YJHU - ECOLI - GREMLIN Contacts

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YJHU - Uncharacterized transcriptional regulator YjhU

UniProt:	P39356	Sequences: MDRDQTNSSLFNDDPVLHATWLYYQEGKSQTEVAAIMGVSRVTVVKYLQTARENGLVHINLDVNVFGSIDAALQIRDKFNLQRVIIVPDGEHAGKRDDTKLMRTRLSRAGGMYLNQVIENGDVLGVAWGRTIHQMSKTMTPKSCKNVTVIQMLGSMPSQPDLTIIESSSQIAYKLSGRVASLHVPAVVSSARLAMELQAEPIIRSNFDVLTRCTKAFFVVGNALDENPLIRVGVLNKKEMQTYRDLGAVGVICGRFYDKEGMPVVADVDQRILGISLAQLRQIERKIFLAGGERGYDATLGALLGGYVTDLIVDEGTAEFLLACELPH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12604
Length:	328 (305)
Sequences:	2211 (1719)
Seq/√Len:	98.4

ECOLI - YJHU LSRR
BACSU - DEOR CGGR

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
258_D	262_M	7.096	1.00
211_T	279_Q	4.153	1.00
125_G	213_C	3.523	1.00
106_L	291_G	3.276	1.00
259_K	297_D	2.951	1.00
299_T	317_T	2.901	1.00
58_H	62_D	2.863	1.00
79_F	300_L	2.857	1.00
122_D	214_T	2.853	1.00
79_F	303_L	2.792	1.00
257_Y	301_G	2.722	1.00
220_V	288_F	2.683	1.00
300_L	304_L	2.638	1.00
313_V	317_T	2.546	1.00
288_F	308_V	2.539	1.00
113_Y	312_I	2.536	1.00
28_K	36_I	2.497	1.00
194_A	198_Q	2.476	1.00
110_G	289_L	2.450	1.00
149_V	175_L	2.358	1.00
320_F	323_A	2.203	1.00
204_R	208_D	2.194	1.00
74_Q	77_D	2.158	1.00
250_G	301_G	2.156	1.00
123_V	209_V	2.142	1.00
87_V	109_A	2.138	1.00
219_V	288_F	2.129	1.00
214_T	284_E	2.111	1.00
290_A	299_T	2.067	1.00
49_Q	53_E	2.061	1.00
285_R	310_D	2.024	1.00
296_Y	320_F	2.014	1.00
250_G	257_Y	1.994	1.00
121_G	146_N	1.980	1.00
296_Y	321_L	1.958	1.00
110_G	135_M	1.952	1.00
50_T	54_N	1.935	1.00
85_I	109_A	1.930	1.00
296_Y	317_T	1.882	1.00
151_Q	165_I	1.875	1.00
276_S	279_Q	1.873	1.00
135_M	289_L	1.849	1.00
188_V	193_L	1.839	1.00
103_R	130_R	1.813	1.00
136_S	167_S	1.805	1.00
241_Q	245_D	1.805	1.00
73_L	76_R	1.780	1.00
191_A	270_Q	1.779	1.00
75_I	84_V	1.775	1.00
286_K	309_T	1.762	1.00
300_L	321_L	1.760	1.00
88_P	315_E	1.746	1.00
123_V	213_C	1.746	1.00
148_T	180_A	1.741	1.00
215_K	287_I	1.740	1.00
83_R	310_D	1.712	1.00
210_L	213_C	1.706	1.00
218_F	286_K	1.672	1.00
213_C	283_I	1.662	1.00
19_A	39_V	1.661	1.00
152_M	216_A	1.661	1.00
123_V	212_R	1.652	1.00
191_A	195_M	1.640	1.00
189_S	201_P	1.635	1.00
257_Y	298_A	1.623	1.00
218_F	288_F	1.612	1.00
76_R	84_V	1.605	1.00
82_Q	285_R	1.599	1.00
139_M	171_I	1.575	1.00
113_Y	310_D	1.558	1.00
19_A	33_V	1.556	1.00
