YRBC - BACSU - GREMLIN Contacts

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YRBC - Probable transcriptional regulatory protein YrbC

UniProt:	P94447	Sequences: MAGHSKWKNIQKRKNAQDAKRGKIFMKLAKEIYVAAKEGGADPEANSALRLVIEKAKGANMPNENIDRAIKKAAGGQDGSSYEEITYEGYGPSGIAVMVECVTDNKNRTASNVRTAFNKNGGSLGESGCVAFLFERKGFITIDRTERQIEEDELMLDVLEAGGEELRIEEDLYEVFTEPEHFEEVKTALESKYLISSAEVTMLPNTYAEADDQAVEKLETLIDVLEDDDDVQEVYTNYRS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	240 (230)
Sequences:	3293 (1727)
Seq/√Len:	113.9

ECOLI - YEBC YEEN
BACSU - YRBC YEEI

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
135_E	205_N	4.314	1.00
67_D	71_K	3.616	1.00
112_N	228_D	3.551	1.00
13_R	17_Q	3.324	1.00
43_P	53_I	2.880	1.00
99_V	117_F	2.845	1.00
150_E	153_E	2.786	1.00
211_D	214_A	2.717	1.00
41_A	74_A	2.629	1.00
187_T	191_S	2.387	1.00
125_G	129_C	2.325	1.00
16_A	20_K	2.294	1.00
209_E	239_R	2.289	1.00
210_A	218_L	2.118	1.00
181_H	184_E	2.094	1.00
8_K	11_Q	2.086	1.00
138_G	177_T	2.071	1.00
116_A	228_D	2.058	1.00
153_E	156_L	2.053	1.00
89_G	117_F	1.963	1.00
143_D	196_S	1.935	1.00
182_F	198_A	1.879	1.00
156_L	160_E	1.821	1.00
158_V	163_G	1.807	1.00
11_Q	15_N	1.778	1.00
207_Y	239_R	1.775	1.00
28_L	59_A	1.771	1.00
139_F	201_T	1.761	1.00
83_E	106_K	1.716	1.00
31_E	48_A	1.701	1.00
101_C	109_T	1.698	1.00
177_T	185_V	1.693	1.00
120_N	224_V	1.688	1.00
164_E	181_H	1.680	1.00
86_T	100_E	1.641	1.00
178_E	181_H	1.637	1.00
65_N	68_R	1.614	1.00
9_N	13_R	1.567	1.00
157_D	192_K	1.562	1.00
210_A	214_A	1.555	1.00
97_V	221_L	1.551	1.00
221_L	225_L	1.549	1.00
62_P	65_N	1.525	1.00
183_E	187_T	1.498	1.00
9_N	17_Q	1.492	1.00
161_A	188_A	1.448	1.00
36_A	74_A	1.442	1.00
222_I	226_E	1.435	1.00
7_W	11_Q	1.426	1.00
116_A	224_V	1.411	1.00
140_I	182_F	1.411	1.00
69_A	73_A	1.408	1.00
140_I	177_T	1.400	1.00
115_T	118_N	1.394	1.00
86_T	98_M	1.392	1.00
186_K	190_E	1.389	1.00
151_E	168_I	1.387	1.00
149_I	154_L	1.386	1.00
204_P	207_Y	1.380	1.00
100_E	233_E	1.378	1.00
179_P	200_V	1.375	1.00
158_V	166_L	1.363	1.00
63_N	67_D	1.361	1.00
167_R	176_F	1.360	1.00
157_D	193_Y	1.340	1.00
214_A	217_K	1.339	1.00
120_N	220_T	1.330	1.00
89_G	99_V	1.326	1.00
213_Q	217_K	1.323	1.00
51_L	55_K	1.319	1.00
53_I	66_I	1.317	1.00
