RGHR - BACSU - GREMLIN Contacts

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RGHR - HTH-type transcriptional repressor RghR

UniProt:	O32236	Sequences: MESFGEQLRALREERKLTVNQLATYSGVSAAGISRIENGKRGVPKPATIKKLAEALKIPYEGLMYKAGYIEEVHEARAPYETKCKLLEKAEAYDLKNLALLENEKWQYLNKEDLLMLDHYFSFISDEAKKRSADD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	135 (118)
Sequences:	1121 (1019)
Seq/√Len:	93.8

ECOLI - DICA
BACSU - RGHR RGHRB IMMR YQAE ANSR YOBD SLRR YONR SINR XRE YQAF YGZD YAZB
HALSA - O51961 Q9HRZ8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
4_F	8_L	3.417	1.00
22_L	33_I	3.178	1.00
12_R	37_E	2.783	1.00
17_L	55_A	2.748	1.00
54_E	66_K	2.680	1.00
20_N	24_T	2.667	1.00
5_G	39_G	2.660	1.00
20_N	30_A	2.525	1.00
35_R	40_K	2.132	1.00
11_L	56_L	2.130	1.00
28_V	33_I	2.094	1.00
31_A	35_R	2.069	1.00
7_Q	62_G	2.017	1.00
46_P	49_I	1.990	1.00
14_E	70_I	1.949	1.00
22_L	56_L	1.941	1.00
29_S	32_G	1.901	1.00
25_Y	55_A	1.863	1.00
60_Y	64_M	1.784	1.00
31_A	34_S	1.742	1.00
35_R	41_R	1.688	1.00
32_G	35_R	1.652	1.00
110_N	113_D	1.616	1.00
36_I	48_T	1.615	1.00
33_I	36_I	1.591	1.00
21_Q	24_T	1.513	1.00
120_Y	123_F	1.497	1.00
53_A	66_K	1.489	1.00
30_A	34_S	1.485	1.00
22_L	55_A	1.466	1.00
8_L	56_L	1.423	0.99
120_Y	124_I	1.398	0.99
45_K	48_T	1.389	0.99
61_E	66_K	1.383	0.99
116_M	123_F	1.362	0.99
8_L	33_I	1.354	0.99
7_Q	65_Y	1.317	0.99
7_Q	66_K	1.314	0.99
29_S	34_S	1.300	0.99
22_L	52_L	1.279	0.99
19_V	23_A	1.276	0.99
11_L	58_I	1.263	0.99
58_I	62_G	1.244	0.99
36_I	41_R	1.241	0.99
26_S	55_A	1.220	0.98
103_N	108_Y	1.181	0.98
119_H	123_F	1.170	0.98
44_P	61_E	1.168	0.98
26_S	52_L	1.143	0.97
15_R	25_Y	1.128	0.97
113_D	116_M	1.123	0.97
7_Q	68_G	1.122	0.97
6_E	39_G	1.116	0.97
19_V	30_A	1.101	0.97
116_M	124_I	1.089	0.97
12_R	19_V	1.087	0.97
43_V	46_P	1.048	0.96
109_L	121_F	1.046	0.96
22_L	26_S	1.035	0.95
17_L	25_Y	1.014	0.95
34_S	44_P	1.003	0.95
35_R	38_N	0.990	0.94
4_F	46_P	0.959	0.93
28_V	31_A	0.950	0.93
17_L	21_Q	0.939	0.92
36_I	45_K	0.931	0.92
19_V	33_I	0.930	0.92
27_G	51_K	0.921	0.92
117_L	124_I	0.917	0.92
62_G	68_G	0.910	0.91
9_R	13_E	0.908	0.91
17_L	22_L	0.904	0.91
19_V	37_E	0.902	0.91
7_Q	10_A	0.882	0.90
49_I	60_Y	0.870	0.89
4_F	56_L	0.867	0.89
34_S	38_N	0.863	0.89
122_S	125_S	0.858	0.89
15_R	57_K	0.857	0.89
4_F	44_P	0.854	0.88
67_A	70_I	0.845	0.88
116_M	125_S	0.828	0.87
8_L	22_L	0.822	0.86
29_S	35_R	0.820	0.86
118_D	122_S	0.811	0.86
32_G	36_I	0.807	0.85
10_A	14_E	0.802	0.85
20_N	34_S	0.801	0.85
