SOXR - ECOLI - GREMLIN Contacts

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SOXR - Redox-sensitive transcriptional activator SoxR

UniProt:	P0ACS2	Sequences: MEKKLPRIKALLTPGEVAKRSGVAVSALHFYESKGLITSIRNSGNQRRYKRDVLRYVAIIKIAQRIGIPLATIGEAFGVLPEGHTLSAKEWKQLSSQWREELDRRIHTLVALRDELDGCIGCGCLSRSDCPLRNPGDRLGEEGTGARLLEDEQN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10957
Length:	154 (125)
Sequences:	8328 (5954)
Seq/√Len:	532.6

ECOLI - SOXR CUER ZNTR
BACSU - CUER ADHR MTA YFMP YDFL YYAN BLTR BMRR GLNR TNRA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
103_D	113_R	4.429	1.00
50_K	53_V	3.646	1.00
99_R	117_D	3.379	1.00
106_I	110_V	3.132	1.00
30_F	34_K	3.019	1.00
96_S	120_I	2.668	1.00
26_S	33_S	2.432	1.00
98_W	101_E	2.048	1.00
25_V	29_H	1.971	1.00
99_R	113_R	1.897	1.00
103_D	117_D	1.781	1.00
95_S	120_I	1.770	1.00
110_V	113_R	1.749	1.00
61_K	64_Q	1.726	1.00
15_G	19_K	1.712	1.00
42_N	48_R	1.689	1.00
64_Q	70_L	1.655	1.00
34_K	74_G	1.632	1.00
99_R	120_I	1.622	1.00
14_P	29_H	1.614	1.00
113_R	117_D	1.577	1.00
105_R	108_T	1.524	1.00
17_V	54_L	1.501	1.00
56_Y	82_E	1.494	1.00
12_L	48_R	1.481	1.00
106_I	109_L	1.476	1.00
13_T	48_R	1.466	1.00
69_P	72_T	1.436	1.00
104_R	108_T	1.435	1.00
99_R	103_D	1.435	1.00
13_T	16_E	1.427	1.00
17_V	57_V	1.420	1.00
72_T	98_W	1.417	1.00
24_A	27_A	1.401	1.00
106_I	113_R	1.367	1.00
17_V	53_V	1.354	1.00
92_K	96_S	1.342	1.00
101_E	105_R	1.317	1.00
16_E	19_K	1.317	1.00
103_D	106_I	1.309	1.00
107_H	110_V	1.226	1.00
96_S	123_G	1.220	1.00
92_K	123_G	1.213	1.00
65_R	108_T	1.212	1.00
100_E	104_R	1.203	1.00
74_G	78_G	1.196	1.00
56_Y	77_F	1.167	1.00
36_L	60_I	1.165	1.00
27_A	30_F	1.130	1.00
71_A	74_G	1.116	1.00
90_E	93_Q	1.116	1.00
102_L	109_L	1.110	1.00
31_Y	57_V	1.088	1.00
105_R	109_L	1.085	1.00
34_K	71_A	1.076	1.00
39_S	42_N	1.072	1.00
44_G	48_R	1.067	1.00
16_E	20_R	1.059	1.00
40_I	50_K	1.051	1.00
107_H	111_A	1.044	1.00
95_S	116_L	1.037	1.00
101_E	104_R	1.035	1.00
60_I	73_I	1.034	1.00
20_R	54_L	1.024	1.00
102_L	113_R	1.022	1.00
97_Q	100_E	1.018	1.00
72_T	75_E	1.014	1.00
28_L	49_Y	0.997	1.00
18_A	25_V	0.995	1.00
13_T	46_Q	0.968	1.00
28_L	57_V	0.964	1.00
12_L	51_R	0.953	1.00
67_G	105_R	0.935	1.00
109_L	113_R	0.928	1.00
122_C	130_C	0.918	1.00
110_V	114_D	0.907	1.00
15_G	25_V	0.894	1.00
42_N	45_N	0.892	1.00
96_S	100_E	0.891	1.00
102_L	106_I	0.890	1.00
72_T	97_Q	0.888	1.00
103_D	107_H	0.879	1.00
102_L	116_L	0.877	1.00
104_R	107_H	0.876	1.00
37_I	60_I	0.870	1.00
12_L	20_R	0.864	1.00
21_S	57_V	0.857	1.00
32_E	37_I	0.852	1.00
68_I	76_A	0.845	1.00
62_I	108_T	0.845	1.00
32_E	49_Y	0.844	1.00
93_Q	97_Q	0.842	1.00
32_E	38_T	0.835	1.00
