CYMR - BACSU - GREMLIN Contacts

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CYMR - HTH-type transcriptional regulator CymR

UniProt:	O34527	Sequences: MKISTKGRYGLTIMIELAKKHGEGPTSLKSIAQTNNLSEHYLEQLVSPLRNAGLVKSIRGAYGGYVLGSEPDAITAGDIIRVLEGPISPVEVLEDEEPAKRELWIRIRDAVKEVLDSTTLEDLASYTDGEQEAYMFYI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	138 (127)
Sequences:	5611 (3767)
Seq/√Len:	334.2

ECOLI - ISCR NSRR
BACSU - CYMR NSRR YWGB YWNA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
92_V	98_P	3.854	1.00
77_G	116_D	3.843	1.00
72_D	121_E	2.980	1.00
10_G	83_L	2.882	1.00
16_E	34_T	2.818	1.00
56_K	66_V	2.788	1.00
121_E	125_S	2.671	1.00
14_M	54_L	2.612	1.00
106_R	114_V	2.397	1.00
81_R	116_D	2.367	1.00
52_A	82_V	2.354	1.00
14_M	120_L	2.313	1.00
69_S	78_D	2.274	1.00
13_I	46_V	2.089	1.00
77_G	81_R	2.082	1.00
18_A	124_A	2.029	1.00
25_P	66_V	1.954	1.00
17_L	55_V	1.908	1.00
29_K	39_E	1.831	1.00
110_A	114_V	1.795	1.00
110_A	113_E	1.647	1.00
70_E	73_A	1.594	1.00
106_R	118_T	1.585	1.00
58_I	66_V	1.577	1.00
29_K	33_Q	1.568	1.00
16_E	26_T	1.560	1.00
50_R	57_S	1.558	1.00
69_S	73_A	1.537	1.00
7_G	80_I	1.511	1.00
13_I	42_L	1.438	1.00
75_T	119_T	1.433	1.00
107_I	111_V	1.420	1.00
47_S	51_N	1.393	1.00
75_T	78_D	1.363	1.00
37_L	42_L	1.341	1.00
28_L	46_V	1.228	1.00
114_V	117_S	1.207	1.00
112_K	116_D	1.203	1.00
103_L	118_T	1.200	1.00
108_R	112_K	1.191	1.00
21_H	71_P	1.156	1.00
16_E	20_K	1.147	1.00
16_E	35_N	1.146	1.00
13_I	31_I	1.139	1.00
69_S	74_I	1.128	1.00
56_K	68_G	1.113	1.00
7_G	84_E	1.105	1.00
106_R	126_Y	1.086	1.00
20_K	24_G	1.084	1.00
25_P	58_I	1.081	1.00
109_D	113_E	1.079	1.00
81_R	112_K	1.073	1.00
113_E	117_S	1.051	1.00
47_S	50_R	1.047	1.00
20_K	26_T	1.046	1.00
9_Y	37_L	1.026	1.00
33_Q	39_E	1.022	1.00
8_R	12_T	1.019	1.00
80_I	115_L	1.009	1.00
78_D	116_D	1.006	1.00
6_K	44_Q	1.004	1.00
14_M	79_I	0.997	1.00
107_I	115_L	0.996	1.00
27_S	30_S	0.995	1.00
24_G	30_S	0.994	1.00
54_L	74_I	0.981	1.00
105_I	109_D	0.977	1.00
54_L	82_V	0.973	1.00
89_P	108_R	0.947	1.00
102_E	126_Y	0.942	1.00
11_L	76_A	0.942	1.00
46_V	65_Y	0.932	1.00
5_T	41_Y	0.924	1.00
40_H	43_E	0.918	1.00
15_I	124_A	0.907	1.00
46_V	55_V	0.904	1.00
19_K	124_A	0.900	1.00
30_S	34_T	0.895	1.00
6_K	48_P	0.887	1.00
28_L	43_E	0.884	1.00
30_S	33_Q	0.858	1.00
76_A	103_L	0.850	1.00
21_H	24_G	0.830	1.00
78_D	81_R	0.829	1.00
14_M	49_L	0.829	1.00
87_I	112_K	0.819	1.00
92_V	101_R	0.818	1.00
122_D	125_S	0.816	1.00
3_I	104_W	0.812	1.00
21_H	70_E	0.805	1.00
107_I	110_A	0.804	1.00
43_E	65_Y	0.794	1.00
17_L	26_T	0.790	1.00
68_G	74_I	0.782	1.00
114_V	118_T	0.781	1.00
