NADR - BACSU - GREMLIN Contacts

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NADR - Transcription repressor NadR

UniProt:	P39667	Sequences: MTEELKLMGANRRDQLLLWLKESKSPLTGGELAKKANVSRQVIVQDISLLKAKNVPIIATSQGYVYMDAAAQQHQQAERIIACLHGPERTEEELQLIVDEGVTVKDVKIEHPVYGDLTAAIQVGTRKEVSHFIKKINSTNAAYLSQLTDGVHLHTLTAPDEHRIDQACQALEEAGILIKD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	180 (168)
Sequences:	635 (538)
Seq/√Len:	41.5

BACSU - NADR

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
96_L	174_A	4.402	1.00
92_E	176_I	4.331	1.00
102_V	167_A	4.198	1.00
99_D	126_R	4.070	1.00
81_I	156_L	3.799	1.00
106_D	155_T	3.313	1.00
92_E	174_A	2.940	1.00
90_T	143_Y	2.831	1.00
95_Q	130_S	2.812	1.00
97_I	102_V	2.563	1.00
105_K	157_T	2.510	1.00
19_W	27_L	2.510	1.00
89_R	92_E	2.450	1.00
86_G	89_R	2.321	1.00
97_I	167_A	2.294	1.00
94_L	104_V	2.256	1.00
98_V	129_V	2.252	1.00
160_D	163_R	2.227	1.00
91_E	95_Q	2.195	1.00
127_K	166_Q	2.194	1.00
82_A	153_L	2.151	0.99
91_E	130_S	2.105	0.99
158_A	164_I	2.078	0.99
95_Q	129_V	2.062	0.99
169_Q	173_E	1.887	0.99
79_R	161_E	1.838	0.98
9_G	49_L	1.827	0.98
48_S	51_K	1.790	0.98
54_N	119_A	1.768	0.98
9_G	13_R	1.764	0.98
103_T	157_T	1.748	0.98
106_D	118_T	1.722	0.97
170_A	173_E	1.706	0.97
79_R	168_C	1.705	0.97
95_Q	99_D	1.670	0.97
102_V	156_L	1.647	0.97
79_R	165_D	1.638	0.96
39_S	45_Q	1.605	0.96
19_W	36_A	1.569	0.95
18_L	22_E	1.566	0.95
15_Q	18_L	1.496	0.94
87_P	145_S	1.481	0.94
45_Q	157_T	1.477	0.94
17_L	55_V	1.448	0.93
92_E	96_L	1.433	0.93
79_R	158_A	1.427	0.92
95_Q	126_R	1.425	0.92
82_A	151_V	1.366	0.91
19_W	35_K	1.353	0.90
7_L	66_Y	1.341	0.90
96_L	100_E	1.319	0.89
78_E	105_K	1.315	0.89
91_E	129_V	1.300	0.88
80_I	155_T	1.283	0.88
113_V	136_I	1.255	0.86
103_T	124_G	1.238	0.86
42_V	45_Q	1.236	0.86
15_Q	36_A	1.234	0.86
82_A	116_D	1.207	0.84
8_M	11_N	1.195	0.84
29_G	45_Q	1.179	0.83
84_L	149_D	1.132	0.80
112_P	141_A	1.099	0.78
123_V	129_V	1.096	0.78
77_A	158_A	1.083	0.77
9_G	39_S	1.076	0.77
20_L	128_E	1.072	0.76
28_T	62_Q	1.061	0.76
78_E	157_T	1.053	0.75
99_D	127_K	1.043	0.74
90_T	132_F	0.994	0.71
145_S	150_G	0.992	0.71
134_K	137_N	0.987	0.70
159_P	163_R	0.979	0.70
91_E	137_N	0.971	0.69
116_D	120_A	0.953	0.67
49_L	52_A	0.944	0.67
