HXLR - BACSU - GREMLIN Contacts

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HXLR - HTH-type transcriptional activator HxlR

UniProt:	P42406	Sequences: MSRMDDKRFNCEKELTLAVIGGKWKMLILWHLGKEGTKRFNELKTLIPDITQKILVNQLRELEQDMIVHREVYPVVPPKVEYSLTPHGESLMPILEAMYEWGKGYMELIDIDKNVMKESL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	120 (99)
Sequences:	9992 (6023)
Seq/√Len:	605.3

ECOLI - YTFH
BACSU - HXLR YTCD YDEP YKVN YYBR YODB YDZF YVAP
HALSA - Q9HRG9 Q9HPZ4
SULSO - Q97UU6 Q97U48

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
69_H	83_S	2.775	1.00
44_K	52_Q	2.751	1.00
53_K	57_N	2.631	1.00
90_S	104_G	2.580	1.00
33_G	92_M	2.543	1.00
71_E	83_S	2.465	1.00
75_V	79_K	2.454	1.00
32_L	68_V	2.280	1.00
31_H	46_L	2.112	1.00
69_H	85_T	2.044	1.00
73_Y	81_E	1.890	1.00
87_H	105_Y	1.841	1.00
73_Y	79_K	1.714	1.00
32_L	43_L	1.678	1.00
28_I	58_Q	1.663	1.00
94_I	97_A	1.660	1.00
97_A	100_E	1.659	1.00
93_P	97_A	1.644	1.00
84_L	88_G	1.609	1.00
60_R	63_E	1.564	1.00
38_K	46_L	1.539	1.00
37_T	83_S	1.512	1.00
37_T	81_E	1.505	1.00
54_I	57_N	1.452	1.00
89_E	92_M	1.358	1.00
25_K	61_E	1.356	1.00
67_I	88_G	1.322	1.00
25_K	58_Q	1.312	1.00
90_S	101_W	1.308	1.00
86_P	89_E	1.302	1.00
70_R	80_V	1.297	1.00
16_T	98_M	1.296	1.00
87_H	90_S	1.273	1.00
22_G	61_E	1.256	1.00
52_Q	56_V	1.166	1.00
99_Y	103_K	1.155	1.00
87_H	108_L	1.125	1.00
63_E	68_V	1.118	1.00
19_V	65_D	1.118	1.00
16_T	102_G	1.117	1.00
15_L	106_M	1.101	1.00
25_K	62_L	1.096	1.00
32_L	38_K	1.092	1.00
73_Y	77_P	1.088	1.00
71_E	81_E	1.082	1.00
38_K	42_E	1.081	1.00
22_G	58_Q	1.076	1.00
41_N	45_T	1.051	1.00
72_V	78_P	1.046	1.00
22_G	25_K	1.045	1.00
39_R	81_E	1.043	1.00
83_S	89_E	1.039	1.00
72_V	80_V	1.024	1.00
90_S	105_Y	1.011	1.00
29_L	84_L	1.006	1.00
72_V	77_P	1.006	1.00
67_I	91_L	1.004	1.00
74_P	77_P	0.995	1.00
40_F	56_V	0.979	1.00
56_V	60_R	0.974	1.00
19_V	67_I	0.972	1.00
26_M	95_L	0.965	1.00
73_Y	76_V	0.958	1.00
28_I	47_I	0.935	1.00
54_I	58_Q	0.931	1.00
73_Y	78_P	0.922	1.00
92_M	96_E	0.908	1.00
91_L	101_W	0.901	1.00
41_N	44_K	0.895	1.00
42_E	45_T	0.890	1.00
93_P	100_E	0.880	1.00
33_G	84_L	0.866	1.00
40_F	52_Q	0.862	1.00
50_I	55_L	0.860	1.00
66_M	87_H	0.848	1.00
100_E	104_G	0.848	1.00
35_E	38_K	0.840	1.00
31_H	43_L	0.836	1.00
14_E	18_A	0.810	1.00
61_E	65_D	0.797	1.00
51_T	54_I	0.793	1.00
72_V	76_V	0.792	1.00
47_I	50_I	0.789	1.00
30_W	99_Y	0.788	1.00
12_E	103_K	0.776	1.00
25_K	65_D	0.766	1.00
96_E	100_E	0.761	1.00
33_G	96_E	0.752	1.00
9_F	18_A	0.733	1.00
94_I	98_M	0.733	1.00
28_I	50_I	0.724	1.00
38_K	43_L	0.706	1.00
102_G	106_M	0.688	1.00
30_W	33_G	0.683	1.00
15_L	105_Y	0.679	1.00
75_V	78_P	0.674	1.00
9_F	14_E	0.673	1.00
76_V	80_V	0.664	1.00
24_W	50_I	0.662	1.00
72_V	75_V	0.660	1.00
105_Y	108_L	0.654	1.00
36_G	89_E	0.651	1.00
9_F	15_L	0.642	1.00
103_K	106_M	0.639	1.00
27_L	31_H	0.627	1.00
96_E	99_Y	0.625	1.00
50_I	80_V	0.625	1.00
57_N	61_E	0.622	1.00
100_E	103_K	0.618	1.00
62_L	67_I	0.615	1.00
44_K	55_L	0.614	1.00
91_L	94_I	0.607	1.00
31_H	35_E	0.605	1.00
27_L	47_I	0.603	1.00
39_R	73_Y	0.601	1.00
17_L	26_M	0.598	1.00
31_H	38_K	0.592	1.00
29_L	91_L	0.592	1.00
39_R	42_E	0.592	1.00
101_W	105_Y	0.590	1.00
75_V	81_E	0.587	1.00
40_F	44_K	0.579	1.00
17_L	98_M	0.576	1.00
17_L	91_L	0.575	1.00
37_T	71_E	0.573	1.00
13_K	106_M	0.569	1.00
42_E	46_L	0.564	1.00
32_L	37_T	0.563	1.00
87_H	106_M	0.556	1.00
63_E	70_R	0.556	1.00
86_P	90_S	0.553	0.99
41_N	52_Q	0.551	0.99
13_K	30_W	0.540	0.99
16_T	67_I	0.539	0.99
15_L	18_A	0.537	0.99
94_I	102_G	0.534	0.99
14_E	48_P	0.531	0.99
93_P	96_E	0.530	0.99
32_L	63_E	0.530	0.99
90_S	93_P	0.525	0.99
77_P	80_V	0.524	0.99
63_E	72_V	0.522	0.99
104_G	107_E	0.521	0.99
14_E	26_M	0.515	0.99
75_V	80_V	0.513	0.99
35_E	46_L	0.511	0.99
83_S	86_P	0.507	0.99
89_E	93_P	0.500	0.99

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
4gcvA	3	0.9	99.9	0.381	Contact Map
1yyvA	2	0.925	99.7	0.479	Contact Map
4a5nA	2	0.875	99.7	0.49	Contact Map
2hztA	2	0.7917	99.7	0.504	Contact Map
2fswA	2	0.8583	99.7	0.507	Contact Map
1z7uA	2	0.925	99.7	0.507	Contact Map
2f2eA	4	0.95	99.7	0.509	Contact Map
4hw0A	2	0.775	99.5	0.557	Contact Map
3df8A	2	0.85	99.5	0.561	Contact Map
4hqeA	2	0.8917	99.4	0.595	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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