GLNR - BACSU - GREMLIN Contacts

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GLNR - HTH-type transcriptional regulator GlnR

UniProt:	P37582	Sequences: MSDNIRRSMPLFPIGIVMQLTELSARQIRYYEENGLIFPARSEGNRRLFSFHDVDKLLEIKHLIEQGVNMAGIKQILAKAEAEPEQKQNEKTKKPMKHDLSDDELRQLLKNELMQAGRFQRGNTFRQGDMSRFFH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	135 (113)
Sequences:	572 (386)
Seq/√Len:	36.3

BACSU - 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
64_I	73_I	3.691	1.00
90_E	93_K	3.511	1.00
68_V	76_I	3.035	1.00
83_E	86_Q	2.496	1.00
82_A	87_K	2.479	1.00
97_K	100_L	2.447	1.00
25_A	45_N	2.436	1.00
88_Q	92_T	2.029	0.99
12_F	54_V	2.028	0.99
51_F	54_V	1.972	0.98
59_E	62_H	1.924	0.98
89_N	92_T	1.782	0.97
69_N	72_G	1.730	0.96
68_V	72_G	1.703	0.96
24_S	27_Q	1.694	0.96
36_L	60_I	1.692	0.96
21_T	30_Y	1.666	0.95
106_R	109_L	1.657	0.95
20_L	58_L	1.631	0.95
56_K	77_L	1.622	0.94
71_A	74_K	1.563	0.93
32_E	64_I	1.553	0.93
72_G	76_I	1.546	0.93
8_S	52_H	1.517	0.92
82_A	85_E	1.487	0.91
106_R	112_E	1.478	0.91
12_F	51_F	1.465	0.91
63_L	72_G	1.458	0.90
66_Q	75_Q	1.391	0.88
10_P	50_S	1.387	0.88
65_E	69_N	1.385	0.88
111_N	118_R	1.384	0.88
82_A	90_E	1.341	0.86
96_M	99_D	1.332	0.86
56_K	81_E	1.320	0.85
114_M	117_G	1.292	0.84
12_F	39_P	1.272	0.83
53_D	56_K	1.270	0.83
7_R	55_D	1.252	0.82
89_N	94_K	1.251	0.82
11_L	105_L	1.244	0.82
10_P	70_M	1.233	0.81
100_L	104_E	1.224	0.81
95_P	98_H	1.202	0.80
61_K	73_I	1.196	0.79
42_S	45_N	1.196	0.79
32_E	37_I	1.192	0.79
14_I	39_P	1.183	0.78
76_I	79_K	1.168	0.78
81_E	85_E	1.162	0.77
43_E	55_D	1.149	0.76
32_E	61_K	1.126	0.75
27_Q	64_I	1.081	0.72
24_S	64_I	1.070	0.71
57_L	73_I	1.063	0.71
115_Q	118_R	1.046	0.69
68_V	82_A	1.031	0.68
10_P	30_Y	1.018	0.67
40_A	65_E	1.015	0.67
44_G	57_L	1.008	0.66
17_V	21_T	0.995	0.65
14_I	58_L	0.992	0.65
63_L	76_I	0.988	0.65
20_L	57_L	0.982	0.64
8_S	55_D	0.978	0.64
21_T	58_L	0.976	0.64
25_A	30_Y	0.966	0.63
85_E	89_N	0.964	0.63
42_S	48_L	0.946	0.61
81_E	92_T	0.931	0.60
45_N	48_L	0.921	0.59
75_Q	78_A	0.913	0.59
111_N	114_M	0.913	0.59
75_Q	80_A	0.895	0.57
79_K	83_E	0.875	0.55
33_E	76_I	0.867	0.55
8_S	99_D	0.859	0.54
63_L	68_V	0.853	0.53
106_R	111_N	0.843	0.53
69_N	74_K	0.843	0.53
20_L	100_L	0.836	0.52
113_L	118_R	0.833	0.52
44_G	49_F	0.833	0.52
35_G	38_F	0.828	0.51
105_L	109_L	0.827	0.51
7_R	45_N	0.826	0.51
22_E	78_A	0.824	0.51