118_I	124_L	1.542	1.00
292_G	314_D	1.486	1.00
104_T	138_T	1.472	1.00
259_K	301_G	1.468	1.00
16_V	47_Y	1.459	1.00
236_N	239_E	1.456	1.00
172_A	179_V	1.453	1.00
127_A	253_C	1.444	1.00
42_V	45_V	1.435	1.00
260_E	304_L	1.432	1.00
220_V	298_A	1.432	1.00
107_S	134_Q	1.429	1.00
239_E	271_R	1.427	1.00
113_Y	117_V	1.415	1.00
76_R	83_R	1.392	0.99
124_L	215_K	1.378	0.99
137_K	170_Q	1.368	0.99
293_E	320_F	1.356	0.99
315_E	319_E	1.352	0.99
148_T	209_V	1.328	0.99
266_A	269_D	1.306	0.99
24_Y	59_I	1.295	0.99
242_T	246_L	1.288	0.99
125_G	152_M	1.287	0.99
299_T	313_V	1.282	0.99
124_L	149_V	1.279	0.99
16_V	56_L	1.269	0.99
207_F	210_L	1.262	0.99
258_D	264_V	1.257	0.99
19_A	37_M	1.256	0.99
189_S	200_E	1.248	0.99
111_G	139_M	1.248	0.99
170_Q	173_Y	1.232	0.99
28_K	32_E	1.227	0.99
134_Q	137_K	1.215	0.99
27_G	52_R	1.214	0.99
216_A	283_I	1.213	0.99
114_L	215_K	1.213	0.99
180_A	209_V	1.211	0.99
70_D	74_Q	1.205	0.98
242_T	245_D	1.204	0.98
136_S	171_I	1.193	0.98
188_V	197_L	1.187	0.98
78_K	321_L	1.180	0.98
21_W	25_Q	1.178	0.98
125_G	128_W	1.173	0.98
208_D	212_R	1.170	0.98
135_M	217_F	1.165	0.98
123_V	214_T	1.161	0.98
290_A	313_V	1.154	0.98
19_A	47_Y	1.146	0.98
15_P	47_Y	1.133	0.98
203_I	207_F	1.105	0.97
117_V	285_R	1.098	0.97
16_V	50_T	1.094	0.97
122_D	215_K	1.092	0.97
155_S	251_V	1.081	0.97
75_I	86_I	1.079	0.97
114_L	217_F	1.074	0.97
73_L	77_D	1.069	0.97
120_N	145_K	1.061	0.97
34_A	44_V	1.056	0.97
74_Q	78_K	1.054	0.96
255_R	274_G	1.053	0.96
22_L	36_I	1.052	0.96
17_L	56_L	1.045	0.96
44_V	48_L	1.034	0.96
241_Q	244_R	1.032	0.96
303_L	308_V	1.029	0.96
23_Y	41_R	1.022	0.96
155_S	163_T	1.015	0.96
136_S	170_Q	1.013	0.96
148_T	178_R	1.010	0.95
78_K	322_L	1.007	0.95
75_I	322_L	1.006	0.95
255_R	269_D	1.004	0.95
220_V	299_T	1.004	0.95
195_M	199_A	1.002	0.95
193_L	200_E	1.001	0.95
75_I	321_L	1.001	0.95
208_D	211_T	0.995	0.95
197_L	273_L	0.985	0.95
13_D	64_N	0.980	0.95
168_S	179_V	0.980	0.95
257_Y	302_A	0.973	0.94
151_Q	163_T	0.971	0.94
222_N	227_N	0.971	0.94
83_R	116_Q	0.964	0.94
218_F	308_V	0.964	0.94
259_K	300_L	0.954	0.94
219_V	290_A	0.950	0.94
216_A	280_L	0.949	0.94
229_L	232_V	0.941	0.93
79_F	84_V	0.939	0.93
205_S	208_D	0.934	0.93
85_I	113_Y	0.933	0.93
319_E	323_A	0.931	0.93
82_Q	309_T	0.929	0.93
259_K	304_L	0.928	0.93
265_V	269_D	0.927	0.93
16_V	19_A	0.925	0.93
29_S	41_R	0.924	0.93
