DUS1 - BACSU - GREMLIN Contacts

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DUS1 - Probable tRNA-dihydrouridine synthase 1

UniProt:	P37567	Sequences: MFKIGDIQLKNRVVLAPMAGVCNSAFRLTVKEFGAGLVCAEMVSDKAILYNNARTMGMLYIDEREKPLSLQIFGGKKETLVEAAKFVDQNTTADIIDINMGCPVPKITKCDAGAKWLLDPDKIYEMVSAVVDAVNKPVTVKMRMGWDEDHIFAVKNAQAVERAGGKAVALHGRTRVQMYEGTANWDIIKEVKQSVSIPVIGNGDVKTPQDAKRMLDETGVDGVMIGRAALGNPWMIYRTVQYLETGKLKEEPQVREKMAVCKLHLDRLIDLKGENVAVREMRKHAAWYLKGVKGNANVRNEINHCETREEFVQLLDAFTVEVEAKELQNAKVG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	333 (304)
Sequences:	6668 (3993)
Seq/√Len:	229.0

ECOLI - DUSB DUSC DUSA
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
32_E	263_L	4.597	1.00
192_K	221_D	4.420	1.00
207_T	210_D	3.311	1.00
88_D	135_N	3.233	1.00
206_K	210_D	2.988	1.00
131_V	166_K	2.872	1.00
213_R	217_E	2.692	1.00
66_K	94_D	2.620	1.00
161_E	196_S	2.617	1.00
127_V	165_G	2.453	1.00
189_K	193_Q	2.448	1.00
186_D	217_E	2.427	1.00
128_S	132_D	2.369	1.00
80_L	98_I	2.352	1.00
307_T	310_E	2.269	1.00
212_K	216_D	2.230	1.00
201_G	214_M	2.218	1.00
118_L	146_W	2.207	1.00
26_F	30_V	2.122	1.00
84_A	134_V	2.081	1.00
144_M	187_I	2.029	1.00
124_Y	163_A	2.009	1.00
212_K	242_Y	2.001	1.00
190_E	193_Q	1.976	1.00
205_V	214_M	1.964	1.00
161_E	197_I	1.897	1.00
100_M	123_I	1.889	1.00
82_E	85_K	1.875	1.00
119_D	122_K	1.869	1.00
134_V	138_V	1.860	1.00
262_K	312_V	1.860	1.00
266_D	312_V	1.857	1.00
78_E	82_E	1.850	1.00
184_N	187_I	1.827	1.00
124_Y	159_A	1.810	1.00
177_Q	184_N	1.804	1.00
213_R	216_D	1.796	1.00
188_I	201_G	1.786	1.00
210_D	213_R	1.773	1.00
123_I	156_N	1.754	1.00
69_S	95_I	1.752	1.00
206_K	228_A	1.724	1.00
111_D	119_D	1.715	1.00
300_N	304_H	1.712	1.00
121_D	125_E	1.711	1.00
85_K	133_A	1.710	1.00
70_L	87_V	1.699	1.00
158_Q	194_S	1.679	1.00
80_L	130_V	1.657	1.00
264_H	288_Y	1.649	1.00
211_A	223_V	1.642	1.00
153_A	191_V	1.641	1.00
37_L	69_S	1.640	1.00
262_K	316_D	1.638	1.00
81_V	133_A	1.637	1.00
76_K	79_T	1.618	1.00
142_M	170_L	1.617	1.00
310_E	313_Q	1.593	1.00
124_Y	162_R	1.585	1.00
241_Q	245_T	1.582	1.00
241_Q	249_K	1.579	1.00
155_K	158_Q	1.579	1.00
124_Y	128_S	1.577	1.00
195_V	199_V	1.559	1.00
121_D	159_A	1.554	1.00
14_V	200_I	1.551	1.00
36_G	240_V	1.549	1.00
201_G	205_V	1.537	1.00
77_K	81_V	1.536	1.00
200_I	222_G	1.533	1.00
187_I	190_E	1.532	1.00
