NRDR - BACSU - GREMLIN Contacts

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NRDR - Transcriptional repressor NrdR

UniProt:	Q45549	Sequences: MKCPSCQHNGTRVLDSRPVDDGKSIRRRRECESCHYRFTTFEKVEETPLIVVKKEGVREEFSREKMLRGLIKACEKRPVSLKTLEDMCFDIEKELRNQGCSEVKSELVGEMVMDRLAKIDEVAYVRFASVYRQFKDINVFIDELKDLIKKER	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	152 (148)
Sequences:	2018 (1073)
Seq/√Len:	88.2

ECOLI - NRDR
BACSU - NRDR

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
90_D	115_R	5.604	1.00
5_S	36_Y	3.939	1.00
80_S	83_T	3.562	1.00
72_K	75_E	3.389	1.00
77_R	120_D	3.334	1.00
70_L	87_M	3.209	1.00
70_L	84_L	2.932	1.00
94_E	115_R	2.870	1.00
143_E	146_D	2.495	1.00
12_R	32_E	2.431	1.00
67_L	84_L	2.407	1.00
67_L	88_C	2.343	1.00
66_M	112_V	2.260	1.00
8_H	33_S	2.233	1.00
51_V	108_V	2.220	1.00
54_K	106_E	2.111	1.00
87_M	119_I	2.067	1.00
141_I	145_K	2.057	1.00
64_E	68_R	2.009	1.00
98_Q	107_L	1.944	1.00
58_R	102_E	1.901	1.00
63_R	92_E	1.891	1.00
83_T	86_D	1.863	1.00
87_M	115_R	1.741	1.00
30_E	35_H	1.727	1.00
10_G	32_E	1.584	1.00
138_N	148_I	1.562	1.00
83_T	119_I	1.554	1.00
87_M	91_I	1.516	1.00
95_L	111_M	1.508	1.00
104_K	107_L	1.488	1.00
54_K	133_Q	1.443	0.99
132_R	143_E	1.405	0.99
100_C	107_L	1.404	0.99
69_G	75_E	1.385	0.99
142_D	145_K	1.380	0.99
63_R	89_F	1.351	0.99
19_V	24_S	1.341	0.99
52_V	102_E	1.340	0.99
138_N	142_D	1.325	0.99
110_E	132_R	1.298	0.99
94_E	114_D	1.270	0.98
125_V	135_K	1.250	0.98
12_R	69_G	1.233	0.98
24_S	43_K	1.198	0.98
94_E	111_M	1.192	0.98
121_E	133_Q	1.185	0.98
91_I	111_M	1.166	0.97
52_V	58_R	1.127	0.97
12_R	30_E	1.121	0.97
18_P	25_I	1.098	0.96
71_I	81_L	1.088	0.96
66_M	108_V	1.078	0.96
68_R	72_K	1.070	0.96
16_S	24_S	1.063	0.95
95_L	103_V	1.062	0.95
76_K	125_V	1.055	0.95
70_L	112_V	1.049	0.95
55_E	69_G	1.047	0.95
10_G	33_S	1.046	0.95
11_T	32_E	1.041	0.95
63_R	67_L	1.011	0.94
102_E	132_R	1.007	0.94
135_K	144_L	1.005	0.94
15_D	120_D	0.993	0.93
111_M	115_R	0.990	0.93
69_G	72_K	0.972	0.93
141_I	148_I	0.964	0.92
77_R	129_S	0.963	0.92
15_D	77_R	0.957	0.92
129_S	140_F	0.953	0.92
106_E	110_E	0.946	0.92
74_C	88_C	0.946	0.92
43_K	92_E	0.944	0.91
18_P	49_L	0.927	0.91
138_N	141_I	0.926	0.91
73_A	95_L	0.911	0.90
56_G	79_V	0.908	0.90
66_M	95_L	0.907	0.90
135_K	139_V	0.905	0.90
74_C	84_L	0.897	0.89
63_R	88_C	0.897	0.89
11_T	25_I	0.896	0.89
113_M	136_D	0.893	0.89
67_L	85_E	0.879	0.88
61_F	96_R	0.877	0.88
58_R	113_M	0.876	0.88
125_V	132_R	0.865	0.87
2_K	7_Q	0.859	0.87
57_V	79_V	0.855	0.87
11_T	20_D	0.850	0.87
11_T	30_E	0.848	0.86
2_K	9_N	0.848	0.86
61_F	92_E	0.845	0.86
122_V	140_F	0.843	0.86
140_F	144_L	0.840	0.86
125_V	138_N	0.839	0.86
98_Q	103_V	0.837	0.86
115_R	118_K	0.835	0.86
121_E	144_L	0.827	0.85
113_M	135_K	0.818	0.84
107_L	111_M	0.818	0.84
30_E	105_S	0.814	0.84
110_E	113_M	0.811	0.84
12_R	143_E	0.806	0.83
2_K	46_E	0.805	0.83
135_K	148_I	0.801	0.83
79_V	119_I	0.799	0.83
138_N	145_K	0.794	0.83
70_L	91_I	0.793	0.82
59_E	69_G	0.776	0.81
