DUSA - ECOLI - GREMLIN Contacts

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DUSA - tRNA-dihydrouridine synthase A

UniProt:	P32695	Sequences: MHGNSEMQKINQTSAMPEKTDVHWSGRFSVAPMLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHGKGDYLAYSEEEHPVALQLGGSDPAALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVTVKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRVYQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDTDADPVAVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLSENAHKAGADINVLEHALKLVADKR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11932
Length:	345 (297)
Sequences:	6475 (3880)
Seq/√Len:	225.1

ECOLI - DUSA DUSB DUSC
BACSU - DUS1 DUS2
HALSA - Q9HPX3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
47_L	281_A	4.768	1.00
215_K	243_D	4.348	1.00
231_S	234_E	3.279	1.00
101_E	147_S	3.228	1.00
230_K	234_E	2.986	1.00
143_R	181_E	2.884	1.00
237_A	241_H	2.764	1.00
79_H	106_D	2.580	1.00
175_S	220_H	2.570	1.00
139_V	180_C	2.473	1.00
212_Y	216_R	2.439	1.00
209_P	241_H	2.334	1.00
140_K	144_D	2.332	1.00
93_L	110_L	2.267	1.00
225_I	238_H	2.218	1.00
236_K	240_Q	2.170	1.00
130_G	158_I	2.149	1.00
41_C	45_L	2.111	1.00
97_A	146_V	2.080	1.00
156_I	210_R	2.024	1.00
213_Q	216_R	2.024	1.00
236_K	264_E	2.014	1.00
175_S	221_L	1.935	1.00
136_A	177_K	1.931	1.00
95_Q	98_K	1.927	1.00
112_V	135_V	1.904	1.00
229_I	238_H	1.871	1.00
146_V	150_V	1.863	1.00
211_V	225_I	1.820	1.00
325_H	328_G	1.811	1.00
91_A	95_Q	1.809	1.00
237_A	240_Q	1.805	1.00
230_K	250_E	1.795	1.00
280_R	330_D	1.789	1.00
212_Y	241_H	1.787	1.00
131_N	134_L	1.783	1.00
207_D	210_R	1.781	1.00
82_A	107_E	1.775	1.00
133_Q	137_D	1.769	1.00
136_A	173_T	1.749	1.00
234_E	237_A	1.727	1.00
318_R	322_E	1.722	1.00
284_P	330_D	1.718	1.00
83_L	100_A	1.712	1.00
98_K	145_V	1.706	1.00
263_R	267_G	1.700	1.00
135_V	170_F	1.696	1.00
123_M	131_N	1.673	1.00
235_A	245_V	1.663	1.00
53_L	82_A	1.662	1.00
93_L	142_M	1.662	1.00
168_C	217_D	1.623	1.00
200_N	207_D	1.619	1.00
52_T	262_D	1.616	1.00
136_A	176_G	1.606	1.00
136_A	140_K	1.597	1.00
169_D	172_N	1.596	1.00
172_N	217_D	1.593	1.00
154_T	185_I	1.586	1.00
133_Q	173_T	1.584	1.00
29_S	224_S	1.579	1.00
89_D	92_A	1.563	1.00
224_S	246_M	1.557	1.00
225_I	229_I	1.553	1.00
167_L	214_L	1.552	1.00
282_M	306_L	1.552	1.00
159_D	162_D	1.551	1.00
212_Y	238_H	1.547	1.00