167_A	200_I	1.531	1.00
209_Q	213_R	1.528	1.00
200_I	224_M	1.519	1.00
154_V	194_S	1.513	1.00
189_K	214_M	1.495	1.00
183_A	204_D	1.488	1.00
125_E	128_S	1.479	1.00
98_I	130_V	1.474	1.00
122_K	125_E	1.461	1.00
88_D	136_K	1.438	1.00
74_G	80_L	1.437	1.00
192_K	199_V	1.428	1.00
88_D	134_V	1.424	1.00
158_Q	161_E	1.423	1.00
232_N	238_R	1.417	1.00
189_K	217_E	1.409	1.00
297_N	300_N	1.396	1.00
312_V	316_D	1.391	1.00
11_N	36_G	1.389	1.00
128_S	163_A	1.386	1.00
87_V	96_I	1.374	1.00
237_Y	256_E	1.373	1.00
140_V	160_V	1.372	1.00
46_K	79_T	1.335	1.00
201_G	220_V	1.309	1.00
13_V	223_V	1.295	1.00
172_G	188_I	1.280	1.00
263_L	267_R	1.273	1.00
253_Q	256_E	1.254	1.00
305_C	310_E	1.251	1.00
157_A	195_V	1.249	1.00
305_C	314_L	1.243	1.00
16_A	226_G	1.228	1.00
13_V	239_T	1.227	1.00
266_D	270_D	1.225	1.00
139_T	167_A	1.221	1.00
158_Q	162_R	1.214	1.00
117_L	142_M	1.209	1.00
127_V	163_A	1.207	1.00
39_C	169_A	1.205	1.00
28_L	32_E	1.190	1.00
114_A	175_R	1.182	1.00
48_I	86_F	1.176	1.00
157_A	191_V	1.173	1.00
144_M	184_N	1.172	1.00
225_I	239_T	1.163	1.00
258_M	262_K	1.162	1.00
190_E	194_S	1.162	1.00
39_C	69_S	1.161	1.00
77_K	122_K	1.159	1.00
309_E	313_Q	1.156	1.00
31_K	65_E	1.148	1.00
155_K	159_A	1.145	1.00
37_L	95_I	1.136	1.00
148_E	177_Q	1.130	1.00
211_A	239_T	1.122	1.00
117_L	156_N	1.120	1.00
140_V	165_G	1.110	1.00
306_E	310_E	1.108	1.00
33_F	260_V	1.108	1.00
261_C	285_A	1.107	1.00
241_Q	247_K	1.106	1.00
242_Y	245_T	1.101	1.00
14_V	37_L	1.093	1.00
161_E	195_V	1.093	1.00
117_L	152_F	1.093	1.00
156_N	160_V	1.092	1.00
240_V	244_E	1.088	1.00
271_L	276_V	1.081	1.00
154_V	190_E	1.077	1.00
144_M	172_G	1.074	1.00
214_M	220_V	1.071	1.00
127_V	160_V	1.066	1.00
170_L	191_V	1.064	1.00
208_P	238_R	1.062	1.00
45_D	83_A	1.048	1.00
46_K	50_Y	1.045	1.00
131_V	138_V	1.042	1.00
264_H	268_L	1.041	1.00
185_W	214_M	1.041	1.00
28_L	267_R	1.041	1.00
80_L	126_M	1.039	1.00
15_L	30_V	1.036	1.00
127_V	140_V	1.035	1.00
28_L	64_R	1.030	1.00
214_M	218_T	1.026	1.00
24_S	28_L	1.026	1.00
297_N	301_E	1.020	1.00
123_I	160_V	1.020	1.00
116_W	126_M	1.019	1.00
85_K	89_Q	1.018	1.00
28_L	62_D	1.015	1.00
242_Y	246_G	1.013	1.00
154_V	195_V	1.004	1.00
308_R	312_V	1.000	1.00
153_A	187_I	0.998	1.00
159_A	163_A	0.997	1.00
205_V	211_A	0.997	1.00
142_M	156_N	0.990	1.00
209_Q	242_Y	0.987	1.00
189_K	219_G	0.985	1.00
120_P	155_K	0.981	1.00
