
72_S79_T0.6720.18
18_E71_H0.6580.17
33_Q52_Q0.6330.17
20_V74_N0.6320.17
36_I79_T0.6240.16
19_R43_V0.6210.16
69_S74_N0.6150.16
70_H79_T0.6110.16
28_N60_S0.6060.16
3_K7_L0.5980.16
67_P71_H0.5950.15
23_S38_S0.5920.15
28_N43_V0.5890.15
15_L32_L0.5840.15
27_V35_Q0.5750.15
29_G60_S0.5690.15
17_R32_L0.5690.15
59_I78_G0.5690.15
14_A65_S0.5620.15
31_K43_V0.5560.14
33_Q62_V0.5440.14
29_G61_T0.5420.14
48_N53_M0.5350.14
28_N70_H0.5240.14
19_R72_S0.5200.14
42_F52_Q0.5190.14
27_V47_K0.5160.13
23_S49_T0.5140.13
10_P15_L0.5110.13
14_A27_V0.5080.13
2_A76_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  
2y90A 3 0.6275 100 0.258 Contact Map
1u1sA 3 0.6569 100 0.304 Contact Map
3sb2A 3 0.6765 100 0.311 Contact Map
1kq1A 5 0.6373 100 0.321 Contact Map
4nl2D 3 0.7157 100 0.331 Contact Map
4pnoA 3 0.6275 100 0.345 Contact Map
3ahuA 3 0.6373 100 0.352 Contact Map
3hfoA 4 0.6078 99.9 0.466 Contact Map
3hfnA 3 0.5882 99.9 0.474 Contact Map
4x9cA 3 0.5588 99.9 0.477 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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