29_S	32_E	0.919	0.93
124_L	171_I	0.917	0.93
166_E	169_S	0.915	0.92
106_L	110_G	0.912	0.92
314_D	317_T	0.911	0.92
127_A	255_R	0.903	0.92
68_S	72_A	0.900	0.92
277_L	307_Y	0.897	0.92
128_W	255_R	0.897	0.92
186_A	254_G	0.893	0.92
123_V	150_I	0.890	0.91
251_V	254_G	0.888	0.91
128_W	251_V	0.887	0.91
265_V	270_Q	0.881	0.91
89_D	316_G	0.880	0.91
119_E	122_D	0.879	0.91
217_F	287_I	0.871	0.90
302_A	305_G	0.869	0.90
127_A	151_Q	0.866	0.90
243_Y	248_A	0.861	0.90
296_Y	300_L	0.840	0.89
108_R	138_T	0.836	0.89
237_K	241_Q	0.835	0.89
126_V	171_I	0.833	0.88
199_A	204_R	0.827	0.88
45_V	63_V	0.826	0.88
184_V	273_L	0.825	0.88
42_V	63_V	0.815	0.87
48_L	52_R	0.812	0.87
74_Q	319_E	0.810	0.87
157_P	163_T	0.809	0.87
33_V	61_L	0.807	0.87
19_A	22_L	0.806	0.87
114_L	135_M	0.803	0.87
165_I	183_H	0.799	0.86
22_L	30_Q	0.799	0.86
275_I	283_I	0.796	0.86
149_V	177_G	0.796	0.86
20_T	48_L	0.796	0.86
196_E	200_E	0.796	0.86
81_L	311_L	0.791	0.86
248_A	264_V	0.789	0.86
301_G	304_L	0.789	0.86
219_V	299_T	0.788	0.86
107_S	291_G	0.788	0.86
106_L	289_L	0.786	0.85
288_F	299_T	0.785	0.85
168_S	172_A	0.784	0.85
92_H	316_G	0.782	0.85
219_V	308_V	0.782	0.85
134_Q	219_V	0.777	0.85
15_P	18_H	0.775	0.85
21_W	63_V	0.775	0.85
187_V	272_I	0.774	0.84
31_T	35_A	0.774	0.84
22_L	33_V	0.773	0.84
19_A	44_V	0.772	0.84
15_P	39_V	0.769	0.84
13_D	54_N	0.763	0.84
301_G	305_G	0.762	0.84
68_S	86_I	0.761	0.83
187_V	271_R	0.760	0.83
126_V	167_S	0.759	0.83
71_A	86_I	0.758	0.83
188_V	273_L	0.758	0.83
186_A	223_A	0.753	0.83
198_Q	207_F	0.748	0.82
113_Y	287_I	0.745	0.82
118_I	175_L	0.743	0.82
278_A	281_R	0.741	0.82
79_F	321_L	0.740	0.82
39_V	44_V	0.739	0.82
71_A	319_E	0.738	0.82
291_G	299_T	0.736	0.81
306_G	309_T	0.736	0.81
110_G	219_V	0.730	0.81
21_W	45_V	0.724	0.80
119_E	214_T	0.724	0.80
128_W	151_Q	0.723	0.80
152_M	253_C	0.721	0.80
290_A	295_G	0.719	0.80
106_L	313_V	0.718	0.80
18_H	21_W	0.718	0.80
24_Y	48_L	0.717	0.80
75_I	79_F	0.716	0.80
170_Q	174_K	0.715	0.79
113_Y	116_Q	0.713	0.79
33_V	46_K	0.711	0.79
208_D	297_D	0.710	0.79
30_Q	45_V	0.709	0.79
291_G	317_T	0.704	0.78
208_D	323_A	0.702	0.78
117_V	309_T	0.700	0.78
275_I	279_Q	0.700	0.78
17_L	63_V	0.700	0.78
115_N	175_L	0.694	0.77
292_G	295_G	0.693	0.77
205_S	209_V	0.692	0.77
219_V	272_I	0.692	0.77
22_L	28_K	0.691	0.77
171_I	298_A	0.689	0.77
117_V	215_K	0.688	0.77
255_R	272_I	0.682	0.76