161_A	185_V	1.307	1.00
93_S	214_A	1.305	1.00
144_R	168_I	1.304	1.00
164_E	178_E	1.290	0.99
34_V	102_V	1.279	0.99
8_K	12_K	1.273	0.99
151_E	155_M	1.270	0.99
86_T	202_M	1.270	0.99
97_V	117_F	1.266	0.99
25_F	61_M	1.264	0.99
213_Q	216_E	1.261	0.99
142_I	175_V	1.249	0.99
137_K	164_E	1.247	0.99
141_T	174_E	1.235	0.99
85_I	101_C	1.221	0.99
139_F	174_E	1.212	0.99
218_L	238_Y	1.211	0.99
168_I	173_Y	1.201	0.99
97_V	218_L	1.198	0.99
53_I	70_I	1.195	0.99
42_D	45_A	1.192	0.99
90_Y	96_A	1.191	0.99
91_G	218_L	1.178	0.99
137_K	203_L	1.173	0.99
222_I	236_T	1.170	0.99
85_I	106_K	1.163	0.99
155_M	159_L	1.143	0.99
190_E	195_I	1.127	0.99
9_N	12_K	1.116	0.98
70_I	73_A	1.113	0.98
144_R	171_D	1.107	0.98
124_L	127_S	1.100	0.98
113_V	228_D	1.079	0.98
53_I	57_K	1.077	0.98
187_T	190_E	1.076	0.98
188_A	192_K	1.074	0.98
12_K	16_A	1.072	0.98
188_A	191_S	1.071	0.98
142_I	195_I	1.067	0.98
77_Q	80_S	1.056	0.98
24_I	59_A	1.054	0.98
57_K	63_N	1.045	0.98
132_F	206_T	1.041	0.98
153_E	157_D	1.035	0.97
57_K	62_P	1.024	0.97
14_K	18_D	1.016	0.97
167_R	174_E	1.014	0.97
93_S	218_L	1.006	0.97
212_D	216_E	1.005	0.97
33_Y	73_A	1.003	0.97
111_S	115_T	0.976	0.96
64_E	68_R	0.975	0.96
141_T	172_L	0.974	0.96
139_F	203_L	0.970	0.96
6_K	11_Q	0.968	0.96
91_G	97_V	0.967	0.96
220_T	223_D	0.955	0.96
115_T	120_N	0.954	0.96
154_L	173_Y	0.950	0.96
9_N	21_R	0.949	0.96
212_D	215_V	0.948	0.96
74_A	77_Q	0.944	0.96
140_I	186_K	0.942	0.96
172_L	196_S	0.939	0.96
100_E	136_R	0.937	0.95
133_L	205_N	0.922	0.95
27_K	227_D	0.917	0.95
115_T	119_K	0.917	0.95
21_R	25_F	0.915	0.95
151_E	173_Y	0.908	0.95
215_V	238_Y	0.905	0.95
10_I	18_D	0.905	0.95
87_Y	106_K	0.904	0.95
95_I	238_Y	0.902	0.94
163_G	175_V	0.901	0.94
226_E	234_V	0.896	0.94
183_E	186_K	0.889	0.94
10_I	13_R	0.880	0.94
55_K	199_E	0.877	0.94
24_I	28_L	0.872	0.93
33_Y	72_K	0.868	0.93
15_N	21_R	0.863	0.93
89_G	125_G	0.861	0.93
71_K	77_Q	0.857	0.93
41_A	70_I	0.855	0.93
61_M	65_N	0.855	0.93
126_E	132_F	0.852	0.93
137_K	178_E	0.852	0.93
93_S	210_A	0.851	0.93
166_L	175_V	0.849	0.92
95_I	218_L	0.848	0.92
12_K	15_N	0.846	0.92
6_K	9_N	0.841	0.92
169_E	174_E	0.840	0.92
95_I	210_A	0.833	0.92
139_F	176_F	0.832	0.92
136_R	202_M	0.831	0.92
182_F	200_V	0.830	0.92
11_Q	17_Q	0.830	0.92
