NSRR - ECOLI - GREMLIN Contacts

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NSRR - HTH-type transcriptional repressor NsrR

UniProt:	P0AF63	Sequences: MQLTSFTDYGLRALIYMASLPEGRMTSISEVTDVYGVSRNHMVKIINQLSRAGYVTAVRGKNGGIRLGKPASAIRIGDVVRELEPLSLVNCSSEFCHITPACRLKQALSKAVQSFLTELDNYTLADLVEENQPLYKLLLVE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11212
Length:	141 (131)
Sequences:	5764 (3902)
Seq/√Len:	340.9

ECOLI - NSRR ISCR
BACSU - NSRR YWGB CYMR 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
77_G	120_D	3.794	1.00
91_C	102_C	3.040	1.00
72_S	125_A	2.996	1.00
56_T	66_R	2.796	1.00
16_Y	34_V	2.775	1.00
10_G	83_L	2.734	1.00
125_A	129_E	2.642	1.00
14_L	54_Y	2.578	1.00
110_K	118_E	2.404	1.00
52_A	82_E	2.394	1.00
69_K	78_D	2.351	1.00
14_L	124_L	2.199	1.00
81_R	120_D	2.171	1.00
91_C	96_C	2.157	1.00
77_G	81_R	2.072	1.00
13_A	46_I	2.050	1.00
18_A	128_V	2.039	1.00
25_M	66_R	1.971	1.00
96_C	102_C	1.919	1.00
29_S	39_R	1.900	1.00
17_M	55_V	1.843	1.00
114_S	118_E	1.837	1.00
114_S	117_T	1.726	1.00
16_Y	26_T	1.634	1.00
70_P	73_A	1.631	1.00
29_S	33_D	1.585	1.00
110_K	122_Y	1.576	1.00
50_S	57_A	1.569	1.00
58_V	66_R	1.540	1.00
69_K	73_A	1.539	1.00
47_N	51_R	1.483	1.00
7_T	80_V	1.469	1.00
75_R	123_T	1.462	1.00
20_L	24_R	1.437	1.00
111_A	115_F	1.430	1.00
37_V	42_M	1.396	1.00
13_A	42_M	1.350	1.00
75_R	78_D	1.319	1.00
21_P	71_A	1.291	1.00
116_L	120_D	1.287	1.00
28_I	46_I	1.274	1.00
112_V	116_L	1.214	1.00
107_A	122_Y	1.207	1.00
118_E	121_N	1.201	1.00
7_T	84_E	1.172	1.00
81_R	116_L	1.162	1.00
69_K	74_I	1.137	1.00
13_A	31_V	1.128	1.00
113_Q	117_T	1.121	1.00
56_T	68_G	1.121	1.00
16_Y	20_L	1.111	1.00
16_Y	35_Y	1.097	1.00
117_T	121_N	1.073	1.00
110_K	130_E	1.068	1.00
47_N	50_S	1.055	1.00
27_S	30_E	1.050	1.00
20_L	26_T	1.043	1.00
25_M	58_V	1.043	1.00
6_F	44_K	1.034	1.00
111_A	119_L	1.030	1.00
9_Y	37_V	1.005	1.00
54_Y	74_I	1.000	1.00
109_S	113_Q	0.998	1.00
54_Y	82_E	0.985	1.00
80_V	119_L	0.983	1.00
33_D	39_R	0.978	1.00
46_I	65_I	0.967	1.00
14_L	79_V	0.960	1.00
8_D	12_R	0.953	1.00
15_I	128_V	0.930	1.00
86_L	116_L	0.920	1.00
78_D	120_D	0.918	1.00
6_F	48_Q	0.917	1.00
24_R	30_E	0.911	1.00
46_I	55_V	0.904	1.00
76_I	107_A	0.904	1.00
11_L	76_I	0.898	1.00
30_E	34_V	0.898	1.00
106_Q	130_E	0.894	1.00
5_S	41_H	0.893	1.00
14_L	49_L	0.887	1.00
88_L	112_V	0.880	1.00
30_E	33_D	0.865	1.00
40_N	43_V	0.865	1.00
78_D	81_R	0.855	1.00
111_A	114_S	0.848	1.00
110_K	114_S	0.822	1.00
28_I	43_V	0.820	1.00
17_M	26_T	0.818	1.00
47_N	57_A	0.809	1.00
70_P	125_A	0.809	1.00
50_S	55_V	0.806	1.00
126_D	129_E	0.800	1.00
21_P	24_R	0.800	1.00
6_F	10_G	0.796	1.00
47_N	65_I	0.792	1.00
28_I	39_R	0.788	1.00
123_T	126_D	0.785	1.00