100_E	103_D	0.835	1.00
72_T	101_E	0.815	1.00
21_S	54_L	0.799	1.00
14_P	18_A	0.796	1.00
61_K	65_R	0.796	1.00
68_I	98_W	0.795	1.00
30_F	70_L	0.789	1.00
18_A	28_L	0.781	1.00
92_K	120_I	0.777	1.00
39_S	53_V	0.777	1.00
20_R	58_A	0.773	1.00
68_I	72_T	0.771	1.00
108_T	111_A	0.768	1.00
59_I	63_A	0.761	1.00
88_A	91_W	0.759	1.00
52_D	55_R	0.757	1.00
98_W	105_R	0.753	1.00
129_D	133_R	0.752	1.00
87_S	90_E	0.751	1.00
111_A	114_D	0.750	1.00
20_R	51_R	0.744	1.00
30_F	33_S	0.741	1.00
21_S	28_L	0.739	1.00
128_S	131_P	0.729	1.00
38_T	53_V	0.726	1.00
23_V	61_K	0.722	1.00
112_L	115_E	0.717	1.00
40_I	48_R	0.717	1.00
99_R	102_L	0.713	1.00
63_A	68_I	0.711	1.00
99_R	116_L	0.710	1.00
51_R	55_R	0.700	1.00
124_C	127_R	0.691	1.00
102_L	112_L	0.690	1.00
15_G	46_Q	0.685	1.00
24_A	30_F	0.672	1.00
32_E	41_R	0.667	1.00
53_V	56_Y	0.665	1.00
64_Q	73_I	0.663	1.00
23_V	27_A	0.654	1.00
21_S	25_V	0.650	1.00
58_A	61_K	0.648	1.00
57_V	64_Q	0.647	1.00
129_D	132_L	0.642	1.00
17_V	21_S	0.633	1.00
83_G	86_L	0.625	1.00
26_S	30_F	0.624	1.00
24_A	33_S	0.623	1.00
55_R	58_A	0.620	1.00
34_K	70_L	0.617	1.00
40_I	53_V	0.617	1.00
37_I	53_V	0.613	1.00
119_C	122_C	0.611	1.00
96_S	99_R	0.609	1.00
28_L	32_E	0.606	1.00
130_C	134_N	0.606	1.00
32_E	47_R	0.605	1.00
66_I	112_L	0.595	1.00
35_G	38_T	0.594	1.00
133_R	136_G	0.588	0.99
127_R	130_C	0.578	0.99
21_S	31_Y	0.571	0.99
134_N	137_D	0.570	0.99
51_R	58_A	0.567	0.99
56_Y	78_G	0.565	0.99
114_D	118_G	0.564	0.99
38_T	82_E	0.555	0.99
64_Q	69_P	0.550	0.99
127_R	131_P	0.550	0.99
117_D	121_G	0.550	0.99
75_E	78_G	0.549	0.99
12_L	54_L	0.548	0.99
93_Q	96_S	0.547	0.99
54_L	58_A	0.547	0.99
17_V	37_I	0.545	0.99
21_S	61_K	0.543	0.99
23_V	73_I	0.542	0.99
103_D	110_V	0.538	0.99
89_K	93_Q	0.535	0.99
64_Q	98_W	0.532	0.99
75_E	90_E	0.531	0.99
15_G	18_A	0.529	0.99
18_A	24_A	0.529	0.99
39_S	49_Y	0.528	0.99
114_D	117_D	0.527	0.99
75_E	94_L	0.526	0.99
23_V	57_V	0.525	0.99
125_L	129_D	0.522	0.99
118_G	121_G	0.521	0.99
121_G	124_C	0.520	0.99
43_S	48_R	0.520	0.99
128_S	134_N	0.510	0.99
130_C	133_R	0.506	0.98
65_R	105_R	0.504	0.98
133_R	137_D	0.500	0.98

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
2zhgA	2	0.7857	100	0.192	Contact Map
1q06A	2	0.8117	100	0.276	Contact Map
3hh0A	4	0.8571	100	0.286	Contact Map
2dg6A	2	0.8636	99.9	0.289	Contact Map
3gp4A	4	0.8442	99.9	0.3	Contact Map
3gpvA	2	0.7403	99.9	0.301	Contact Map
3qaoA	2	0.8766	99.9	0.309	Contact Map
4ua1A	2	0.7922	99.9	0.312	Contact Map
2vz4A	2	0.6429	99.9	0.335	Contact Map
1r8dA	2	0.7013	99.9	0.348	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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