132_F	205_N	0.826	0.91
219_E	238_Y	0.825	0.91
68_R	71_K	0.825	0.91
74_A	78_D	0.822	0.91
38_E	48_A	0.819	0.91
208_A	237_N	0.819	0.91
190_E	194_L	0.819	0.91
54_E	186_K	0.817	0.91
157_D	161_A	0.809	0.91
10_I	14_K	0.804	0.90
98_M	131_A	0.804	0.90
10_I	15_N	0.801	0.90
116_A	120_N	0.799	0.90
156_L	159_L	0.796	0.90
7_W	18_D	0.795	0.90
184_E	187_T	0.793	0.90
116_A	225_L	0.791	0.90
99_V	231_V	0.791	0.90
51_L	54_E	0.790	0.89
176_F	203_L	0.788	0.89
210_A	215_V	0.788	0.89
124_L	225_L	0.786	0.89
144_R	173_Y	0.784	0.89
132_F	208_A	0.783	0.89
169_E	172_L	0.783	0.89
28_L	66_I	0.775	0.89
48_A	51_L	0.775	0.89
101_C	126_E	0.774	0.89
23_K	227_D	0.774	0.89
91_G	95_I	0.773	0.88
141_T	197_S	0.772	0.88
18_D	21_R	0.770	0.88
15_N	19_A	0.766	0.88
19_A	22_G	0.764	0.88
32_I	66_I	0.764	0.88
166_L	173_Y	0.761	0.88
133_L	206_T	0.759	0.88
17_Q	20_K	0.753	0.87
140_I	195_I	0.752	0.87
117_F	124_L	0.751	0.87
62_P	68_R	0.749	0.87
216_E	219_E	0.748	0.87
85_I	103_T	0.746	0.87
29_A	33_Y	0.744	0.86
186_K	198_A	0.743	0.86
218_L	236_T	0.732	0.86
28_L	31_E	0.731	0.86
97_V	222_I	0.730	0.85
29_A	65_N	0.730	0.85
216_E	220_T	0.728	0.85
36_A	73_A	0.722	0.85
220_T	224_V	0.720	0.85
87_Y	110_A	0.716	0.84
36_A	41_A	0.715	0.84
110_A	124_L	0.711	0.84
29_A	61_M	0.708	0.84
142_I	173_Y	0.706	0.84
15_N	18_D	0.704	0.83
31_E	50_R	0.697	0.83
215_V	219_E	0.696	0.83
90_Y	130_V	0.689	0.82
149_I	153_E	0.687	0.82
47_S	50_R	0.680	0.81
137_K	176_F	0.680	0.81
82_Y	102_V	0.679	0.81
40_G	46_N	0.678	0.81
18_D	22_G	0.677	0.81
142_I	193_Y	0.676	0.81
140_I	189_L	0.670	0.80
6_K	18_D	0.669	0.80
12_K	17_Q	0.665	0.80
46_N	49_L	0.662	0.79
26_M	33_Y	0.656	0.79
40_G	45_A	0.653	0.78
89_G	122_G	0.653	0.78
78_D	81_S	0.653	0.78
30_K	109_T	0.649	0.78
36_A	69_A	0.648	0.78
119_K	224_V	0.648	0.78
35_A	52_V	0.641	0.77
20_K	23_K	0.640	0.77
153_E	193_Y	0.639	0.77
153_E	160_E	0.639	0.77
28_L	52_V	0.639	0.77
72_K	82_Y	0.638	0.77
219_E	223_D	0.636	0.77
210_A	238_Y	0.635	0.77
27_K	30_K	0.635	0.77
182_F	195_I	0.634	0.76
48_A	52_V	0.633	0.76
222_I	238_Y	0.628	0.76
136_R	200_V	0.628	0.76
54_E	58_G	0.624	0.75
23_K	47_S	0.618	0.75
15_N	57_K	0.617	0.74
10_I	21_R	0.614	0.74
54_E	197_S	0.612	0.74
201_T	235_Y	0.611	0.74
102_V	232_Q	0.608	0.73
90_Y	126_E	0.607	0.73