48_Q	52_A	0.785	1.00
57_A	65_I	0.784	1.00
43_V	65_I	0.781	1.00
76_I	127_L	0.776	1.00
19_S	128_V	0.771	1.00
105_K	109_S	0.765	1.00
118_E	122_Y	0.765	1.00
3_L	108_L	0.757	1.00
67_L	71_A	0.753	1.00
77_G	116_L	0.750	1.00
43_V	50_S	0.746	1.00
68_G	74_I	0.746	1.00
110_K	121_N	0.745	1.00
6_F	41_H	0.738	0.99
109_S	112_V	0.735	0.99
16_Y	31_V	0.732	0.99
54_Y	78_D	0.723	0.99
81_R	85_P	0.722	0.99
10_G	45_I	0.713	0.99
41_H	45_I	0.706	0.99
39_R	43_V	0.702	0.99
32_T	37_V	0.698	0.99
3_L	80_V	0.697	0.99
7_T	83_L	0.684	0.99
110_K	113_Q	0.680	0.99
9_Y	45_I	0.678	0.99
16_Y	30_E	0.674	0.99
21_P	70_P	0.674	0.99
94_E	99_T	0.673	0.99
74_I	79_V	0.671	0.99
91_C	105_K	0.660	0.99
78_D	82_E	0.657	0.99
80_V	84_E	0.656	0.99
8_D	104_L	0.656	0.99
75_R	120_D	0.643	0.99
74_I	124_L	0.643	0.99
4_T	7_T	0.642	0.99
71_A	128_V	0.639	0.98
27_S	62_N	0.635	0.98
111_A	118_E	0.632	0.98
108_L	115_F	0.628	0.98
87_S	93_S	0.621	0.98
40_N	44_K	0.621	0.98
48_Q	51_R	0.620	0.98
117_T	120_D	0.615	0.98
79_V	124_L	0.610	0.98
19_S	34_V	0.610	0.98
79_V	82_E	0.609	0.98
15_I	127_L	0.607	0.98
19_S	103_R	0.604	0.98
96_C	105_K	0.598	0.98
54_Y	69_K	0.597	0.98
38_S	41_H	0.595	0.98
53_G	68_G	0.592	0.98
107_A	110_K	0.592	0.98
4_T	41_H	0.591	0.98
98_I	101_A	0.590	0.97
17_M	46_I	0.584	0.97
75_R	121_N	0.584	0.97
114_S	119_L	0.578	0.97
3_L	7_T	0.576	0.97
125_A	128_V	0.569	0.97
14_L	18_A	0.566	0.97
31_V	46_I	0.565	0.97
9_Y	41_H	0.564	0.97
52_A	78_D	0.563	0.97
4_T	84_E	0.560	0.97
44_K	47_N	0.557	0.96
20_L	34_V	0.549	0.96
72_S	126_D	0.546	0.96
89_V	92_S	0.545	0.96
102_C	105_K	0.545	0.96
87_S	95_F	0.545	0.96
107_A	118_E	0.542	0.96
50_S	65_I	0.541	0.96
27_S	59_R	0.540	0.96
97_H	101_A	0.539	0.96
113_Q	116_L	0.536	0.96
59_R	108_L	0.533	0.95
71_A	74_I	0.530	0.95
97_H	100_P	0.529	0.95
55_V	59_R	0.529	0.95
41_H	59_R	0.529	0.95
12_R	35_Y	0.527	0.95
72_S	129_E	0.524	0.95
68_G	71_A	0.524	0.95
9_Y	35_Y	0.518	0.95
99_T	105_K	0.518	0.95
28_I	65_I	0.517	0.95
104_L	108_L	0.515	0.95
69_K	72_S	0.512	0.94
17_M	31_V	0.510	0.94
9_Y	115_F	0.510	0.94
98_I	109_S	0.508	0.94
5_S	90_N	0.504	0.94
8_D	88_L	0.501	0.94
90_N	93_S	0.500	0.94
71_A	124_L	0.500	0.94

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
4hf1A	2	0.9787	100	0.227	Contact Map
1xd7A	2	0.8085	100	0.266	Contact Map
4hf0A	3	0.8652	100	0.276	Contact Map
3k69A	2	0.9645	100	0.281	Contact Map
1ylfA	5	0.8511	100	0.295	Contact Map
3lwfA	5	0.9574	100	0.301	Contact Map
4cicA	2	0.922	100	0.308	Contact Map
3t8rA	2	0.8511	99.9	0.346	Contact Map
2y75A	5	0.9007	99.9	0.382	Contact Map
2jscA	2	0.6312	98.5	0.745	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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