182_L	273_L	0.682	0.76
129_G	315_E	0.680	0.76
188_V	203_I	0.680	0.76
221_G	251_V	0.680	0.76
120_N	146_N	0.680	0.76
140_T	174_K	0.679	0.76
68_S	88_P	0.678	0.76
57_V	61_L	0.678	0.76
110_G	312_I	0.678	0.76
30_Q	42_V	0.672	0.75
81_L	309_T	0.671	0.75
31_T	41_R	0.668	0.75
87_V	106_L	0.666	0.75
124_L	260_E	0.664	0.74
41_R	52_R	0.659	0.74
151_Q	183_H	0.656	0.73
84_V	104_T	0.656	0.73
70_D	284_E	0.654	0.73
20_T	51_A	0.651	0.73
19_A	43_T	0.645	0.72
47_Y	179_V	0.642	0.72
118_I	147_V	0.639	0.71
226_E	229_L	0.637	0.71
151_Q	200_E	0.635	0.71
185_P	188_V	0.635	0.71
47_Y	51_A	0.635	0.71
287_I	309_T	0.633	0.71
192_R	195_M	0.632	0.71
87_V	102_M	0.630	0.70
73_L	316_G	0.628	0.70
42_V	186_A	0.628	0.70
149_V	171_I	0.626	0.70
252_I	302_A	0.626	0.70
280_L	283_I	0.626	0.70
195_M	269_D	0.625	0.70
18_H	76_R	0.623	0.70
84_V	303_L	0.623	0.70
242_T	267_D	0.622	0.69
42_V	153_L	0.620	0.69
14_D	21_W	0.618	0.69
46_K	271_R	0.617	0.69
45_V	251_V	0.617	0.69
169_S	183_H	0.617	0.69
193_L	197_L	0.616	0.69
150_I	206_N	0.613	0.68
44_V	280_L	0.611	0.68
104_T	134_Q	0.611	0.68
214_T	283_I	0.611	0.68
299_T	311_L	0.611	0.68
34_A	141_P	0.610	0.68
117_V	310_D	0.607	0.68
255_R	276_S	0.606	0.67
151_Q	224_L	0.606	0.67
46_K	183_H	0.605	0.67
72_A	84_V	0.603	0.67
263_P	277_L	0.602	0.67
127_A	180_A	0.600	0.67
269_D	276_S	0.600	0.67
37_M	109_A	0.598	0.66
23_Y	30_Q	0.597	0.66
128_W	152_M	0.595	0.66
80_N	306_G	0.595	0.66
23_Y	45_V	0.595	0.66
112_M	115_N	0.595	0.66
222_N	244_R	0.594	0.66
22_L	26_E	0.594	0.66
104_T	137_K	0.593	0.66
78_K	304_L	0.593	0.66
153_L	186_A	0.591	0.66
249_V	301_G	0.591	0.66
226_E	294_R	0.591	0.66
126_V	164_I	0.590	0.65
211_T	282_Q	0.590	0.65
249_V	264_V	0.589	0.65
200_E	254_G	0.588	0.65
132_I	167_S	0.588	0.65
248_A	256_F	0.587	0.65
33_V	110_G	0.586	0.65
85_I	310_D	0.584	0.65
223_A	298_A	0.583	0.64
269_D	272_I	0.581	0.64
15_P	37_M	0.580	0.64
118_I	144_C	0.580	0.64
207_F	273_L	0.579	0.64
149_V	168_S	0.579	0.64
122_D	146_N	0.578	0.64
41_R	186_A	0.578	0.64
15_P	72_A	0.577	0.64
208_D	242_T	0.577	0.64
291_G	314_D	0.572	0.63
152_M	210_L	0.572	0.63
155_S	184_V	0.571	0.63
165_I	219_V	0.571	0.63
14_D	72_A	0.570	0.63
155_S	165_I	0.570	0.63
25_Q	127_A	0.570	0.63
73_L	293_E	0.569	0.63
302_A	306_G	0.568	0.62
48_L	251_V	0.568	0.62
220_V	308_V	0.567	0.62
42_V	61_L	0.567	0.62
117_V	287_I	0.566	0.62
143_S	176_S	0.565	0.62