44_P	48_T	0.799	0.85
44_P	49_I	0.792	0.84
4_F	63_L	0.792	0.84
118_D	121_F	0.789	0.84
36_I	44_P	0.775	0.83
23_A	35_R	0.760	0.82
28_V	36_I	0.754	0.81
49_I	61_E	0.750	0.81
23_A	33_I	0.747	0.81
121_F	125_S	0.747	0.81
41_R	46_P	0.739	0.80
30_A	40_K	0.728	0.79
28_V	32_G	0.722	0.78
35_R	45_K	0.721	0.78
53_A	65_Y	0.711	0.77
116_M	121_F	0.697	0.76
30_A	38_N	0.695	0.76
118_D	125_S	0.668	0.73
23_A	31_A	0.668	0.73
113_D	119_H	0.666	0.73
11_L	62_G	0.659	0.72
116_M	120_Y	0.658	0.72
99_A	103_N	0.657	0.72
30_A	33_I	0.648	0.71
53_A	60_Y	0.641	0.70
21_Q	25_Y	0.640	0.70
23_A	37_E	0.638	0.69
121_F	124_I	0.636	0.69
115_L	119_H	0.631	0.69
12_R	23_A	0.631	0.69
116_M	119_H	0.618	0.67
48_T	52_L	0.616	0.67
82_T	89_K	0.613	0.66
19_V	35_R	0.613	0.66
117_L	121_F	0.612	0.66
30_A	35_R	0.610	0.66
110_N	116_M	0.608	0.66
36_I	52_L	0.606	0.65
86_L	89_K	0.603	0.65
61_E	64_M	0.600	0.65
23_A	28_V	0.600	0.65
65_Y	68_G	0.593	0.64
31_A	41_R	0.591	0.64
62_G	67_A	0.587	0.63
103_N	120_Y	0.587	0.63
104_E	118_D	0.586	0.63
92_A	113_D	0.585	0.63
120_Y	125_S	0.585	0.63
34_S	41_R	0.583	0.63
32_G	40_K	0.581	0.62
55_A	58_I	0.580	0.62
34_S	45_K	0.578	0.62
49_I	64_M	0.573	0.61
35_R	46_P	0.573	0.61
109_L	113_D	0.573	0.61
22_L	25_Y	0.567	0.60
26_S	56_L	0.566	0.60
87_L	117_L	0.560	0.59
86_L	90_A	0.548	0.58
15_R	55_A	0.548	0.58
29_S	44_P	0.547	0.58
60_Y	66_K	0.542	0.57
69_Y	72_E	0.542	0.57
23_A	30_A	0.541	0.57
111_K	114_L	0.541	0.57
85_K	89_K	0.540	0.57
62_G	65_Y	0.539	0.57
27_G	31_A	0.538	0.56
6_E	10_A	0.538	0.56
32_G	38_N	0.536	0.56
31_A	40_K	0.534	0.56
33_I	43_V	0.533	0.56
113_D	125_S	0.529	0.55
86_L	100_L	0.528	0.55
5_G	34_S	0.526	0.55
50_K	66_K	0.524	0.54
90_A	94_D	0.521	0.54
99_A	102_E	0.520	0.54
65_Y	70_I	0.520	0.54
38_N	45_K	0.518	0.54
89_K	100_L	0.518	0.54
7_Q	11_L	0.515	0.53
58_I	70_I	0.511	0.53
13_E	33_I	0.510	0.53
103_N	109_L	0.509	0.52
96_K	101_L	0.505	0.52
93_Y	97_N	0.501	0.51
62_G	70_I	0.500	0.51
19_V	32_G	0.500	0.51

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
4ndwA	2	0.8741	99.8	0.413	Contact Map
3r1fA	2	0.8741	99.7	0.419	Contact Map
3op9A	4	0.7852	99.7	0.432	Contact Map
3qwgA	2	0.6074	99.7	0.434	Contact Map
4o8bA	2	0.7185	99.7	0.436	Contact Map
3ivpA	2	0.8	99.7	0.441	Contact Map
1b0nA	2	0.7556	99.7	0.448	Contact Map
3mlfA	2	0.6593	99.7	0.454	Contact Map
4jcyA	2	0.6519	99.7	0.461	Contact Map
2ebyA	2	0.7407	99.6	0.469	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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