256_E	259_A	0.980	1.00
81_V	85_K	0.973	1.00
52_N	55_T	0.971	1.00
275_N	279_R	0.960	1.00
305_C	311_F	0.959	1.00
78_E	129_A	0.953	1.00
267_R	270_D	0.952	1.00
254_V	257_K	0.947	1.00
111_D	115_K	0.945	1.00
15_L	229_A	0.938	1.00
257_K	292_V	0.937	1.00
31_K	67_P	0.935	1.00
229_A	235_M	0.930	1.00
144_M	151_I	0.927	1.00
289_L	295_N	0.926	1.00
301_E	305_C	0.924	1.00
33_F	237_Y	0.922	1.00
229_A	236_I	0.917	1.00
154_V	191_V	0.915	1.00
128_S	162_R	0.912	1.00
85_K	88_D	0.910	1.00
262_K	266_D	0.904	0.99
156_N	159_A	0.904	0.99
84_A	130_V	0.904	0.99
264_H	285_A	0.900	0.99
279_R	282_R	0.898	0.99
169_A	224_M	0.894	0.99
228_A	232_N	0.893	0.99
129_A	132_D	0.893	0.99
165_G	168_V	0.881	0.99
121_D	124_Y	0.875	0.99
158_Q	195_V	0.873	0.99
205_V	223_V	0.872	0.99
69_S	139_T	0.866	0.99
79_T	82_E	0.864	0.99
264_H	281_M	0.863	0.99
25_A	267_R	0.856	0.99
160_V	165_G	0.855	0.99
104_V	107_I	0.855	0.99
49_L	82_E	0.851	0.99
234_W	257_K	0.849	0.99
273_G	277_A	0.846	0.99
123_I	127_V	0.842	0.99
24_S	60_Y	0.838	0.99
252_P	256_E	0.837	0.99
14_V	39_C	0.837	0.99
77_K	125_E	0.835	0.99
108_T	115_K	0.833	0.99
167_A	198_P	0.833	0.99
170_L	199_V	0.829	0.99
309_E	312_V	0.825	0.99
61_I	68_L	0.824	0.99
25_A	271_L	0.819	0.99
177_Q	181_G	0.813	0.99
87_V	93_A	0.809	0.99
60_Y	91_T	0.805	0.99
208_P	212_K	0.804	0.99
204_D	227_R	0.797	0.99
21_V	287_W	0.796	0.99
81_V	129_A	0.796	0.99
289_L	298_V	0.795	0.99
77_K	126_M	0.793	0.99
86_F	89_Q	0.792	0.99
296_A	300_N	0.792	0.99
101_G	202_N	0.791	0.99
255_R	259_A	0.790	0.99
13_V	236_I	0.790	0.99
82_E	86_F	0.789	0.99
266_D	269_I	0.786	0.99
149_D	152_F	0.785	0.99
272_K	280_E	0.785	0.99
142_M	153_A	0.785	0.99
148_E	151_I	0.783	0.98
57_G	60_Y	0.782	0.98
259_A	263_L	0.781	0.98
215_L	223_V	0.781	0.98
261_C	264_H	0.775	0.98
265_L	269_I	0.774	0.98
12_R	36_G	0.770	0.98
15_L	22_C	0.768	0.98
95_I	139_T	0.767	0.98
269_I	312_V	0.764	0.98
16_A	224_M	0.760	0.98
97_D	169_A	0.757	0.98
230_L	287_W	0.756	0.98
131_V	165_G	0.755	0.98
100_M	140_V	0.754	0.98
49_L	79_T	0.753	0.98
30_V	229_A	0.750	0.98
209_Q	212_K	0.749	0.98
283_K	287_W	0.748	0.98
269_I	273_G	0.746	0.98
81_V	134_V	0.740	0.98
257_K	261_C	0.738	0.98
53_A	57_G	0.733	0.98
188_I	199_V	0.732	0.98
245_T	249_K	0.731	0.98
271_L	274_E	0.730	0.98
40_A	68_L	0.727	0.98
157_A	168_V	0.724	0.98
147_D	174_T	0.722	0.97
215_L	220_V	0.722	0.97
