NSRR - BACSU - GREMLIN Contacts

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NSRR - HTH-type transcriptional regulator NsrR

UniProt:	O07573	Sequences: MKLTNYTDYSLRVLIFLAAERPGELSNIKQIAETYSISKNHLMKVIYRLGQLGYVETIRGRGGGIRLGMDPEDINIGEVVRKTEDDFNIVECFDANKNLCVISPVCGLKHVLNEALLAYLAVLDKYTLRDLVKNKEDIMKLLKMKE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	146 (134)
Sequences:	5890 (4074)
Seq/√Len:	351.9

ECOLI - ISCR NSRR
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	124_D	3.869	1.00
72_E	129_R	3.019	1.00
92_C	106_C	2.895	1.00
56_E	66_R	2.857	1.00
16_F	34_T	2.830	1.00
10_S	83_T	2.702	1.00
129_R	133_K	2.660	1.00
14_L	54_Y	2.600	1.00
114_E	122_V	2.496	1.00
52_L	82_K	2.384	1.00
69_M	78_E	2.376	1.00
81_R	124_D	2.262	1.00
14_L	128_L	2.237	1.00
77_G	81_R	2.160	1.00
13_V	46_I	2.064	1.00
25_L	66_R	2.040	1.00
18_A	132_V	2.022	1.00
92_C	100_C	1.921	1.00
118_A	122_V	1.909	1.00
17_L	55_V	1.881	1.00
29_K	39_K	1.835	1.00
100_C	106_C	1.773	1.00
118_A	121_A	1.747	1.00
16_F	26_S	1.659	1.00
70_D	73_D	1.647	1.00
29_K	33_E	1.613	1.00
69_M	73_D	1.602	1.00
58_I	66_R	1.592	1.00
114_E	126_Y	1.575	1.00
50_G	57_T	1.509	1.00
75_N	127_T	1.500	1.00
7_T	80_V	1.497	1.00
47_Y	51_Q	1.476	1.00
20_E	24_E	1.452	1.00
37_I	42_L	1.438	1.00
115_A	119_Y	1.432	1.00
13_V	42_L	1.397	1.00
75_N	78_E	1.324	1.00
28_I	46_I	1.311	1.00
122_V	125_K	1.310	1.00
120_L	124_D	1.294	1.00
81_R	120_L	1.283	1.00
116_L	120_L	1.252	1.00
111_V	126_Y	1.203	1.00
16_F	20_E	1.180	1.00
69_M	74_I	1.178	1.00
7_T	84_E	1.165	1.00
13_V	31_I	1.161	1.00
56_E	68_G	1.143	1.00
117_L	121_A	1.108	1.00
16_F	35_Y	1.104	1.00
47_Y	50_G	1.098	1.00
27_N	30_Q	1.095	1.00
114_E	134_N	1.092	1.00
21_R	24_E	1.077	1.00
115_A	123_L	1.074	1.00
6_Y	44_K	1.072	1.00
54_Y	74_I	1.068	1.00
121_A	125_K	1.066	1.00
20_E	26_S	1.051	1.00
9_Y	37_I	1.035	1.00
25_L	58_I	1.029	1.00
80_V	123_L	1.021	1.00
46_I	65_I	1.015	1.00
15_I	132_V	0.997	1.00
8_D	12_R	0.986	1.00
14_L	79_V	0.984	1.00
54_Y	82_K	0.978	1.00
113_N	117_L	0.973	1.00
24_E	30_Q	0.951	1.00
78_E	124_D	0.944	1.00
33_E	39_K	0.940	1.00
11_L	76_I	0.916	1.00
30_Q	34_T	0.900	1.00
110_H	134_N	0.896	1.00
40_N	43_M	0.893	1.00
19_A	132_V	0.890	1.00
115_A	118_A	0.887	1.00
14_L	49_L	0.883	1.00
5_N	41_H	0.874	1.00
17_L	26_S	0.873	1.00
6_Y	48_R	0.872	1.00
28_I	43_M	0.871	1.00
30_Q	33_E	0.870	1.00
77_G	120_L	0.860	1.00
67_L	71_P	0.853	1.00
89_I	116_L	0.852	1.00
46_I	55_V	0.847	1.00
122_V	126_Y	0.841	1.00
48_R	52_L	0.833	1.00
57_T	65_I	0.832	1.00
76_I	111_V	0.819	1.00
127_T	130_D	0.819	1.00
114_E	118_A	0.816	1.00
50_G	55_V	0.816	1.00
47_Y	65_I	0.811	1.00
43_M	65_I	0.810	1.00
87_F	120_L	0.808	1.00
6_Y	10_S	0.804	1.00
47_Y	57_T	0.803	1.00
78_E	81_R	0.801	1.00