25_A	74_K	0.815	0.50
65_E	70_M	0.813	0.50
59_E	80_A	0.807	0.49
32_E	39_P	0.803	0.49
26_R	33_E	0.790	0.48
42_S	113_L	0.771	0.46
14_I	28_I	0.765	0.46
86_Q	90_E	0.763	0.46
63_L	77_L	0.756	0.45
46_R	49_F	0.756	0.45
88_Q	94_K	0.748	0.44
25_A	64_I	0.743	0.44
92_T	96_M	0.739	0.44
55_D	95_P	0.738	0.43
20_L	109_L	0.736	0.43
10_P	77_L	0.733	0.43
16_I	60_I	0.732	0.43
21_T	57_L	0.719	0.42
30_Y	46_R	0.716	0.42
49_F	76_I	0.709	0.41
15_G	85_E	0.692	0.40
32_E	46_R	0.680	0.39
38_F	84_P	0.671	0.38
63_L	79_K	0.669	0.38
24_S	61_K	0.668	0.38
14_I	68_V	0.665	0.37
91_K	95_P	0.663	0.37
8_S	62_H	0.662	0.37
72_G	79_K	0.661	0.37
10_P	118_R	0.661	0.37
9_M	40_A	0.656	0.37
30_Y	34_N	0.653	0.36
104_E	107_Q	0.643	0.36
23_L	30_Y	0.641	0.35
25_A	71_A	0.634	0.35
20_L	54_V	0.629	0.34
34_N	63_L	0.629	0.34
22_E	43_E	0.624	0.34
30_Y	45_N	0.621	0.34
40_A	87_K	0.621	0.34
35_G	85_E	0.619	0.34
111_N	115_Q	0.618	0.34
108_L	111_N	0.618	0.34
75_Q	79_K	0.615	0.33
16_I	22_E	0.602	0.32
17_V	58_L	0.600	0.32
96_M	101_S	0.596	0.32
51_F	55_D	0.594	0.32
105_L	111_N	0.594	0.32
17_V	23_L	0.589	0.31
9_M	59_E	0.576	0.30
25_A	46_R	0.574	0.30
10_P	38_F	0.567	0.30
32_E	66_Q	0.566	0.30
92_T	107_Q	0.564	0.29
13_P	58_L	0.559	0.29
18_M	27_Q	0.551	0.29
8_S	102_D	0.548	0.28
23_L	37_I	0.546	0.28
53_D	72_G	0.546	0.28
24_S	33_E	0.542	0.28
30_Y	37_I	0.542	0.28
30_Y	61_K	0.539	0.28
83_E	97_K	0.538	0.28
33_E	54_V	0.538	0.28
27_Q	34_N	0.535	0.27
43_E	91_K	0.533	0.27
68_V	77_L	0.533	0.27
83_E	96_M	0.533	0.27
23_L	27_Q	0.531	0.27
111_N	116_A	0.530	0.27
93_K	97_K	0.527	0.27
49_F	99_D	0.526	0.27
40_A	75_Q	0.526	0.27
94_K	98_H	0.523	0.27
21_T	54_V	0.522	0.27
17_V	34_N	0.521	0.26
48_L	66_Q	0.518	0.26
75_Q	117_G	0.514	0.26
78_A	83_E	0.507	0.26
113_L	117_G	0.504	0.25
41_R	57_L	0.502	0.25
26_R	30_Y	0.500	0.25

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
3ucsA	2	0.7333	99.7	0.633	Contact Map
2zhgA	2	0.837	99.7	0.635	Contact Map
3qaoA	2	0.9111	99.7	0.636	Contact Map
3gpvA	2	0.7926	99.7	0.639	Contact Map
4r4eB	2	0.6222	99.7	0.639	Contact Map
2vz4A	2	0.7333	99.7	0.639	Contact Map
3gp4A	4	0.8889	99.7	0.64	Contact Map
4r24B	2	0.6296	99.7	0.649	Contact Map
2dg6A	2	0.837	99.7	0.655	Contact Map
3hh0A	4	0.8963	99.7	0.656	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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