168_V	197_I	0.721	0.97
30_V	35_A	0.718	0.97
263_L	266_D	0.718	0.97
272_K	276_V	0.716	0.97
186_D	190_E	0.714	0.97
241_Q	246_G	0.701	0.97
142_M	157_A	0.700	0.97
208_P	242_Y	0.700	0.97
89_Q	92_T	0.700	0.97
75_G	111_D	0.699	0.97
45_D	80_L	0.698	0.97
234_W	252_P	0.697	0.97
189_K	220_V	0.696	0.97
210_D	214_M	0.696	0.97
161_E	168_V	0.695	0.97
208_P	211_A	0.694	0.97
154_V	158_Q	0.693	0.97
44_S	73_F	0.693	0.97
19_A	42_M	0.692	0.97
310_E	314_L	0.692	0.97
311_F	314_L	0.689	0.97
276_V	280_E	0.687	0.97
299_R	303_N	0.686	0.97
130_V	138_V	0.685	0.97
29_T	267_R	0.684	0.96
37_L	167_A	0.680	0.96
115_K	118_L	0.679	0.96
72_I	80_L	0.678	0.96
31_K	38_V	0.678	0.96
61_I	65_E	0.678	0.96
137_P	166_K	0.676	0.96
212_K	243_L	0.675	0.96
266_D	308_R	0.670	0.96
96_I	134_V	0.665	0.96
12_R	222_G	0.663	0.96
105_P	109_K	0.663	0.96
45_D	79_T	0.657	0.96
129_A	133_A	0.657	0.96
159_A	162_R	0.654	0.95
92_T	136_K	0.654	0.95
108_T	146_W	0.653	0.95
13_V	211_A	0.652	0.95
118_L	152_F	0.647	0.95
30_V	33_F	0.646	0.95
117_L	123_I	0.645	0.95
111_D	122_K	0.643	0.95
55_T	58_M	0.643	0.95
105_P	178_M	0.641	0.95
152_F	156_N	0.641	0.95
24_S	62_D	0.638	0.95
48_I	91_T	0.638	0.95
276_V	281_M	0.637	0.95
189_K	218_T	0.636	0.95
21_V	230_L	0.636	0.95
199_V	220_V	0.635	0.95
212_K	215_L	0.634	0.95
147_D	176_V	0.634	0.95
239_T	243_L	0.634	0.95
169_A	200_I	0.632	0.95
168_V	195_V	0.629	0.94
258_M	261_C	0.627	0.94
142_M	168_V	0.626	0.94
120_P	159_A	0.625	0.94
258_M	315_L	0.624	0.94
157_A	170_L	0.624	0.94
25_A	28_L	0.623	0.94
30_V	236_I	0.622	0.94
167_A	222_G	0.621	0.94
154_V	157_A	0.621	0.94
185_W	201_G	0.620	0.94
225_I	235_M	0.620	0.94
208_P	239_T	0.620	0.94
40_A	70_L	0.620	0.94
32_E	64_R	0.619	0.94
289_L	299_R	0.619	0.94
206_K	226_G	0.618	0.94
238_R	251_E	0.618	0.94
84_A	96_I	0.613	0.94
75_G	112_A	0.612	0.94
131_V	163_A	0.609	0.93
53_A	58_M	0.608	0.93
81_V	132_D	0.608	0.93
191_V	194_S	0.606	0.93
14_V	167_A	0.602	0.93
225_I	236_I	0.599	0.93
286_A	303_N	0.595	0.93
179_Y	204_D	0.595	0.93
189_K	205_V	0.595	0.93
48_I	53_A	0.595	0.93
313_Q	316_D	0.593	0.93
61_I	66_K	0.591	0.92
269_I	308_R	0.591	0.92
257_K	260_V	0.591	0.92
14_V	169_A	0.590	0.92
70_L	93_A	0.583	0.92
154_V	187_I	0.583	0.92
105_P	108_T	0.582	0.92
44_S	47_A	0.580	0.92
247_K	250_E	0.579	0.92
151_I	154_V	0.576	0.91
104_V	178_M	0.571	0.91
98_I	127_V	0.571	0.91
