YCZG - BACSU - GREMLIN Contacts

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YCZG - Uncharacterized HTH-type transcriptional regulator YczG

UniProt:	O31480	Sequences: MNIPNHPETETLQLTKVLHALSDPLRLELVKQLAEAKEKTCSTCADVQVAKSTLSHHFKVLRESGIAQVRIEGKRRYYSLRAEDLEKAFPGLLEAVLNVDQDRW	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	104 (95)
Sequences:	927 (563)
Seq/√Len:	57.7

BACSU - YCZG YCEK

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
38_E	70_R	4.928	1.00
9_T	84_D	3.465	1.00
9_T	12_L	3.372	1.00
12_L	84_D	3.092	1.00
9_T	87_K	2.909	1.00
66_I	85_L	2.684	1.00
86_E	94_E	2.596	1.00
55_S	69_V	2.342	1.00
82_A	86_E	2.331	1.00
49_V	53_T	2.106	1.00
58_F	78_Y	2.058	1.00
28_E	32_Q	1.946	1.00
82_A	94_E	1.876	1.00
15_T	27_L	1.833	0.99
68_Q	79_S	1.768	0.99
13_Q	16_K	1.693	0.99
36_A	39_K	1.690	0.99
30_V	80_L	1.640	0.99
67_A	78_Y	1.631	0.99
41_C	76_R	1.583	0.98
55_S	59_K	1.580	0.98
6_H	68_Q	1.556	0.98
74_K	78_Y	1.519	0.98
32_Q	39_K	1.473	0.98
34_A	97_L	1.462	0.97
47_V	54_L	1.455	0.97
95_A	99_V	1.334	0.96
71_I	76_R	1.279	0.94
17_V	85_L	1.221	0.93
34_A	82_A	1.187	0.92
20_A	53_T	1.160	0.91
50_A	53_T	1.149	0.91
15_T	22_S	1.130	0.90
94_E	98_N	1.092	0.88
23_D	64_S	1.090	0.88
20_A	60_V	1.089	0.88
35_E	98_N	1.080	0.88
38_E	77_Y	1.078	0.87
4_P	76_R	1.064	0.87
19_H	22_S	1.060	0.87
18_L	95_A	1.013	0.84
72_E	77_Y	0.969	0.81
73_G	89_F	0.944	0.80
4_P	63_E	0.940	0.79
25_L	28_E	0.936	0.79
33_L	80_L	0.928	0.78
56_H	60_V	0.927	0.78
4_P	96_V	0.916	0.77
8_E	11_T	0.908	0.77
69_V	78_Y	0.906	0.77
7_P	84_D	0.898	0.76
9_T	88_A	0.880	0.75
58_F	74_K	0.873	0.74
38_E	79_S	0.845	0.71
28_E	46_D	0.838	0.71
14_L	95_A	0.837	0.71
12_L	16_K	0.835	0.71
22_S	27_L	0.827	0.70
58_F	69_V	0.822	0.69
20_A	93_L	0.821	0.69
14_L	89_F	0.820	0.69
35_E	83_E	0.810	0.68
66_I	84_D	0.798	0.67
71_I	75_R	0.788	0.66
93_L	96_V	0.783	0.66
32_Q	45_A	0.779	0.65
15_T	51_K	0.773	0.65
83_E	98_N	0.772	0.65
69_V	76_R	0.769	0.64
10_E	98_N	0.761	0.63
72_E	75_R	0.755	0.63
33_L	61_L	0.747	0.62
48_Q	53_T	0.740	0.61
10_E	13_Q	0.732	0.60
11_T	51_K	0.730	0.60
45_A	56_H	0.730	0.60
27_L	30_V	0.726	0.60
29_L	43_T	0.706	0.58
4_P	59_K	0.704	0.57
29_L	45_A	0.703	0.57
84_D	88_A	0.697	0.57
17_V	66_I	0.696	0.57
5_N	79_S	0.695	0.56
42_S	70_R	0.693	0.56
14_L	92_L	0.671	0.54
48_Q	74_K	0.667	0.53
54_L	88_A	0.663	0.53
22_S	73_G	0.663	0.53
5_N	63_E	0.661	0.53
86_E	91_G	0.660	0.53
22_S	59_K	0.658	0.52
50_A	74_K	0.654	0.52
30_V	33_L	0.654	0.52
54_L	76_R	0.654	0.52
29_L	48_Q	0.654	0.52
58_F	76_R	0.652	0.52
37_K	54_L	0.651	0.52
93_L	97_L	0.646	0.51
68_Q	95_A	0.645	0.51
4_P	88_A	0.639	0.50
5_N	75_R	0.632	0.50
5_N	37_K	0.625	0.49
19_H	50_A	0.612	0.47
50_A	71_I	0.608	0.47
12_L	17_V	0.608	0.47
32_Q	43_T	0.606	0.47
11_T	22_S	0.602	0.46
18_L	93_L	0.600	0.46
56_H	59_K	0.597	0.46
88_A	95_A	0.589	0.45
25_L	78_Y	0.585	0.44
25_L	32_Q	0.584	0.44
41_C	91_G	0.581	0.44
31_K	64_S	0.580	0.44
34_A	37_K	0.554	0.41
55_S	75_R	0.553	0.41
36_A	49_V	0.549	0.40
45_A	50_A	0.548	0.40
54_L	57_H	0.548	0.40
27_L	97_L	0.546	0.40
24_P	98_N	0.539	0.39
9_T	14_L	0.538	0.39
23_D	76_R	0.537	0.39
15_T	19_H	0.535	0.39
34_A	80_L	0.533	0.39
13_Q	22_S	0.531	0.39
22_S	51_K	0.530	0.38
19_H	42_S	0.527	0.38
40_T	67_A	0.521	0.38
31_K	82_A	0.517	0.37
6_H	67_A	0.516	0.37
23_D	78_Y	0.516	0.37
45_A	69_V	0.516	0.37
41_C	58_F	0.516	0.37
23_D	58_F	0.515	0.37
5_N	16_K	0.514	0.37
22_S	25_L	0.514	0.37
53_T	64_S	0.507	0.36
20_A	56_H	0.504	0.36
45_A	71_I	0.503	0.36
23_D	47_V	0.502	0.36
66_I	88_A	0.500	0.35

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
1q1hA	1	0.7692	98.9	0.728	Contact Map
1r1tA	2	0.8558	98.9	0.73	Contact Map
1r1uA	2	0.9231	98.8	0.731	Contact Map
2jscA	2	0.875	98.8	0.737	Contact Map
2kkoA	2	0.9423	98.7	0.742	Contact Map
3f6vA	2	0.8558	98.7	0.743	Contact Map
4k2eA	2	0.8846	98.6	0.751	Contact Map
1u2wA	2	0.9519	98.6	0.753	Contact Map
4g6qA	4	0.9327	98.5	0.759	Contact Map
2zkzA	2	0.8173	98.5	0.76	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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