HFQ - ECOLI - GREMLIN Contacts

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HFQ - RNA-binding protein Hfq

UniProt:	P0A6X3	Sequences: MAKGQSLQDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVSHHSNNAGGGTSSNYHHGSSAQNTSAQQDSEETE	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

ECOLI - HFQ
BACSU - HFQ

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_I	59_I	3.751	0.99
42_F	51_S	3.660	0.99
7_L	62_V	3.250	0.98
44_I	72_S	2.274	0.86
20_V	68_V	2.189	0.83
41_Q	50_V	1.946	0.75
28_N	61_T	1.928	0.75
32_L	46_L	1.914	0.74
6_S	42_F	1.901	0.73
66_R	78_G	1.726	0.66
69_S	76_G	1.720	0.65
3_K	22_V	1.708	0.65
43_V	53_M	1.601	0.60
37_E	47_K	1.586	0.59
31_K	47_K	1.558	0.58
9_D	36_I	1.528	0.56
73_N	77_G	1.370	0.48
36_I	75_A	1.369	0.48
30_I	43_V	1.357	0.47
38_S	63_V	1.351	0.47
54_V	77_G	1.301	0.44
73_N	76_G	1.297	0.44
21_P	67_P	1.244	0.41
55_Y	64_P	1.240	0.41
76_G	79_T	1.206	0.39
32_L	52_Q	1.169	0.38
33_Q	51_S	1.116	0.35
70_H	75_A	1.108	0.35
1_M	6_S	1.076	0.33
5_Q	47_K	1.073	0.33
31_K	37_E	1.048	0.32
17_R	78_G	1.024	0.31
31_K	51_S	1.013	0.30
11_F	46_L	1.008	0.30
7_L	38_S	1.008	0.30
41_Q	63_V	1.001	0.30
38_S	45_L	0.999	0.30
30_I	51_S	0.994	0.30
35_Q	78_G	0.991	0.29
37_E	51_S	0.978	0.29
37_E	43_V	0.971	0.29
31_K	38_S	0.971	0.29
9_D	54_V	0.971	0.29
3_K	10_P	0.959	0.28
49_T	54_V	0.944	0.27
68_V	76_G	0.937	0.27
6_S	51_S	0.935	0.27
25_Y	77_G	0.934	0.27
37_E	53_M	0.930	0.27
47_K	51_S	0.926	0.27
9_D	14_A	0.922	0.27
13_N	17_R	0.896	0.26
6_S	36_I	0.875	0.25
33_Q	47_K	0.875	0.25
3_K	47_K	0.872	0.25
67_P	70_H	0.870	0.25
23_S	48_N	0.864	0.24
43_V	51_S	0.858	0.24
24_I	38_S	0.855	0.24
33_Q	37_E	0.841	0.23
30_I	37_E	0.835	0.23
2_A	11_F	0.833	0.23
9_D	35_Q	0.827	0.23
45_L	50_V	0.824	0.23
30_I	63_V	0.822	0.23
27_V	61_T	0.810	0.22
5_Q	24_I	0.807	0.22
73_N	78_G	0.799	0.22
35_Q	77_G	0.794	0.22
65_S	79_T	0.786	0.21
6_S	44_I	0.775	0.21
23_S	53_M	0.753	0.20
70_H	73_N	0.745	0.20
7_L	10_P	0.743	0.20
33_Q	43_V	0.739	0.20
13_N	16_R	0.733	0.20
5_Q	31_K	0.731	0.20
74_N	78_G	0.728	0.19
14_A	18_E	0.724	0.19
5_Q	14_A	0.715	0.19
68_V	78_G	0.714	0.19
52_Q	60_S	0.710	0.19
7_L	55_Y	0.709	0.19
21_P	48_N	0.705	0.19
33_Q	54_V	0.702	0.19
66_R	74_N	0.702	0.19
48_N	52_Q	0.685	0.18
72_S	79_T	0.672	0.18
18_E	71_H	0.658	0.17
33_Q	52_Q	0.633	0.17
20_V	74_N	0.632	0.17
36_I	79_T	0.624	0.16
19_R	43_V	0.621	0.16
69_S	74_N	0.615	0.16
70_H	79_T	0.611	0.16
28_N	60_S	0.606	0.16
3_K	7_L	0.598	0.16
67_P	71_H	0.595	0.15
23_S	38_S	0.592	0.15
28_N	43_V	0.589	0.15
15_L	32_L	0.584	0.15
27_V	35_Q	0.575	0.15
29_G	60_S	0.569	0.15
17_R	32_L	0.569	0.15
59_I	78_G	0.569	0.15
14_A	65_S	0.562	0.15
31_K	43_V	0.556	0.14
33_Q	62_V	0.544	0.14
29_G	61_T	0.542	0.14
48_N	53_M	0.535	0.14
28_N	70_H	0.524	0.14
19_R	72_S	0.520	0.14
42_F	52_Q	0.519	0.14
27_V	47_K	0.516	0.13
23_S	49_T	0.514	0.13
10_P	15_L	0.511	0.13
14_A	27_V	0.508	0.13
2_A	76_G	0.500	0.13

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

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

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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