YQAF - BACSU - GREMLIN Contacts

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YQAF - Uncharacterized HTH-type transcriptional regulator YqaF

UniProt:	P45903	Sequences: MMRKWLKKNRLEKGFTQEEVAKAAQIGRAYYTMIENGTRKPSVIVSKKIGEKLGFDWTIFFEDVCNETKHNSKDSA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	76 (64)
Sequences:	964 (840)
Seq/√Len:	105.0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
10_R	35_E	4.507	1.00
20_V	31_Y	3.452	1.00
18_E	28_R	2.966	1.00
18_E	22_K	2.613	1.00
23_A	52_K	2.108	1.00
29_A	33_M	1.839	1.00
33_M	38_T	1.806	1.00
64_V	67_E	1.718	1.00
5_W	59_I	1.692	1.00
40_K	43_V	1.591	1.00
12_E	67_E	1.548	1.00
20_V	53_L	1.461	1.00
45_V	48_K	1.417	1.00
29_A	32_T	1.415	1.00
51_E	63_D	1.415	1.00
9_N	53_L	1.383	1.00
17_Q	28_R	1.335	0.99
46_S	57_W	1.310	0.99
33_M	36_N	1.284	0.99
30_Y	33_M	1.265	0.99
50_G	57_W	1.224	0.99
59_I	62_E	1.198	0.99
57_W	61_F	1.173	0.99
24_A	53_L	1.090	0.98
5_W	8_K	1.085	0.98
26_I	31_Y	1.065	0.97
46_S	61_F	1.041	0.97
16_T	19_E	1.040	0.97
20_V	49_I	1.025	0.97
33_M	39_R	1.008	0.96
27_G	30_Y	0.999	0.96
27_G	33_M	0.992	0.96
58_T	63_D	0.982	0.96
6_L	31_Y	0.975	0.95
30_Y	34_I	0.963	0.95
34_I	45_V	0.961	0.95
32_T	36_N	0.944	0.95
28_R	32_T	0.940	0.94
24_A	52_K	0.911	0.93
9_N	55_F	0.906	0.93
17_Q	35_E	0.898	0.93
13_K	23_A	0.889	0.93
24_A	34_I	0.885	0.92
47_K	51_E	0.883	0.92
17_Q	31_Y	0.850	0.91
19_E	23_A	0.835	0.90
34_I	39_R	0.831	0.90
13_K	54_G	0.829	0.90
5_W	63_D	0.812	0.89
28_R	31_Y	0.807	0.89
7_K	11_L	0.804	0.88
55_F	59_I	0.794	0.88
43_V	47_K	0.792	0.88
55_F	60_F	0.792	0.88
26_I	30_Y	0.752	0.85
4_K	8_K	0.733	0.83
42_S	47_K	0.717	0.82
9_N	52_K	0.710	0.81
47_K	65_C	0.710	0.81
21_A	31_Y	0.708	0.81
19_E	22_K	0.707	0.81
5_W	65_C	0.700	0.80
21_A	26_I	0.688	0.79
11_L	16_T	0.687	0.79
10_R	17_Q	0.687	0.79
8_K	12_E	0.679	0.78
51_E	54_G	0.678	0.78
21_A	28_R	0.674	0.78
7_K	35_E	0.672	0.78
41_P	45_V	0.664	0.77
47_K	54_G	0.663	0.77
9_N	20_V	0.657	0.76
41_P	46_S	0.650	0.75
15_F	52_K	0.633	0.73
27_G	32_T	0.609	0.70
50_G	63_D	0.588	0.68
7_K	10_R	0.577	0.66
16_T	24_A	0.572	0.66
53_L	57_W	0.571	0.65
40_K	45_V	0.564	0.65
17_Q	32_T	0.557	0.64
40_K	44_I	0.552	0.63
47_K	57_W	0.552	0.63
13_K	53_L	0.552	0.63
4_K	46_S	0.547	0.62
21_A	24_A	0.546	0.62
50_G	60_F	0.545	0.62
16_T	20_V	0.520	0.58
26_I	34_I	0.510	0.57
4_K	40_K	0.508	0.57
10_R	15_F	0.507	0.56
9_N	13_K	0.506	0.56
4_K	65_C	0.502	0.56
37_G	44_I	0.501	0.56
9_N	54_G	0.500	0.55
4_K	36_N	0.500	0.55

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
2p5tA	2	0.1842	99.5	0.254	Contact Map
4o8bA	2	1	99.5	0.269	Contact Map
4ndwA	2	1	99.5	0.286	Contact Map
3u3wA	2	0.9868	99.4	0.293	Contact Map
1b0nA	2	0.9342	99.4	0.296	Contact Map
4jcyA	2	1	99.4	0.296	Contact Map
3op9A	4	0.9737	99.4	0.297	Contact Map
3r1fA	2	1	99.4	0.297	Contact Map
1y9qA	1	1	99.4	0.298	Contact Map
3mlfA	2	1	99.4	0.298	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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