PERR - BACSU - GREMLIN Contacts

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PERR - Peroxide operon regulator

UniProt:	P71086	Sequences: MAAHELKEALETLKETGVRITPQRHAILEYLVNSMAHPTADDIYKALEGKFPNMSVATVYNNLRVFRESGLVKELTYGDASSRFDFVTSDHYHAICENCGKIVDFHYPGLDEVEQLAAHVTGFKVSHHRLEIYGVCQECSKKENH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	145 (132)
Sequences:	7245 (4765)
Seq/√Len:	414.8

ECOLI - ZUR FUR
BACSU - PERR FUR ZUR
SULSO - Q97WH5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
97_E	126_S	4.024	1.00
98_N	135_V	3.627	1.00
101_K	138_E	3.312	1.00
124_K	140_S	3.119	1.00
31_L	72_V	2.819	1.00
125_V	132_I	2.355	1.00
30_Y	46_A	2.264	1.00
122_G	137_Q	2.193	1.00
20_I	25_H	2.098	1.00
67_R	74_E	2.072	1.00
97_E	133_Y	2.070	1.00
10_L	25_H	2.049	1.00
97_E	135_V	1.932	1.00
40_A	63_L	1.877	1.00
99_C	136_C	1.841	1.00
74_E	82_S	1.837	1.00
45_K	48_E	1.813	1.00
34_S	46_A	1.806	1.00
44_Y	56_V	1.794	1.00
67_R	72_V	1.790	1.00
64_R	74_E	1.775	1.00
11_E	15_E	1.711	1.00
18_V	69_S	1.681	1.00
94_A	103_V	1.656	1.00
27_I	62_N	1.654	1.00
126_S	135_V	1.642	1.00
37_H	85_D	1.591	1.00
99_C	139_C	1.555	1.00
96_C	99_C	1.542	1.00
29_E	33_N	1.503	1.00
92_Y	128_H	1.460	1.00
103_V	123_F	1.459	1.00
116_L	120_V	1.440	1.00
94_A	123_F	1.429	1.00
30_Y	43_I	1.380	1.00
44_Y	48_E	1.377	1.00
136_C	139_C	1.310	1.00
28_L	66_F	1.308	1.00
12_T	16_T	1.298	1.00
96_C	136_C	1.294	1.00
39_T	42_D	1.281	1.00
46_A	49_G	1.280	1.00
23_Q	58_T	1.274	1.00
123_F	137_Q	1.269	1.00
26_A	29_E	1.267	1.00
25_H	29_E	1.227	1.00
30_Y	47_L	1.223	1.00
26_A	50_K	1.219	1.00
115_Q	119_H	1.134	1.00
38_P	83_R	1.125	1.00
90_D	128_H	1.119	1.00
62_N	65_V	1.114	1.00
37_H	93_H	1.111	1.00
112_E	116_L	1.099	1.00
65_V	69_S	1.081	1.00
34_S	38_P	1.072	1.00
124_K	135_V	1.061	1.00
44_Y	59_V	1.048	1.00
30_Y	38_P	1.033	1.00
95_I	100_G	1.031	1.00
38_P	46_A	1.018	1.00
37_H	104_D	1.006	1.00
12_T	15_E	0.998	1.00
66_F	71_L	0.997	1.00
36_A	46_A	0.992	1.00
95_I	133_Y	0.992	1.00
10_L	14_K	0.981	1.00
95_I	131_E	0.968	1.00
103_V	121_T	0.958	1.00
137_Q	141_K	0.955	1.00
123_F	134_G	0.954	1.00
24_R	65_V	0.953	1.00
91_H	104_D	0.950	1.00
107_Y	113_V	0.948	1.00
18_V	65_V	0.938	1.00
94_A	134_G	0.936	1.00
30_Y	50_K	0.932	1.00
23_Q	54_M	0.919	1.00
96_C	139_C	0.908	1.00
45_K	49_G	0.907	1.00
108_P	128_H	0.896	1.00
107_Y	110_L	0.895	1.00
41_D	45_K	0.894	1.00
127_H	133_Y	0.893	1.00
37_H	91_H	0.887	1.00
122_G	140_S	0.882	1.00
38_P	43_I	0.878	1.00
135_V	140_S	0.877	1.00
36_A	42_D	0.876	1.00
37_H	102_I	0.860	1.00
40_A	59_V	0.860	1.00
31_L	38_P	0.854	1.00
22_P	26_A	0.849	1.00
64_R	67_R	0.849	1.00
109_G	112_E	0.846	1.00
48_E	56_V	0.845	1.00
75_L	104_D	0.833	1.00
26_A	51_F	0.824	1.00
47_L	54_M	0.822	1.00
