RCNR - ECOLI - GREMLIN Contacts

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RCNR - Transcriptional repressor RcnR

UniProt:	P64530	Sequences: MSHTIRDKQKLKARASKIQGQVVALKKMLDEPHECAAVLQQIAAIRGAVNGLMREVIKGHLTEHIVHQGDELKREEDLDVVLKVLDSYIK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG14070
Length:	90 (90)
Sequences:	435 (287)
Seq/√Len:	30.2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
42_I	56_V	4.569	1.00
19_Q	23_V	3.496	1.00
45_I	49_V	2.893	1.00
18_I	22_V	2.703	1.00
8_K	32_P	2.319	0.99
23_V	27_K	2.264	0.99
4_T	8_K	2.067	0.98
16_S	26_K	1.940	0.97
78_L	81_V	1.898	0.96
58_K	62_T	1.881	0.96
49_V	53_M	1.813	0.95
61_L	81_V	1.731	0.93
15_A	29_L	1.728	0.93
53_M	89_I	1.704	0.93
44_A	53_M	1.693	0.93
2_S	64_H	1.574	0.90
24_A	28_M	1.533	0.88
58_K	82_L	1.533	0.88
11_L	64_H	1.513	0.88
70_D	74_R	1.507	0.88
24_A	40_Q	1.495	0.87
29_L	50_N	1.465	0.86
11_L	84_V	1.449	0.85
34_E	37_A	1.379	0.82
85_L	89_I	1.369	0.82
54_R	89_I	1.367	0.82
12_K	16_S	1.358	0.81
25_L	41_Q	1.350	0.81
15_A	52_L	1.314	0.79
62_T	82_L	1.292	0.78
4_T	11_L	1.284	0.77
9_Q	13_A	1.276	0.77
61_L	85_L	1.188	0.72
2_S	5_I	1.173	0.71
39_L	57_I	1.110	0.66
25_L	44_A	1.102	0.66
3_H	64_H	1.078	0.64
40_Q	44_A	1.069	0.63
13_A	17_K	1.066	0.63
3_H	11_L	1.026	0.60
7_D	56_V	1.022	0.60
19_Q	26_K	1.017	0.59
77_D	90_K	1.011	0.59
15_A	26_K	0.998	0.58
57_I	66_V	0.957	0.55
28_M	31_E	0.945	0.54
45_I	89_I	0.943	0.54
70_D	73_K	0.936	0.53
61_L	78_L	0.921	0.52
18_I	45_I	0.913	0.51
61_L	70_D	0.911	0.51
57_I	78_L	0.910	0.51
28_M	33_H	0.909	0.51
28_M	57_I	0.892	0.50
57_I	62_T	0.881	0.49
39_L	50_N	0.878	0.49
49_V	69_G	0.870	0.48
43_A	86_D	0.869	0.48
4_T	59_G	0.863	0.47
27_K	30_D	0.858	0.47
72_L	75_E	0.847	0.46
63_E	87_S	0.839	0.45
5_I	32_P	0.839	0.45
10_K	23_V	0.837	0.45
8_K	76_E	0.830	0.45
42_I	53_M	0.830	0.45
63_E	67_H	0.827	0.44
10_K	32_P	0.825	0.44
77_D	84_V	0.793	0.42
36_A	46_R	0.790	0.42
59_G	68_Q	0.789	0.42
61_L	82_L	0.788	0.41
25_L	32_P	0.776	0.41
4_T	64_H	0.775	0.40
71_E	75_E	0.756	0.39
2_S	11_L	0.746	0.38
4_T	32_P	0.740	0.38
41_Q	48_A	0.737	0.38
27_K	46_R	0.732	0.37
8_K	12_K	0.731	0.37
12_K	28_M	0.728	0.37
44_A	48_A	0.725	0.37
10_K	37_A	0.723	0.37
77_D	86_D	0.722	0.36
64_H	84_V	0.720	0.36
22_V	25_L	0.720	0.36
54_R	85_L	0.713	0.36
27_K	41_Q	0.708	0.35
11_L	79_D	0.693	0.34
66_V	78_L	0.689	0.34
45_I	78_L	0.681	0.33
73_K	82_L	0.676	0.33
14_R	20_G	0.657	0.32
54_R	78_L	0.655	0.32
71_E	74_R	0.648	0.31
59_G	83_K	0.648	0.31
11_L	59_G	0.645	0.31
16_S	86_D	0.626	0.30
19_Q	87_S	0.617	0.29
15_A	38_V	0.616	0.29
13_A	45_I	0.616	0.29
36_A	80_V	0.610	0.29
10_K	69_G	0.610	0.29
57_I	85_L	0.599	0.28
42_I	52_L	0.599	0.28
9_Q	40_Q	0.598	0.28
55_E	83_K	0.596	0.28
38_V	75_E	0.586	0.27
23_V	80_V	0.584	0.27
30_D	71_E	0.584	0.27
56_V	65_I	0.582	0.27
75_E	79_D	0.581	0.27
69_G	75_E	0.581	0.27
24_A	49_V	0.571	0.26
55_E	75_E	0.568	0.26
23_V	54_R	0.568	0.26
7_D	83_K	0.561	0.26
10_K	19_Q	0.556	0.25
36_A	76_E	0.548	0.25
53_M	68_Q	0.543	0.24
18_I	68_Q	0.540	0.24
5_I	59_G	0.536	0.24
50_N	88_Y	0.536	0.24
67_H	90_K	0.532	0.24
25_L	59_G	0.532	0.24
3_H	38_V	0.530	0.24
50_N	90_K	0.527	0.24
37_A	40_Q	0.527	0.24
51_G	84_V	0.523	0.23
1_M	35_C	0.521	0.23
19_Q	44_A	0.519	0.23
17_K	86_D	0.512	0.23
5_I	10_K	0.511	0.23
40_Q	83_K	0.504	0.22
54_R	87_S	0.500	0.22

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
4m1pA	3	1	99.9	0.319	Contact Map
2hh7A	3	0.9333	99.9	0.339	Contact Map
4adzA	4	0.9667	99.9	0.363	Contact Map
3aaiA	3	0.8889	99.9	0.392	Contact Map
2okuA	2	0.5667	61.9	0.894	Contact Map
2fb5A	3	0.9111	44	0.904	Contact Map
2ffhA	4	0.4889	18.3	0.921	Contact Map
3dm5A	4	0.5333	15.2	0.924	Contact Map
2xxaA	1	0.4778	14.1	0.925	Contact Map
4hubG	1	0.8889	10.3	0.929	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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