263_R	271_T	1.529	1.00
206_L	228_G	1.522	1.00
182_M	224_S	1.510	1.00
94_A	145_V	1.505	1.00
224_S	244_G	1.502	1.00
210_R	213_Q	1.490	1.00
137_D	140_K	1.460	1.00
134_L	137_D	1.457	1.00
90_P	94_A	1.442	1.00
87_G	93_L	1.440	1.00
259_A	274_D	1.439	1.00
110_L	142_M	1.437	1.00
101_E	148_I	1.428	1.00
233_E	237_A	1.423	1.00
101_E	146_V	1.422	1.00
152_V	174_V	1.409	1.00
100_A	108_I	1.404	1.00
328_G	331_I	1.393	1.00
280_R	334_L	1.385	1.00
26_G	52_T	1.367	1.00
315_Q	318_R	1.366	1.00
254_N	260_A	1.347	1.00
215_K	223_M	1.324	1.00
172_N	175_S	1.297	1.00
225_I	242_M	1.294	1.00
28_F	245_V	1.275	1.00
140_K	177_K	1.274	1.00
187_A	211_V	1.262	1.00
163_S	166_F	1.251	1.00
62_G	92_A	1.232	1.00
28_F	261_V	1.228	1.00
126_A	190_A	1.218	1.00
276_V	280_R	1.218	1.00
31_A	248_G	1.217	1.00
323_N	332_N	1.216	1.00
172_N	176_G	1.210	1.00
160_D	200_N	1.200	1.00
284_P	288_R	1.191	1.00
175_S	219_P	1.177	1.00
247_V	261_V	1.173	1.00
43_Y	47_L	1.167	1.00
190_A	199_E	1.164	1.00
55_Y	184_I	1.161	1.00
151_T	182_M	1.155	1.00
156_I	207_D	1.152	1.00
238_H	242_M	1.151	1.00
171_I	214_L	1.149	1.00
48_L	278_V	1.148	1.00
129_M	154_T	1.148	1.00
219_P	223_M	1.146	1.00
281_A	285_Y	1.144	1.00
53_L	107_E	1.143	1.00
323_N	328_G	1.140	1.00
213_Q	217_D	1.140	1.00
90_P	134_L	1.140	1.00
43_Y	285_Y	1.136	1.00
169_D	173_T	1.127	1.00
208_Y	238_H	1.126	1.00
185_I	214_L	1.126	1.00
330_D	334_L	1.125	1.00
289_E	294_T	1.121	1.00
64_I	99_L	1.118	1.00
46_R	78_E	1.115	1.00
324_A	328_G	1.112	1.00
168_C	213_Q	1.110	1.00
55_Y	82_A	1.110	1.00
43_Y	77_E	1.102	1.00
129_M	166_F	1.100	1.00
232_L	260_A	1.098	1.00
235_A	261_V	1.097	1.00
143_R	150_V	1.092	1.00
327_A	331_I	1.082	1.00
139_V	177_K	1.078	1.00
152_V	180_C	1.072	1.00
29_S	53_L	1.070	1.00
156_I	163_S	1.068	1.00
128_L	138_C	1.056	1.00
167_L	210_R	1.054	1.00
279_V	303_M	1.053	1.00
156_I	187_A	1.050	1.00
40_H	289_E	1.050	1.00
297_G	300_T	1.047	1.00
98_K	102_A	1.044	1.00
139_V	174_V	1.042	1.00
170_F	174_V	1.037	1.00
173_T	177_K	1.035	1.00
233_E	270_D	1.031	1.00
62_G	66_H	1.031	1.00
39_R	43_Y	1.030	1.00
282_M	303_M	1.026	1.00
289_E	292_Q	1.017	1.00
129_M	170_F	1.016	1.00
293_G	297_G	1.014	1.00
170_F	173_T	1.011	1.00
274_D	277_A	1.010	1.00
30_V	45_L	1.008	1.00
30_V	251_A	0.991	1.00
315_Q	319_Y	0.985	1.00
264_E	267_G	0.980	1.00
154_T	170_F	0.980	1.00
256_G	275_P	0.976	1.00