116_D	132_F	0.939	0.66
62_Q	83_C	0.932	0.66
100_E	166_Q	0.929	0.65
89_R	176_I	0.917	0.64
89_R	173_E	0.917	0.64
51_K	167_A	0.910	0.64
133_I	137_N	0.892	0.62
156_L	167_A	0.891	0.62
122_Q	153_L	0.889	0.62
28_T	122_Q	0.875	0.61
100_E	167_A	0.870	0.60
29_G	158_A	0.868	0.60
28_T	83_C	0.867	0.60
7_L	36_A	0.850	0.58
51_K	61_S	0.838	0.57
50_L	57_I	0.833	0.57
136_I	143_Y	0.832	0.57
108_K	155_T	0.830	0.57
110_E	141_A	0.827	0.56
134_K	138_S	0.820	0.56
113_V	121_I	0.812	0.55
79_R	164_I	0.811	0.55
76_Q	159_P	0.807	0.55
121_I	143_Y	0.805	0.54
29_G	47_I	0.804	0.54
87_P	146_Q	0.796	0.54
108_K	116_D	0.792	0.53
77_A	164_I	0.789	0.53
100_E	170_A	0.789	0.53
30_G	39_S	0.787	0.53
82_A	110_E	0.783	0.52
15_Q	35_K	0.781	0.52
7_L	51_K	0.780	0.52
45_Q	48_S	0.780	0.52
96_L	170_A	0.778	0.52
33_A	52_A	0.777	0.52
118_T	155_T	0.771	0.51
16_L	27_L	0.770	0.51
31_E	35_K	0.769	0.51
59_A	62_Q	0.765	0.51
16_L	47_I	0.763	0.50
28_T	31_E	0.756	0.50
59_A	139_T	0.753	0.50
70_A	88_E	0.750	0.49
50_L	147_L	0.731	0.47
91_E	133_I	0.723	0.47
83_C	158_A	0.722	0.47
124_G	128_E	0.721	0.47
11_N	14_D	0.717	0.46
14_D	18_L	0.715	0.46
21_K	66_Y	0.710	0.46
29_G	127_K	0.708	0.45
50_L	55_V	0.703	0.45
82_A	178_I	0.698	0.44
80_I	108_K	0.697	0.44
29_G	51_K	0.696	0.44
18_L	69_A	0.693	0.44
27_L	32_L	0.691	0.44
102_V	163_R	0.690	0.44
49_L	61_S	0.685	0.43
76_Q	157_T	0.683	0.43
36_A	48_S	0.681	0.43
162_H	169_Q	0.679	0.43
110_E	132_F	0.676	0.42
33_A	175_G	0.670	0.42
109_I	127_K	0.664	0.41
146_Q	149_D	0.655	0.40
36_A	118_T	0.649	0.40
42_V	52_A	0.649	0.40
82_A	112_P	0.647	0.40
113_V	133_I	0.647	0.40
52_A	148_T	0.646	0.40
110_E	151_V	0.645	0.40
29_G	164_I	0.643	0.39
45_Q	158_A	0.640	0.39
163_R	166_Q	0.639	0.39
126_R	129_V	0.636	0.39
158_A	165_D	0.636	0.39
110_E	116_D	0.631	0.38
159_P	164_I	0.630	0.38
108_K	153_L	0.628	0.38
116_D	153_L	0.625	0.38
128_E	143_Y	0.622	0.38
42_V	62_Q	0.619	0.37
118_T	135_K	0.615	0.37
151_V	178_I	0.614	0.37
161_E	165_D	0.610	0.37
24_K	137_N	0.609	0.36
24_K	162_H	0.609	0.36
58_I	65_V	0.603	0.36
33_A	43_I	0.603	0.36
88_E	113_V	0.601	0.36
59_A	122_Q	0.600	0.36
139_T	147_L	0.595	0.35
124_G	159_P	0.593	0.35
118_T	142_A	0.593	0.35
169_Q	172_E	0.588	0.35
30_G	34_K	0.588	0.35
25_S	169_Q	0.585	0.34