106_R	110_A	0.779	1.00
41_Y	45_L	0.778	1.00
47_S	57_S	0.777	1.00
43_E	50_R	0.775	1.00
6_K	10_G	0.763	1.00
47_S	65_Y	0.762	1.00
28_L	39_E	0.756	1.00
50_R	55_V	0.752	1.00
105_I	108_R	0.752	1.00
104_W	111_V	0.750	0.99
98_P	101_R	0.743	0.99
76_A	123_L	0.742	0.99
54_L	78_D	0.734	0.99
48_P	52_A	0.732	0.99
39_E	43_E	0.731	0.99
6_K	41_Y	0.728	0.99
101_R	105_I	0.724	0.99
32_A	37_L	0.723	0.99
57_S	65_Y	0.721	0.99
10_G	45_L	0.718	0.99
54_L	69_S	0.715	0.99
79_I	120_L	0.714	0.99
119_T	122_D	0.711	0.99
67_L	71_P	0.711	0.99
77_G	112_K	0.709	0.99
70_E	121_E	0.704	0.99
16_E	31_I	0.699	0.99
106_R	117_S	0.697	0.99
9_Y	45_L	0.695	0.99
74_I	79_I	0.695	0.99
71_P	124_A	0.693	0.99
4_S	7_G	0.690	0.99
27_S	62_Y	0.690	0.99
8_R	100_K	0.689	0.99
78_D	82_V	0.672	0.99
81_R	86_P	0.656	0.99
7_G	83_L	0.644	0.98
16_E	30_S	0.641	0.98
75_T	117_S	0.630	0.98
106_R	109_D	0.627	0.98
75_T	116_D	0.624	0.98
15_I	123_L	0.616	0.98
5_T	91_E	0.612	0.98
91_E	94_E	0.609	0.98
3_I	80_I	0.601	0.98
3_I	7_G	0.600	0.98
89_P	98_P	0.599	0.98
4_S	41_Y	0.596	0.97
20_K	34_T	0.595	0.97
40_H	44_Q	0.594	0.97
31_I	46_V	0.590	0.97
12_T	98_P	0.587	0.97
17_L	46_V	0.583	0.97
72_D	122_D	0.574	0.97
100_K	104_W	0.574	0.97
27_S	59_R	0.571	0.97
72_D	125_S	0.571	0.97
48_P	51_N	0.568	0.97
88_S	94_E	0.567	0.97
44_Q	47_S	0.566	0.97
68_G	71_P	0.556	0.96
88_S	93_L	0.556	0.96
38_S	41_Y	0.556	0.96
59_R	104_W	0.555	0.96
19_K	34_T	0.555	0.96
53_G	68_G	0.554	0.96
107_I	114_V	0.551	0.96
9_Y	41_Y	0.549	0.96
4_S	84_E	0.542	0.96
80_I	84_E	0.542	0.96
57_S	85_G	0.542	0.96
19_K	127_T	0.541	0.96
50_R	65_Y	0.540	0.96
12_T	35_N	0.539	0.96
14_M	18_A	0.533	0.95
110_A	115_L	0.533	0.95
79_I	82_V	0.532	0.95
69_S	72_D	0.531	0.95
19_K	99_A	0.530	0.95
103_L	106_R	0.524	0.95
74_I	120_L	0.522	0.95
121_E	124_A	0.518	0.94
31_I	35_N	0.517	0.94
33_Q	36_N	0.515	0.94
5_T	36_N	0.514	0.94
71_P	74_I	0.514	0.94
71_P	120_L	0.510	0.94
3_I	13_I	0.510	0.94
83_L	101_R	0.509	0.94
8_R	89_P	0.508	0.94
89_P	92_V	0.505	0.94
12_T	92_V	0.504	0.94
13_I	84_E	0.504	0.94
92_V	100_K	0.500	0.93
5_T	43_E	0.500	0.93

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
3lwfA	5	0.9928	100	0.254	Contact Map
4hf1A	2	0.9855	100	0.26	Contact Map
4cicA	2	0.9348	100	0.28	Contact Map
3t8rA	2	0.8696	100	0.294	Contact Map
1xd7A	2	0.7826	100	0.298	Contact Map
4hf0A	3	0.8623	100	0.307	Contact Map
1ylfA	5	0.8478	100	0.338	Contact Map
3k69A	2	0.971	100	0.348	Contact Map
2y75A	5	0.9203	99.9	0.385	Contact Map
2jscA	2	0.6159	98.2	0.774	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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