100_G	103_V	0.816	1.00
92_Y	105_F	0.810	1.00
30_Y	34_S	0.803	1.00
28_L	71_L	0.803	1.00
114_E	128_H	0.801	1.00
97_E	127_H	0.801	1.00
118_A	125_V	0.800	1.00
47_L	51_F	0.792	1.00
92_Y	114_E	0.785	1.00
64_R	68_E	0.782	1.00
22_P	25_H	0.779	1.00
24_R	62_N	0.767	1.00
128_H	132_I	0.766	1.00
29_E	50_K	0.760	1.00
42_D	45_K	0.759	1.00
94_A	121_T	0.757	1.00
90_D	111_D	0.751	1.00
92_Y	130_L	0.729	1.00
71_L	86_F	0.727	1.00
41_D	81_S	0.727	1.00
14_K	20_I	0.722	1.00
23_Q	55_S	0.714	1.00
79_D	83_R	0.710	1.00
110_L	113_V	0.707	1.00
37_H	55_S	0.702	1.00
63_L	67_R	0.702	1.00
27_I	43_I	0.695	1.00
13_L	28_L	0.691	1.00
32_V	86_F	0.690	1.00
33_N	46_A	0.682	1.00
40_A	56_V	0.681	1.00
41_D	56_V	0.680	1.00
138_E	141_K	0.673	1.00
39_T	83_R	0.672	1.00
92_Y	108_P	0.669	0.99
95_I	102_I	0.663	0.99
128_H	133_Y	0.661	0.99
75_L	131_E	0.659	0.99
33_N	50_K	0.656	0.99
37_H	41_D	0.654	0.99
106_H	109_G	0.651	0.99
110_L	114_E	0.648	0.99
58_T	62_N	0.645	0.99
116_L	119_H	0.642	0.99
129_R	133_Y	0.631	0.99
23_Q	62_N	0.625	0.99
27_I	30_Y	0.622	0.99
41_D	44_Y	0.621	0.99
43_I	59_V	0.621	0.99
18_V	24_R	0.613	0.99
63_L	72_V	0.602	0.99
31_L	43_I	0.601	0.99
108_P	132_I	0.599	0.99
10_L	20_I	0.596	0.99
73_K	129_R	0.596	0.99
73_K	87_V	0.590	0.99
126_S	134_G	0.588	0.99
137_Q	140_S	0.588	0.99
35_M	87_V	0.588	0.99
44_Y	54_M	0.585	0.99
123_F	140_S	0.585	0.99
43_I	72_V	0.584	0.99
28_L	32_V	0.581	0.99
109_G	116_L	0.580	0.99
58_T	61_N	0.574	0.98
31_L	86_F	0.573	0.98
26_A	47_L	0.572	0.98
26_A	30_Y	0.569	0.98
114_E	117_A	0.568	0.98
77_Y	129_R	0.563	0.98
92_Y	132_I	0.562	0.98
94_A	117_A	0.561	0.98
13_L	65_V	0.556	0.98
89_S	106_H	0.555	0.98
13_L	18_V	0.552	0.98
84_F	104_D	0.549	0.98
11_E	14_K	0.547	0.98
21_T	25_H	0.545	0.98
112_E	115_Q	0.539	0.98
107_Y	120_V	0.539	0.98
40_A	81_S	0.536	0.98
21_T	58_T	0.532	0.97
106_H	120_V	0.532	0.97
107_Y	112_E	0.530	0.97
96_C	123_F	0.525	0.97
16_T	69_S	0.522	0.97
41_D	74_E	0.521	0.97
83_R	86_F	0.520	0.97
20_I	28_L	0.519	0.97
30_Y	33_N	0.519	0.97
13_L	20_I	0.517	0.97
31_L	39_T	0.516	0.97
103_V	138_E	0.516	0.97
77_Y	82_S	0.509	0.97
26_A	54_M	0.509	0.97
98_N	101_K	0.508	0.97
66_F	72_V	0.506	0.97
47_L	52_P	0.503	0.96
42_D	46_A	0.500	0.96

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
2fe3A	2	0.9862	100	0.088	Contact Map
2xigA	4	0.9931	100	0.132	Contact Map
4mtdA	2	1	100	0.136	Contact Map
4etsA	2	1	100	0.154	Contact Map
3eyyA	2	0.9103	100	0.157	Contact Map
3mwmA	2	0.8621	100	0.163	Contact Map
2w57A	2	0.8897	100	0.182	Contact Map
2o03A	2	0.8828	100	0.191	Contact Map
4lmyA	2	1	100	0.198	Contact Map
1mzbA	4	0.9034	100	0.218	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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