144_R	154_L	0.606	0.73
142_I	189_L	0.606	0.73
110_A	114_R	0.603	0.73
151_E	159_L	0.601	0.73
154_L	166_L	0.601	0.73
109_T	113_V	0.601	0.73
158_V	162_G	0.597	0.72
113_V	116_A	0.597	0.72
159_L	163_G	0.596	0.72
98_M	127_S	0.593	0.72
8_K	13_R	0.592	0.71
75_G	232_Q	0.592	0.71
112_N	115_T	0.590	0.71
117_F	221_L	0.588	0.71
84_E	100_E	0.588	0.71
130_V	133_L	0.587	0.71
86_T	136_R	0.586	0.71
30_K	38_E	0.586	0.71
107_N	111_S	0.585	0.71
185_V	188_A	0.584	0.70
115_T	224_V	0.583	0.70
50_R	61_M	0.582	0.70
141_T	167_R	0.575	0.69
39_G	46_N	0.571	0.69
111_S	118_N	0.568	0.68
87_Y	230_D	0.568	0.68
7_W	10_I	0.567	0.68
20_K	24_I	0.564	0.68
107_N	110_A	0.564	0.68
13_R	16_A	0.560	0.67
77_Q	81_S	0.557	0.67
35_A	39_G	0.556	0.67
73_A	132_F	0.556	0.67
25_F	50_R	0.555	0.67
15_N	59_A	0.554	0.66
110_A	127_S	0.554	0.66
17_Q	21_R	0.553	0.66
109_T	228_D	0.553	0.66
99_V	113_V	0.552	0.66
135_E	164_E	0.551	0.66
184_E	188_A	0.549	0.66
95_I	208_A	0.541	0.65
7_W	14_K	0.540	0.64
96_A	125_G	0.539	0.64
98_M	202_M	0.537	0.64
77_Q	84_E	0.534	0.64
155_M	158_V	0.534	0.64
48_A	84_E	0.534	0.64
209_E	212_D	0.534	0.64
28_L	61_M	0.533	0.63
106_K	110_A	0.531	0.63
182_F	199_E	0.530	0.63
84_E	102_V	0.530	0.63
10_I	17_Q	0.530	0.63
119_K	237_N	0.529	0.63
97_V	236_T	0.528	0.63
173_Y	193_Y	0.520	0.62
47_S	52_V	0.519	0.61
62_P	82_Y	0.519	0.61
10_I	16_A	0.519	0.61
150_E	156_L	0.518	0.61
101_C	110_A	0.518	0.61
61_M	140_I	0.516	0.61
22_G	28_L	0.515	0.61
106_K	126_E	0.515	0.61
90_Y	125_G	0.514	0.61
24_I	60_N	0.511	0.60
55_K	233_E	0.510	0.60
150_E	184_E	0.506	0.59
9_N	16_A	0.505	0.59
109_T	124_L	0.504	0.59
51_L	62_P	0.504	0.59
163_G	166_L	0.503	0.59
29_A	72_K	0.501	0.59
140_I	185_V	0.500	0.59

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
1lfpA	1	0.975	100	0.013	Contact Map
1konA	1	0.925	100	0.019	Contact Map
4f3qA	1	0.9458	100	0.025	Contact Map
1mw7A	1	0.8875	100	0.066	Contact Map
4pt7A	3	0.4583	57.8	0.954	Contact Map
2jsxA	1	0.3167	54.5	0.955	Contact Map
4ptaD	3	0.4208	47.7	0.957	Contact Map
2ra5A	2	0.3833	42.4	0.958	Contact Map
1pdnC	1	0.4833	38.5	0.959	Contact Map
4h0eA	2	0.3375	34.3	0.96	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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