139_V	152_V	0.972	1.00
135_V	174_V	0.971	1.00
264_E	268_S	0.967	1.00
323_N	329_A	0.964	1.00
93_L	138_C	0.960	1.00
262_D	266_F	0.959	1.00
251_A	257_I	0.954	1.00
61_T	96_C	0.953	1.00
43_Y	75_S	0.953	1.00
282_M	286_I	0.952	1.00
94_A	98_K	0.951	1.00
263_R	269_S	0.946	1.00
132_A	169_D	0.944	1.00
91_A	141_A	0.938	1.00
40_H	285_Y	0.933	1.00
229_I	235_A	0.930	1.00
46_R	80_P	0.916	0.99
287_E	291_S	0.906	0.99
251_A	258_L	0.905	0.99
263_R	268_S	0.904	0.99
48_L	259_A	0.902	0.99
250_E	254_N	0.901	0.99
133_Q	136_A	0.899	0.99
280_R	284_P	0.890	0.99
319_Y	323_N	0.888	0.99
177_K	180_C	0.887	0.99
307_F	313_A	0.882	0.99
180_C	183_F	0.870	0.99
277_A	281_A	0.869	0.99
174_V	180_C	0.867	0.99
98_K	101_E	0.867	0.99
82_A	151_T	0.862	0.99
229_I	245_V	0.861	0.99
285_Y	288_R	0.861	0.99
282_M	299_I	0.858	0.99
99_L	102_A	0.858	0.99
116_S	119_V	0.857	0.99
97_A	142_M	0.855	0.99
290_L	298_H	0.854	0.99
291_S	295_Y	0.852	0.99
90_P	137_D	0.851	0.99
171_I	183_F	0.848	0.99
73_A	103_R	0.845	0.99
200_N	204_P	0.844	0.99
140_K	176_G	0.840	0.99
233_E	264_E	0.839	0.99
73_A	76_E	0.838	0.99
184_I	246_M	0.827	0.99
29_S	55_Y	0.826	0.99
141_A	144_D	0.825	0.99
232_L	264_E	0.825	0.99
120_Q	127_C	0.823	0.99
135_V	139_V	0.823	0.99
301_R	305_G	0.820	0.99
64_I	69_G	0.818	0.99
168_C	214_L	0.812	0.99
65_I	95_Q	0.812	0.99
182_M	222_T	0.808	0.99
30_V	37_T	0.808	0.99
95_Q	99_L	0.807	0.99
261_V	265_I	0.806	0.99
162_D	166_F	0.801	0.99
65_I	92_A	0.797	0.99
263_R	270_D	0.794	0.99
92_A	95_Q	0.793	0.99
185_I	223_M	0.793	0.99
232_L	236_K	0.792	0.99
39_R	73_A	0.790	0.98
123_M	127_C	0.790	0.98
27_R	52_T	0.789	0.98
154_T	167_L	0.788	0.98
275_P	310_I	0.787	0.98
239_L	245_V	0.787	0.98
99_L	103_R	0.785	0.98
94_A	141_A	0.783	0.98
307_F	316_W	0.778	0.98
100_A	105_Y	0.777	0.98
28_F	258_L	0.777	0.98
233_E	236_K	0.774	0.98
113_G	226_N	0.773	0.98
212_Y	242_M	0.767	0.98
239_L	242_M	0.764	0.98
45_L	251_A	0.764	0.98
56_T	81_V	0.759	0.98
228_G	249_R	0.758	0.98
117_D	121_N	0.757	0.98
36_W	305_G	0.757	0.98
74_Y	81_V	0.750	0.98
142_M	150_V	0.749	0.98
314_R	318_R	0.749	0.98
209_P	213_Q	0.748	0.98
127_C	130_G	0.748	0.98
225_I	241_H	0.748	0.98
112_V	152_V	0.745	0.98
27_R	244_G	0.744	0.98
159_D	189_K	0.737	0.98
326_K	330_D	0.735	0.98
283_Y	326_K	0.730	0.97
90_P	138_C	0.729	0.97
284_P	287_E	0.728	0.97
141_A	145_V	0.727	0.97