21_R	71_P	0.800	1.00
98_N	103_S	0.799	1.00
28_I	39_K	0.794	1.00
6_Y	41_H	0.793	1.00
70_D	129_R	0.785	1.00
114_E	125_K	0.784	1.00
76_I	131_L	0.781	1.00
109_K	113_N	0.774	1.00
68_G	74_I	0.772	1.00
96_N	99_L	0.772	1.00
10_S	45_V	0.768	1.00
54_Y	78_E	0.759	1.00
43_M	50_G	0.753	1.00
16_F	31_I	0.747	1.00
3_L	112_L	0.742	1.00
130_D	133_K	0.738	1.00
81_R	86_D	0.722	0.99
113_N	116_L	0.718	0.99
3_L	80_V	0.718	0.99
39_K	43_M	0.708	0.99
78_E	82_K	0.707	0.99
41_H	45_V	0.705	0.99
9_Y	45_V	0.705	0.99
74_I	79_V	0.704	0.99
80_V	84_E	0.699	0.99
16_F	30_Q	0.685	0.99
38_S	41_H	0.677	0.99
7_T	83_T	0.676	0.99
121_A	124_D	0.664	0.99
111_V	114_E	0.652	0.99
32_A	37_I	0.646	0.99
115_A	122_V	0.643	0.99
74_I	128_L	0.640	0.99
53_G	68_G	0.639	0.99
40_N	44_K	0.637	0.99
112_L	119_Y	0.636	0.99
79_V	128_L	0.629	0.99
79_V	82_K	0.628	0.98
4_T	7_T	0.621	0.98
31_I	46_I	0.621	0.98
54_Y	69_M	0.621	0.98
75_N	125_K	0.620	0.98
71_P	132_V	0.617	0.98
114_E	117_L	0.615	0.98
108_L	112_L	0.614	0.98
75_N	124_D	0.608	0.98
15_I	131_L	0.605	0.98
48_R	51_Q	0.604	0.98
4_T	84_E	0.601	0.98
41_H	59_R	0.601	0.98
52_L	78_E	0.598	0.98
9_Y	41_H	0.597	0.98
44_K	47_Y	0.596	0.98
3_L	7_T	0.588	0.98
72_E	133_K	0.586	0.98
4_T	41_H	0.584	0.98
91_E	94_D	0.582	0.98
92_C	109_K	0.581	0.98
106_C	109_K	0.580	0.97
55_V	59_R	0.579	0.97
129_R	132_V	0.579	0.97
17_L	46_I	0.576	0.97
27_N	62_G	0.576	0.97
50_G	65_I	0.575	0.97
5_N	91_E	0.574	0.97
118_A	123_L	0.573	0.97
8_D	108_L	0.566	0.97
59_R	112_L	0.565	0.97
94_D	98_N	0.562	0.97
19_A	34_T	0.558	0.97
12_R	35_Y	0.553	0.97
68_G	71_P	0.552	0.97
22_P	70_D	0.550	0.97
94_D	97_K	0.547	0.96
72_E	130_D	0.546	0.96
20_E	34_T	0.543	0.96
71_P	74_I	0.543	0.96
88_N	94_D	0.543	0.96
101_V	105_V	0.536	0.96
69_M	72_E	0.534	0.96
19_A	107_G	0.533	0.96
5_N	36_S	0.532	0.96
71_P	128_L	0.528	0.96
103_S	109_K	0.524	0.95
101_V	104_P	0.524	0.95
31_I	35_Y	0.521	0.95
9_Y	35_Y	0.521	0.95
117_L	120_L	0.517	0.95
27_N	59_R	0.517	0.95
36_S	101_V	0.516	0.95
126_Y	131_L	0.513	0.95
21_R	70_D	0.510	0.95
44_K	48_R	0.509	0.95
28_I	65_I	0.508	0.95
111_V	122_V	0.506	0.95
57_T	85_D	0.505	0.94
6_Y	43_M	0.504	0.94
89_I	106_C	0.502	0.94
13_V	45_V	0.500	0.94
102_I	105_V	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	0.9384	100	0.2	Contact Map
1xd7A	2	0.7808	100	0.239	Contact Map
4hf0A	3	0.8356	100	0.252	Contact Map
3k69A	2	0.9452	100	0.275	Contact Map
1ylfA	5	0.8219	100	0.276	Contact Map
3lwfA	5	0.9452	100	0.282	Contact Map
4cicA	2	0.9041	100	0.283	Contact Map
3t8rA	2	0.8288	100	0.326	Contact Map
2y75A	5	0.8767	99.9	0.359	Contact Map
2jscA	2	0.6027	98.4	0.749	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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