14_D	137_N	0.583	0.34
65_V	175_G	0.582	0.34
21_K	68_D	0.581	0.34
31_E	34_K	0.580	0.34
129_V	133_I	0.574	0.33
158_A	168_C	0.574	0.33
97_I	100_E	0.573	0.33
29_G	53_K	0.569	0.33
55_V	66_Y	0.569	0.33
58_I	103_T	0.567	0.33
116_D	128_E	0.567	0.33
18_L	113_V	0.566	0.33
33_A	136_I	0.564	0.33
105_K	119_A	0.563	0.33
9_G	32_L	0.563	0.33
52_A	55_V	0.562	0.32
50_L	106_D	0.561	0.32
51_K	67_M	0.560	0.32
135_K	172_E	0.560	0.32
24_K	30_G	0.556	0.32
58_I	178_I	0.555	0.32
28_T	67_M	0.553	0.32
32_L	156_L	0.553	0.32
112_P	132_F	0.551	0.32
25_S	123_V	0.550	0.31
100_E	109_I	0.550	0.31
82_A	119_A	0.549	0.31
100_E	163_R	0.548	0.31
81_I	96_L	0.548	0.31
15_Q	19_W	0.548	0.31
68_D	140_N	0.548	0.31
136_I	149_D	0.547	0.31
29_G	116_D	0.545	0.31
61_S	127_K	0.545	0.31
15_Q	47_I	0.545	0.31
82_A	122_Q	0.541	0.31
108_K	118_T	0.541	0.31
20_L	47_I	0.541	0.31
19_W	32_L	0.541	0.31
29_G	62_Q	0.540	0.31
131_H	166_Q	0.540	0.31
17_L	21_K	0.539	0.31
10_A	13_R	0.537	0.30
34_K	68_D	0.536	0.30
117_L	124_G	0.536	0.30
14_D	161_E	0.535	0.30
61_S	67_M	0.535	0.30
75_Q	137_N	0.535	0.30
83_C	164_I	0.534	0.30
66_Y	140_N	0.532	0.30
81_I	168_C	0.531	0.30
100_E	125_T	0.527	0.30
9_G	164_I	0.525	0.30
54_N	61_S	0.523	0.29
29_G	178_I	0.523	0.29
15_Q	58_I	0.523	0.29
134_K	173_E	0.522	0.29
75_Q	173_E	0.521	0.29
24_K	70_A	0.521	0.29
37_N	133_I	0.518	0.29
14_D	135_K	0.513	0.29
23_S	177_L	0.512	0.29
125_T	128_E	0.510	0.28
18_L	76_Q	0.509	0.28
47_I	106_D	0.509	0.28
7_L	15_Q	0.509	0.28
49_L	148_T	0.507	0.28
77_A	161_E	0.506	0.28
95_Q	98_V	0.505	0.28
7_L	102_V	0.505	0.28
164_I	167_A	0.504	0.28
87_P	90_T	0.504	0.28
128_E	163_R	0.503	0.28
112_P	153_L	0.502	0.28
30_G	53_K	0.500	0.28
24_K	76_Q	0.500	0.28

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
1j5yA	4	0.95	99.9	0.663	Contact Map
2lnbA	1	0.3889	99.1	0.83	Contact Map
2heoA	1	0.3278	98.5	0.863	Contact Map
1biaA	1	0.6833	98.3	0.871	Contact Map
2p5vA	5	0.85	98.2	0.876	Contact Map
3sqnA	2	0.8556	98.2	0.876	Contact Map
4r6iA	2	0.8833	97.8	0.886	Contact Map
3rkxA	1	0.6667	97.8	0.889	Contact Map
2cfxA	5	0.7778	97.7	0.889	Contact Map
2cyyA	2	0.8389	97.5	0.895	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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