252_Y	305_G	0.726	0.97
31_A	246_M	0.723	0.97
294_T	298_H	0.721	0.97
107_E	151_T	0.721	0.97
45_L	50_R	0.719	0.97
331_I	334_L	0.717	0.97
74_Y	78_E	0.716	0.97
143_R	180_C	0.716	0.97
283_Y	287_E	0.711	0.97
234_E	238_H	0.709	0.97
109_N	184_I	0.708	0.97
260_A	273_A	0.707	0.97
60_T	86_G	0.707	0.97
168_C	172_N	0.703	0.97
281_A	284_P	0.702	0.97
47_L	77_E	0.702	0.97
53_L	182_M	0.701	0.97
175_S	183_F	0.701	0.97
327_A	330_D	0.700	0.97
230_K	248_G	0.691	0.97
94_A	146_V	0.690	0.96
154_T	171_I	0.690	0.96
211_V	223_M	0.689	0.96
166_F	170_F	0.685	0.96
46_R	54_L	0.684	0.96
45_L	258_L	0.684	0.96
293_G	324_A	0.682	0.96
313_A	317_R	0.678	0.96
317_R	321_S	0.678	0.96
117_D	120_Q	0.678	0.96
223_M	242_M	0.678	0.96
72_L	78_E	0.677	0.96
328_G	332_N	0.677	0.96
200_N	206_L	0.674	0.96
72_L	75_S	0.672	0.96
28_F	235_A	0.670	0.96
275_P	279_V	0.668	0.96
34_L	58_M	0.662	0.96
104_G	148_I	0.660	0.95
85_L	93_L	0.659	0.95
159_D	199_E	0.657	0.95
264_E	270_D	0.657	0.95
120_Q	158_I	0.652	0.95
183_F	221_L	0.651	0.95
108_I	146_V	0.650	0.95
163_S	210_R	0.649	0.95
267_G	271_T	0.646	0.95
61_T	93_L	0.643	0.95
47_L	285_Y	0.643	0.95
110_L	139_V	0.641	0.95
212_Y	229_I	0.637	0.95
61_T	92_A	0.636	0.94
182_M	244_G	0.634	0.94
154_T	183_F	0.629	0.94
171_I	185_I	0.629	0.94
88_S	123_M	0.628	0.94
163_S	168_C	0.627	0.94
36_W	252_Y	0.627	0.94
45_L	48_L	0.626	0.94
40_H	43_Y	0.626	0.94
268_S	271_T	0.625	0.94
184_I	224_S	0.624	0.94
112_V	174_V	0.623	0.94
161_Q	166_F	0.621	0.94
44_F	285_Y	0.620	0.94
270_D	273_A	0.620	0.94
214_L	217_D	0.618	0.94
88_S	124_F	0.616	0.94
232_L	261_V	0.616	0.94
296_L	300_T	0.615	0.93
247_V	251_A	0.615	0.93
74_Y	79_H	0.613	0.93
80_P	106_D	0.612	0.93
279_V	282_M	0.610	0.93
160_D	199_E	0.608	0.93
180_C	221_L	0.607	0.93
130_G	159_D	0.607	0.93
202_E	228_G	0.607	0.93
132_A	173_T	0.607	0.93
295_Y	298_H	0.604	0.93
149_P	181_E	0.603	0.93
232_L	235_A	0.602	0.93
56_T	83_L	0.601	0.93
129_M	135_V	0.598	0.93
167_L	185_I	0.598	0.93
247_V	257_I	0.592	0.92
247_V	258_L	0.591	0.92
254_N	257_I	0.591	0.92
71_Y	74_Y	0.591	0.92
97_A	150_V	0.590	0.92
208_Y	225_I	0.590	0.92
97_A	108_I	0.589	0.92
236_K	239_L	0.585	0.92
62_G	89_D	0.585	0.92
168_C	171_I	0.584	0.92
116_S	201_R	0.579	0.91
173_T	176_G	0.578	0.91
304_L	321_S	0.577	0.91
29_S	182_M	0.576	0.91
208_Y	241_H	0.574	0.91
119_V	124_F	0.573	0.91
316_W	319_Y	0.573	0.91