20_D	139_V	0.773	0.81
50_I	81_L	0.766	0.80
49_L	105_S	0.756	0.79
32_E	144_L	0.755	0.79
49_L	95_L	0.755	0.79
21_D	98_Q	0.752	0.79
43_K	72_K	0.751	0.79
45_E	101_S	0.749	0.79
51_V	95_L	0.748	0.79
102_E	108_V	0.746	0.78
11_T	18_P	0.740	0.78
61_F	139_V	0.731	0.77
91_I	112_V	0.730	0.77
9_N	86_D	0.730	0.77
54_K	63_R	0.729	0.77
41_F	45_E	0.718	0.76
3_C	6_C	0.716	0.76
58_R	76_K	0.714	0.75
66_M	70_L	0.713	0.75
86_D	90_D	0.706	0.75
64_E	93_K	0.694	0.73
128_A	131_Y	0.687	0.73
18_P	139_V	0.687	0.73
89_F	93_K	0.675	0.71
121_E	125_V	0.673	0.71
78_P	120_D	0.670	0.71
51_V	61_F	0.670	0.71
59_E	146_D	0.667	0.70
50_I	57_V	0.664	0.70
139_V	143_E	0.662	0.70
93_K	100_C	0.658	0.69
11_T	22_G	0.656	0.69
47_T	93_K	0.655	0.69
136_D	139_V	0.652	0.69
31_C	34_C	0.652	0.69
49_L	96_R	0.650	0.68
67_L	71_I	0.645	0.68
125_V	144_L	0.636	0.67
113_M	128_A	0.634	0.66
114_D	118_K	0.630	0.66
35_H	55_E	0.627	0.66
61_F	111_M	0.625	0.65
74_C	92_E	0.625	0.65
15_D	131_Y	0.625	0.65
33_S	106_E	0.623	0.65
20_D	43_K	0.621	0.65
63_R	85_E	0.621	0.65
69_G	143_E	0.618	0.64
60_E	146_D	0.618	0.64
64_E	67_L	0.617	0.64
79_V	101_S	0.617	0.64
2_K	18_P	0.613	0.64
113_M	125_V	0.609	0.63
1_M	6_C	0.604	0.63
91_I	115_R	0.604	0.63
14_L	133_Q	0.602	0.62
132_R	135_K	0.597	0.62
33_S	123_A	0.597	0.62
67_L	70_L	0.597	0.62
19_V	41_F	0.591	0.61
48_P	71_I	0.590	0.61
30_E	104_K	0.589	0.61
59_E	75_E	0.589	0.61
54_K	148_I	0.589	0.61
73_A	141_I	0.588	0.61
45_E	96_R	0.587	0.61
61_F	106_E	0.584	0.60
114_D	148_I	0.575	0.59
43_K	47_T	0.575	0.59
15_D	70_L	0.574	0.59
5_S	62_S	0.573	0.59
39_T	89_F	0.573	0.59
109_G	130_V	0.565	0.58
131_Y	140_F	0.563	0.57
5_S	11_T	0.560	0.57
1_M	13_V	0.557	0.57
122_V	125_V	0.556	0.56
20_D	24_S	0.555	0.56
76_K	88_C	0.553	0.56
110_E	136_D	0.552	0.56
63_R	74_C	0.552	0.56
51_V	107_L	0.551	0.56
5_S	9_N	0.550	0.56
43_K	93_K	0.548	0.55
127_F	140_F	0.546	0.55
85_E	89_F	0.546	0.55
56_G	59_E	0.542	0.55
79_V	83_T	0.540	0.54
39_T	114_D	0.540	0.54
30_E	75_E	0.540	0.54
92_E	96_R	0.539	0.54
74_C	122_V	0.538	0.54
75_E	130_V	0.532	0.53
20_D	23_K	0.529	0.53
33_S	104_K	0.524	0.52
81_L	85_E	0.523	0.52
76_K	85_E	0.521	0.52
44_V	85_E	0.518	0.51
125_V	147_L	0.514	0.51
90_D	94_E	0.514	0.51
69_G	109_G	0.514	0.51
11_T	44_V	0.509	0.50
5_S	10_G	0.508	0.50
61_F	141_I	0.507	0.50
32_E	41_F	0.506	0.50
137_I	146_D	0.505	0.50
8_H	44_V	0.505	0.50
117_A	121_E	0.505	0.50
54_K	130_V	0.503	0.49
66_M	75_E	0.501	0.49
144_L	147_L	0.500	0.49

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
3ga8A	1	0.4013	98	0.866	Contact Map
1tfiA	1	0.2566	97.9	0.871	Contact Map
3hncA	2	0.6579	97.7	0.875	Contact Map
3k8tA	2	0.1513	97.7	0.876	Contact Map
2xapA	4	0.6382	97.6	0.877	Contact Map
3o9xA	2	0.7697	95	0.907	Contact Map
1qypA	1	0.2632	90.8	0.92	Contact Map
1twfI	1	0.3158	90.5	0.921	Contact Map
3h0gI	1	0.2566	90.2	0.921	Contact Map
4c2mI	1	0.2763	88.5	0.924	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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