265_L	308_R	0.569	0.91
100_M	160_V	0.568	0.91
117_L	145_G	0.568	0.91
118_L	147_D	0.568	0.91
165_G	197_I	0.566	0.91
237_Y	241_Q	0.565	0.91
49_L	83_A	0.565	0.91
241_Q	250_E	0.565	0.91
185_W	217_E	0.564	0.91
232_N	235_M	0.564	0.91
188_I	220_V	0.563	0.90
18_M	21_V	0.557	0.90
298_V	301_E	0.556	0.90
54_R	91_T	0.556	0.90
295_N	299_R	0.554	0.90
119_D	125_E	0.553	0.90
148_E	176_V	0.553	0.90
225_I	229_A	0.552	0.90
24_S	61_I	0.552	0.90
13_V	240_V	0.551	0.90
188_I	214_M	0.550	0.89
39_C	139_T	0.549	0.89
22_C	30_V	0.548	0.89
35_A	38_V	0.546	0.89
126_M	129_A	0.544	0.89
81_V	130_V	0.544	0.89
235_M	239_T	0.538	0.88
285_A	311_F	0.538	0.88
172_G	183_A	0.534	0.88
130_V	134_V	0.534	0.88
275_N	306_E	0.533	0.88
161_E	198_P	0.533	0.88
282_R	306_E	0.532	0.88
153_A	170_L	0.531	0.88
157_A	194_S	0.531	0.88
268_L	272_K	0.530	0.88
307_T	311_F	0.530	0.88
101_G	224_M	0.530	0.88
107_I	112_A	0.529	0.88
32_E	267_R	0.528	0.87
301_E	310_E	0.527	0.87
84_A	88_D	0.526	0.87
308_R	311_F	0.526	0.87
239_T	242_Y	0.525	0.87
274_E	307_T	0.524	0.87
60_Y	63_E	0.524	0.87
187_I	194_S	0.524	0.87
234_W	237_Y	0.523	0.87
13_V	36_G	0.523	0.87
179_Y	183_A	0.523	0.87
61_I	94_D	0.522	0.87
259_A	262_K	0.520	0.87
29_T	33_F	0.519	0.87
72_I	130_V	0.519	0.87
147_D	151_I	0.518	0.86
211_A	215_L	0.517	0.86
124_Y	160_V	0.515	0.86
144_M	153_A	0.514	0.86
185_W	213_R	0.513	0.86
121_D	155_K	0.513	0.86
246_G	249_K	0.513	0.86
265_L	268_L	0.512	0.86
54_R	60_Y	0.512	0.86
36_G	225_I	0.511	0.86
194_S	199_V	0.511	0.86
250_E	253_Q	0.511	0.86
122_K	126_M	0.509	0.86
85_K	132_D	0.507	0.85
289_L	315_L	0.506	0.85
145_G	226_G	0.505	0.85
186_D	189_K	0.505	0.85
263_L	270_D	0.503	0.85
39_C	95_I	0.503	0.85
51_N	56_M	0.503	0.85
277_A	280_E	0.502	0.85
146_W	175_R	0.502	0.85
193_Q	219_G	0.501	0.85
84_A	138_V	0.501	0.85
19_A	43_V	0.500	0.85

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
1vhnA	1	0.9159	100	0.35	Contact Map
3b0pA	1	0.8979	100	0.371	Contact Map
4bfaA	1	0.9219	100	0.373	Contact Map
4xp7A	1	0.8919	100	0.397	Contact Map
1gteA	4	0.97	100	0.589	Contact Map
3tjlA	2	0.8529	100	0.615	Contact Map
3l5aA	1	0.8228	100	0.619	Contact Map
4gbuA	2	0.8168	100	0.619	Contact Map
4tmbA	2	0.8258	100	0.625	Contact Map
1o94A	2	0.8859	100	0.627	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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