HFQ - BACSU - GREMLIN Contacts

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HFQ - RNA-binding protein Hfq

UniProt:	O31796	Sequences: MKPINIQDQFLNQIRKENTYVTVFLLNGFQLRGQVKGFDNFTVLLESEGKQQLIYKHAISTFAPQKNVQLELE	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_V	59_I	5.790	1.00
27_N	61_T	2.449	0.99
6_I	62_F	2.220	0.98
12_N	38_F	2.168	0.98
12_N	15_R	2.143	0.97
31_L	45_L	2.137	0.97
13_Q	17_E	1.995	0.96
42_T	53_L	1.777	0.93
17_E	38_F	1.731	0.92
27_N	60_S	1.726	0.92
30_Q	46_E	1.609	0.88
31_L	52_Q	1.566	0.87
22_T	60_S	1.565	0.87
14_I	68_V	1.518	0.85
10_F	35_V	1.475	0.83
8_D	38_F	1.440	0.82
36_K	46_E	1.423	0.81
6_I	41_F	1.423	0.81
32_R	50_K	1.406	0.80
12_N	16_K	1.365	0.78
17_E	66_K	1.323	0.76
24_F	63_A	1.272	0.73
52_Q	70_L	1.254	0.72
6_I	9_Q	1.219	0.70
47_S	50_K	1.211	0.69
21_V	35_V	1.164	0.66
13_Q	69_Q	1.120	0.63
3_P	70_L	1.118	0.63
14_I	21_V	1.062	0.59
4_I	13_Q	1.058	0.59
5_N	14_I	1.054	0.58
65_Q	68_V	1.003	0.55
30_Q	50_K	0.988	0.53
24_F	70_L	0.987	0.53
23_V	62_F	0.957	0.51
46_E	49_G	0.949	0.51
52_Q	60_S	0.945	0.50
35_V	45_L	0.938	0.50
31_L	47_S	0.932	0.49
24_F	58_A	0.906	0.47
65_Q	69_Q	0.904	0.47
36_K	66_K	0.903	0.47
4_I	70_L	0.900	0.47
6_I	55_Y	0.886	0.46
26_L	60_S	0.884	0.46
37_G	44_L	0.877	0.45
15_R	37_G	0.872	0.45
42_T	51_Q	0.862	0.44
59_I	66_K	0.848	0.43
5_N	51_Q	0.838	0.42
20_Y	66_K	0.834	0.42
44_L	53_L	0.809	0.40
13_Q	21_V	0.802	0.39
28_G	60_S	0.799	0.39
19_T	67_N	0.796	0.39
10_F	21_V	0.793	0.39
6_I	23_V	0.776	0.38
3_P	41_F	0.769	0.37
20_Y	62_F	0.752	0.36
35_V	47_S	0.746	0.35
4_I	69_Q	0.741	0.35
26_L	61_T	0.740	0.35
9_Q	70_L	0.738	0.35
7_Q	11_L	0.726	0.34
26_L	53_L	0.710	0.33
48_E	64_P	0.708	0.33
5_N	68_V	0.692	0.32
30_Q	63_A	0.669	0.30
21_V	41_F	0.657	0.30
4_I	44_L	0.652	0.29
16_K	36_K	0.648	0.29
6_I	37_G	0.627	0.28
15_R	40_N	0.614	0.27
47_S	52_Q	0.612	0.27
27_N	42_T	0.609	0.27
21_V	70_L	0.602	0.26
4_I	14_I	0.597	0.26
36_K	42_T	0.597	0.26
42_T	55_Y	0.594	0.26
19_T	65_Q	0.584	0.25
3_P	32_R	0.583	0.25
4_I	9_Q	0.581	0.25
8_D	53_L	0.576	0.25
46_E	51_Q	0.571	0.24
9_Q	44_L	0.570	0.24
24_F	43_V	0.563	0.24
30_Q	47_S	0.556	0.24
21_V	62_F	0.553	0.23
34_Q	63_A	0.550	0.23
29_F	51_Q	0.538	0.23
5_N	12_N	0.536	0.23
14_I	37_G	0.535	0.22
22_T	58_A	0.532	0.22
5_N	8_D	0.523	0.22
12_N	37_G	0.518	0.22
22_T	34_Q	0.515	0.21
34_Q	54_I	0.514	0.21
34_Q	65_Q	0.510	0.21
22_T	48_E	0.509	0.21
18_N	42_T	0.508	0.21
28_G	58_A	0.507	0.21
46_E	53_L	0.500	0.21

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

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
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.

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