89_D	314_D	0.564	0.62
136_S	174_K	0.564	0.62
81_L	310_D	0.564	0.62
308_V	311_L	0.564	0.62
62_D	200_E	0.561	0.62
193_L	196_E	0.561	0.62
88_P	109_A	0.561	0.62
48_L	64_N	0.559	0.61
163_T	254_G	0.555	0.61
16_V	51_A	0.555	0.61
74_Q	80_N	0.555	0.61
188_V	280_L	0.553	0.60
133_H	170_Q	0.551	0.60
87_V	268_V	0.551	0.60
32_E	89_D	0.551	0.60
143_S	192_R	0.551	0.60
110_G	113_Y	0.550	0.60
103_R	289_L	0.549	0.60
21_W	151_Q	0.547	0.60
68_S	315_E	0.546	0.59
295_G	314_D	0.545	0.59
83_R	113_Y	0.545	0.59
268_V	272_I	0.544	0.59
298_A	301_G	0.543	0.59
255_R	277_L	0.542	0.59
149_V	172_A	0.542	0.59
121_G	142_K	0.541	0.59
125_G	132_I	0.540	0.59
243_Y	256_F	0.540	0.59
102_M	291_G	0.539	0.58
141_P	176_S	0.539	0.58
118_I	142_K	0.538	0.58
149_V	255_R	0.538	0.58
89_D	172_A	0.537	0.58
74_Q	322_L	0.536	0.58
131_T	292_G	0.536	0.58
115_N	140_T	0.535	0.58
164_I	274_G	0.530	0.57
43_T	47_Y	0.529	0.57
40_S	185_P	0.529	0.57
218_F	309_T	0.528	0.57
189_S	193_L	0.528	0.57
210_L	275_I	0.527	0.57
13_D	21_W	0.526	0.57
115_N	142_K	0.525	0.57
211_T	241_Q	0.524	0.56
268_V	289_L	0.524	0.56
48_L	57_V	0.523	0.56
150_I	193_L	0.523	0.56
187_V	191_A	0.523	0.56
186_A	251_V	0.522	0.56
51_A	63_V	0.520	0.56
114_L	171_I	0.519	0.56
267_D	296_Y	0.519	0.56
41_R	45_V	0.518	0.56
92_H	101_L	0.517	0.55
107_S	264_V	0.517	0.55
238_K	245_D	0.516	0.55
186_A	256_F	0.515	0.55
293_E	316_G	0.515	0.55
303_L	321_L	0.514	0.55
129_G	272_I	0.513	0.55
18_H	315_E	0.512	0.55
242_T	266_A	0.511	0.55
192_R	212_R	0.510	0.54
210_L	254_G	0.509	0.54
127_A	136_S	0.508	0.54
208_D	238_K	0.508	0.54
310_D	313_V	0.508	0.54
78_K	262_M	0.506	0.54
77_D	262_M	0.506	0.54
238_K	241_Q	0.505	0.54
102_M	314_D	0.504	0.54
70_D	281_R	0.504	0.54
40_S	64_N	0.502	0.53
290_A	317_T	0.501	0.53
282_Q	323_A	0.501	0.53
152_M	275_I	0.500	0.53
226_E	257_Y	0.500	0.53

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
2w48A	3	0.9451	100	0.388	Contact Map
4l5jA	4	0.9268	100	0.395	Contact Map
4l4yA	2	0.7256	100	0.461	Contact Map
3efbA	2	0.7561	100	0.468	Contact Map
2r5fA	1	0.6555	100	0.481	Contact Map
2o0mA	1	0.7409	100	0.482	Contact Map
3kv1A	2	0.7652	100	0.485	Contact Map
2gnpA	1	0.7957	100	0.486	Contact Map
4r9nA	1	0.753	100	0.488	Contact Map
4oqpA	2	0.7713	100	0.49	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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