TNRA - BACSU - GREMLIN Contacts

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TNRA - HTH-type transcriptional regulator TnrA

UniProt:	Q45666	Sequences: MTTEDHSYKDKKVISIGIVSELTGLSVRQIRYYEERKLIYPQRSSRGTRKYSFADVERLMDIANKREDGVQTAEILKDMRKKEQMLKNDPQVRKKMLEGQLNAHFRYKNR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	110 (91)
Sequences:	953 (556)
Seq/√Len:	58.3

BACSU - TNRA GLNR

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
66_R	75_I	3.623	1.00
84_Q	89_D	3.513	1.00
85_M	88_N	3.210	1.00
70_V	78_D	2.974	1.00
91_Q	94_K	2.483	1.00
10_D	54_A	2.296	1.00
9_K	57_E	2.231	1.00
38_L	62_I	1.972	1.00
73_A	76_L	1.904	1.00
71_Q	74_E	1.820	0.99
61_D	64_N	1.818	0.99
70_V	74_E	1.722	0.99
61_D	82_K	1.718	0.99
63_A	67_E	1.694	0.99
14_I	53_F	1.675	0.99
47_G	50_K	1.561	0.98
14_I	56_V	1.550	0.98
58_R	83_E	1.518	0.98
29_Q	66_R	1.485	0.98
65_K	74_E	1.481	0.98
68_D	77_K	1.478	0.98
44_S	47_G	1.453	0.97
95_K	98_E	1.451	0.97
27_V	47_G	1.432	0.97
84_Q	87_K	1.388	0.97
26_S	29_Q	1.385	0.97
22_L	60_M	1.381	0.96
77_K	80_R	1.361	0.96
74_E	78_D	1.330	0.96
46_R	51_Y	1.298	0.95
23_T	60_M	1.195	0.92
53_F	56_V	1.185	0.92
91_Q	95_K	1.152	0.91
12_K	52_S	1.119	0.90
78_D	81_K	1.106	0.89
82_K	86_L	1.067	0.87
92_V	95_K	1.035	0.86
16_I	30_I	1.034	0.86
83_E	94_K	1.032	0.85
23_T	32_Y	1.031	0.85
26_S	66_R	1.021	0.85
81_K	85_M	1.004	0.84
58_R	79_M	1.003	0.84
83_E	90_P	0.998	0.83
34_E	66_R	0.995	0.83
24_G	50_K	0.989	0.83
53_F	57_E	0.985	0.83
20_S	27_V	0.957	0.81
34_E	63_A	0.953	0.80
19_V	25_L	0.953	0.80
25_L	29_Q	0.944	0.80
65_K	78_D	0.940	0.80
19_V	56_V	0.937	0.79
55_D	58_R	0.934	0.79
70_V	94_K	0.911	0.77
77_K	82_K	0.911	0.77
11_K	53_F	0.905	0.77
12_K	53_F	0.893	0.76
83_E	87_K	0.887	0.75
12_K	32_Y	0.873	0.74
26_S	63_A	0.852	0.72
14_I	18_I	0.848	0.72
63_A	75_I	0.843	0.72
44_S	50_K	0.840	0.71
48_T	51_Y	0.839	0.71
14_I	74_E	0.838	0.71
32_Y	48_T	0.836	0.71
83_E	96_M	0.834	0.71
23_T	77_K	0.816	0.69
11_K	21_E	0.815	0.69
39_I	62_I	0.813	0.69
14_I	41_P	0.797	0.67
25_L	75_I	0.797	0.67
74_E	81_K	0.788	0.66
85_M	92_V	0.766	0.64
19_V	23_T	0.758	0.63
27_V	66_R	0.756	0.63
28_R	35_E	0.756	0.63
35_E	56_V	0.753	0.63
76_L	80_R	0.745	0.62
35_E	78_D	0.735	0.61
21_E	50_K	0.721	0.60
16_I	41_P	0.708	0.58
11_K	42_Q	0.706	0.58
39_I	56_V	0.698	0.57
66_R	70_V	0.691	0.56
17_G	87_K	0.683	0.55
68_D	79_M	0.679	0.55
39_I	76_L	0.677	0.55
40_Y	45_S	0.676	0.55
13_V	81_K	0.674	0.55
71_Q	75_I	0.673	0.54
84_Q	91_Q	0.668	0.54
34_E	50_K	0.667	0.54
11_K	14_I	0.660	0.53
34_E	53_F	0.647	0.52
34_E	48_T	0.643	0.51
13_V	44_S	0.635	0.50
12_K	72_T	0.629	0.50
70_V	79_M	0.628	0.49
87_K	91_Q	0.622	0.49
34_E	41_P	0.619	0.48
56_V	64_N	0.617	0.48
10_D	64_N	0.615	0.48
22_L	59_L	0.614	0.48
20_S	48_T	0.612	0.48
65_K	72_T	0.607	0.47
84_Q	90_P	0.606	0.47
42_Q	93_R	0.602	0.47
30_I	60_M	0.601	0.46
79_M	89_D	0.601	0.46
12_K	40_Y	0.601	0.46
88_N	92_V	0.594	0.46
13_V	22_L	0.583	0.44
32_Y	63_A	0.582	0.44
83_E	88_N	0.574	0.43
37_K	88_N	0.569	0.43
35_E	39_I	0.567	0.43
80_R	84_Q	0.566	0.43
28_R	32_Y	0.564	0.42
16_I	34_E	0.561	0.42
22_L	90_P	0.559	0.42
26_S	32_Y	0.555	0.41
91_Q	98_E	0.527	0.38
17_G	58_R	0.522	0.38
12_K	58_R	0.520	0.38
34_E	39_I	0.518	0.38
32_Y	44_S	0.516	0.37
36_R	48_T	0.515	0.37
45_S	84_Q	0.515	0.37
11_K	25_L	0.512	0.37
32_Y	36_R	0.510	0.37
39_I	94_K	0.509	0.37
89_D	92_V	0.503	0.36
16_I	70_V	0.501	0.36
90_P	94_K	0.500	0.36

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
3qaoA	2	0.9091	99.7	0.551	Contact Map
2zhgA	2	0.8636	99.7	0.555	Contact Map
2dg6A	2	0.8	99.7	0.556	Contact Map
3ucsA	2	0.9	99.7	0.564	Contact Map
3gp4A	4	0.8909	99.7	0.566	Contact Map
3gpvA	2	0.8909	99.7	0.567	Contact Map
1q06A	2	0.8818	99.7	0.567	Contact Map
4r4eB	2	0.7636	99.7	0.568	Contact Map
4r24B	2	0.7727	99.7	0.568	Contact Map
2vz4A	2	0.8455	99.7	0.569	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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