YBZH - BACSU - GREMLIN Contacts

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YBZH - Uncharacterized HTH-type transcriptional regulator YbzH

UniProt:	C0H3S9	Sequences: MEPIEVFKALSNESRLQILQWLKEPDRHFAPHEGIDMNTIGVCVSQITDKLKMTQSTASQYLTILLRAGLIKAERIGKYTYYKRDEEAIGKLADFLKTEI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	100 (93)
Sequences:	579 (368)
Seq/√Len:	38.2

ECOLI - ARSR
BACSU - YBZH

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
24_E	27_R	4.756	1.00
21_W	50_K	2.873	1.00
69_G	85_D	2.597	1.00
72_K	83_K	2.379	1.00
93_A	96_L	2.367	1.00
4_I	16_L	2.204	0.99
53_M	58_A	2.105	0.99
86_E	89_I	2.089	0.99
73_A	80_T	2.034	0.99
75_R	80_T	2.031	0.99
44_V	61_Y	1.999	0.99
9_A	68_A	1.904	0.98
56_S	63_T	1.836	0.98
62_L	81_Y	1.762	0.97
9_A	64_I	1.714	0.96
62_L	71_I	1.680	0.96
85_D	88_A	1.626	0.95
18_I	47_I	1.553	0.94
40_I	74_E	1.527	0.93
72_K	85_D	1.458	0.92
7_F	95_F	1.455	0.91
43_C	79_Y	1.386	0.89
65_L	71_I	1.372	0.89
7_F	16_L	1.359	0.88
6_V	88_A	1.355	0.88
89_I	93_A	1.348	0.88
24_E	28_H	1.345	0.88
88_A	91_K	1.338	0.88
56_S	77_G	1.335	0.87
31_P	46_Q	1.308	0.86
51_L	58_A	1.239	0.83
32_H	37_M	1.239	0.83
30_A	46_Q	1.195	0.81
54_T	57_T	1.194	0.81
7_F	96_L	1.189	0.81
12_N	61_Y	1.135	0.77
23_K	86_E	1.114	0.76
69_G	72_K	1.103	0.75
5_E	67_R	1.092	0.75
11_S	61_Y	1.062	0.72
6_V	92_L	1.057	0.72
90_G	94_D	1.038	0.71
91_K	95_F	1.022	0.70
28_H	51_L	0.993	0.67
37_M	54_T	0.989	0.67
59_S	77_G	0.978	0.66
12_N	75_R	0.971	0.65
40_I	76_I	0.962	0.65
6_V	70_L	0.961	0.65
7_F	92_L	0.955	0.64
54_T	78_K	0.944	0.63
4_I	13_E	0.940	0.63
61_Y	80_T	0.935	0.63
44_V	75_R	0.923	0.62
25_P	62_L	0.920	0.61
61_Y	75_R	0.917	0.61
37_M	40_I	0.904	0.60
44_V	82_Y	0.903	0.60
32_H	74_E	0.900	0.60
56_S	59_S	0.899	0.59
6_V	12_N	0.892	0.59
12_N	47_I	0.883	0.58
56_S	66_L	0.878	0.58
17_Q	21_W	0.867	0.57
5_E	96_L	0.861	0.56
88_A	95_F	0.856	0.56
6_V	95_F	0.854	0.56
44_V	80_T	0.830	0.53
57_T	63_T	0.824	0.53
9_A	92_L	0.818	0.52
45_S	66_L	0.803	0.51
21_W	51_L	0.801	0.51
36_D	46_Q	0.800	0.51
29_F	32_H	0.780	0.49
88_A	92_L	0.777	0.49
23_K	33_E	0.770	0.48
16_L	92_L	0.754	0.47
44_V	62_L	0.752	0.46
18_I	22_L	0.747	0.46
32_H	36_D	0.745	0.46
31_P	76_I	0.742	0.46
84_R	89_I	0.731	0.45
55_Q	79_Y	0.725	0.44
59_S	80_T	0.725	0.44
23_K	84_R	0.722	0.44
11_S	69_G	0.719	0.43
13_E	16_L	0.712	0.43
85_D	89_I	0.711	0.43
19_L	37_M	0.710	0.43
17_Q	62_L	0.708	0.43
24_E	30_A	0.706	0.42
18_I	42_V	0.703	0.42
9_A	65_L	0.697	0.42
94_D	97_K	0.696	0.41
14_S	17_Q	0.687	0.41
41_G	74_E	0.686	0.41
75_R	82_Y	0.680	0.40
48_T	65_L	0.675	0.40
60_Q	89_I	0.671	0.39
33_E	53_M	0.666	0.39
36_D	42_V	0.661	0.38
38_N	65_L	0.656	0.38
57_T	83_K	0.651	0.38
49_D	75_R	0.647	0.37
38_N	52_K	0.646	0.37
30_A	57_T	0.631	0.36
74_E	78_K	0.610	0.34
47_I	50_K	0.609	0.34
30_A	50_K	0.607	0.34
20_Q	91_K	0.605	0.34
8_K	85_D	0.601	0.34
8_K	25_P	0.587	0.32
12_N	44_V	0.582	0.32
45_S	60_Q	0.581	0.32
56_S	70_L	0.581	0.32
71_I	85_D	0.577	0.32
52_K	92_L	0.577	0.32
29_F	50_K	0.572	0.31
68_A	88_A	0.571	0.31
39_T	74_E	0.571	0.31
57_T	67_R	0.567	0.31
34_G	37_M	0.560	0.30
87_E	91_K	0.558	0.30
44_V	48_T	0.556	0.30
63_T	67_R	0.554	0.30
17_Q	50_K	0.554	0.30
28_H	60_Q	0.553	0.30
23_K	97_K	0.547	0.29
29_F	42_V	0.547	0.29
33_E	38_N	0.545	0.29
60_Q	64_I	0.542	0.29
8_K	79_Y	0.537	0.29
12_N	81_Y	0.533	0.28
68_A	90_G	0.530	0.28
38_N	74_E	0.517	0.27
22_L	42_V	0.516	0.27
26_D	38_N	0.515	0.27
5_E	16_L	0.509	0.27
46_Q	73_A	0.507	0.26
24_E	87_E	0.500	0.26

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
2vxzA	1	0.79	99.6	0.639	Contact Map
1r1tA	2	0.85	99.5	0.677	Contact Map
1u2wA	2	0.86	99.4	0.69	Contact Map
2kkoA	2	0.85	99.3	0.697	Contact Map
1q1hA	1	0.77	99.3	0.699	Contact Map
2jscA	2	0.84	99.3	0.701	Contact Map
1r1uA	2	0.85	99.3	0.702	Contact Map
3pqkA	2	0.85	99.3	0.709	Contact Map
4k2eA	2	0.85	99.3	0.709	Contact Map
2zkzA	2	0.84	99.2	0.713	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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