276_V	333_V	0.573	0.91
238_H	241_H	0.572	0.91
171_I	219_P	0.571	0.91
123_M	134_L	0.571	0.91
29_S	184_I	0.570	0.91
60_T	63_A	0.568	0.90
113_G	246_M	0.561	0.90
44_F	282_M	0.561	0.90
211_V	242_M	0.560	0.90
307_F	317_R	0.560	0.90
236_K	265_I	0.557	0.90
65_I	96_C	0.557	0.90
70_D	103_R	0.555	0.89
33_M	36_W	0.555	0.89
64_I	103_R	0.555	0.89
37_T	45_L	0.555	0.89
94_A	142_M	0.552	0.89
175_S	222_T	0.552	0.89
290_L	294_T	0.552	0.89
64_I	68_K	0.552	0.89
131_N	137_D	0.551	0.89
287_E	326_K	0.551	0.89
50_R	54_L	0.549	0.89
39_R	74_Y	0.548	0.89
259_A	263_R	0.546	0.89
28_F	262_D	0.546	0.89
235_A	239_L	0.545	0.89
158_I	190_A	0.544	0.89
286_I	299_I	0.543	0.88
136_A	174_V	0.540	0.88
168_C	210_R	0.540	0.88
211_V	238_H	0.539	0.88
290_L	295_Y	0.539	0.88
285_Y	289_E	0.539	0.88
239_L	265_I	0.538	0.88
171_I	223_M	0.537	0.88
269_S	272_D	0.536	0.88
44_F	48_L	0.536	0.88
72_L	76_E	0.535	0.88
142_M	146_V	0.533	0.88
260_A	264_E	0.532	0.87
229_I	247_V	0.530	0.87
126_A	129_M	0.527	0.87
83_L	105_Y	0.526	0.87
187_A	206_L	0.526	0.87
286_I	290_L	0.526	0.87
232_L	270_D	0.526	0.87
85_L	142_M	0.526	0.87
287_E	330_D	0.525	0.87
294_T	299_I	0.525	0.87
117_D	201_R	0.525	0.87
28_F	52_T	0.525	0.87
174_V	183_F	0.525	0.87
256_G	259_A	0.520	0.86
91_A	94_A	0.516	0.86
97_A	101_E	0.516	0.86
44_F	281_A	0.514	0.86
261_V	264_E	0.513	0.85
257_I	261_V	0.513	0.85
94_A	144_D	0.512	0.85
216_R	241_H	0.510	0.85
284_P	326_K	0.509	0.85
162_D	189_K	0.508	0.85
98_K	146_V	0.507	0.85
55_Y	107_E	0.506	0.85
73_A	289_E	0.505	0.85
55_Y	151_T	0.505	0.85
82_A	182_M	0.505	0.85
209_P	212_Y	0.503	0.84
64_I	67_G	0.503	0.84
298_H	301_R	0.503	0.84
143_R	177_K	0.503	0.84
98_K	144_D	0.502	0.84
138_C	141_A	0.500	0.84

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
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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
3b0pA	1	0.8754	100	0.372	Contact Map
1vhnA	1	0.8609	100	0.398	Contact Map
4bfaA	1	0.8783	100	0.407	Contact Map
4xp7A	1	0.8319	100	0.45	Contact Map
1gteA	4	0.9507	100	0.625	Contact Map
3l5aA	1	0.8261	100	0.638	Contact Map
3tjlA	2	0.8435	100	0.645	Contact Map
1o94A	2	0.9536	100	0.652	Contact Map
4gbuA	2	0.8203	100	0.652	Contact Map
4jicA	1	0.7739	100	0.656	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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