DUS2 - BACSU - GREMLIN Contacts

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DUS2 - Probable tRNA-dihydrouridine synthase 2

UniProt:	O31546	Sequences: MTENFWRELPRPFFVLAPMEDVTDVVFRHVVSEAGRPDVFFTEFTNSESYCHPDGKDSVRGRLTFTEDEQPIVAHIWGDKPENFRKMSIGMAELGFKGLDINMGCPVPNVAGNGKGSGLICRPAVAAELIQAAKAGGLPVSVKTRLGYTDVDEWREWLTHILKQDIANLSIHLRTRAEMSKVDAHWELIPEIKKLRDEVAPDTLLTINGDIPDRQTGLKLAEQYGVDGIMIGRGIFTNPFAFEKEPKEHSSKELLDLLRLHLDLHDEYSKEEARPYKPLPRFFKIYLRGFRGASELRNQCMNTKSTDEVRALLDDFERKYLDGIE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	325 (293)
Sequences:	6634 (3920)
Seq/√Len:	229.0

ECOLI - DUSB DUSC DUSA
BACSU - DUS2 DUS1
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
33_E	260_L	4.847	1.00
193_K	227_D	3.981	1.00
213_D	216_T	3.360	1.00
92_A	137_G	3.170	1.00
212_P	216_T	3.011	1.00
219_K	223_Q	2.738	1.00
162_L	202_D	2.673	1.00
70_Q	97_K	2.567	1.00
130_I	166_I	2.509	1.00
187_E	223_Q	2.466	1.00
190_P	194_K	2.425	1.00
84_F	101_I	2.367	1.00
131_Q	134_K	2.309	1.00
207_I	220_L	2.297	1.00
218_L	222_E	2.293	1.00
305_S	308_E	2.173	1.00
121_C	148_Y	2.154	1.00
27_F	31_V	2.148	1.00
211_I	220_L	2.066	1.00
88_S	136_G	2.049	1.00
103_M	126_A	2.010	1.00
127_A	164_Q	1.945	1.00
162_L	203_T	1.942	1.00
178_E	185_H	1.942	1.00
146_L	188_L	1.936	1.00
86_K	89_I	1.933	1.00
122_R	125_V	1.894	1.00
259_R	310_R	1.888	1.00
136_G	140_V	1.885	1.00
219_K	222_E	1.883	1.00
191_E	194_K	1.876	1.00
82_E	86_K	1.848	1.00
127_A	160_H	1.836	1.00
298_N	302_N	1.835	1.00
73_V	98_G	1.825	1.00
212_P	234_G	1.810	1.00
216_T	219_K	1.809	1.00
126_A	157_W	1.809	1.00
263_D	310_R	1.792	1.00
89_I	135_A	1.766	1.00
39_V	73_V	1.761	1.00
84_F	133_A	1.756	1.00
74_A	91_M	1.724	1.00
261_H	286_Y	1.687	1.00
217_G	229_I	1.685	1.00
156_E	159_T	1.671	1.00
38_D	246_P	1.644	1.00
124_A	128_E	1.639	1.00
85_R	135_A	1.638	1.00
114_G	122_R	1.626	1.00
144_T	171_I	1.615	1.00
127_A	131_Q	1.610	1.00
157_W	160_H	1.596	1.00
127_A	163_K	1.590	1.00
15_V	206_T	1.585	1.00
206_T	228_G	1.571	1.00
206_T	230_M	1.567	1.00
308_E	311_A	1.565	1.00
168_N	206_T	1.563	1.00
80_K	83_N	1.560	1.00
188_L	191_E	1.529	1.00
124_A	160_H	1.513	1.00
128_E	131_Q	1.511	1.00
207_I	211_I	1.511	1.00
215_Q	219_K	1.510	1.00
190_P	223_Q	1.508	1.00
81_P	85_R	1.496	1.00
101_I	133_A	1.493	1.00
243_E	253_E	1.490	1.00
189_I	207_I	1.490	1.00
92_A	138_L	1.480	1.00
78_G	84_F	1.477	1.00
125_V	128_E	1.471	1.00
238_N	244_K	1.449	1.00
142_V	161_I	1.434	1.00
159_T	162_L	1.408	1.00
131_Q	164_Q	1.396	1.00
184_A	210_D	1.380	1.00
48_E	83_N	1.379	1.00
171_I	192_I	1.374	1.00
92_A	136_G	1.358	1.00
207_I	226_V	1.358	1.00
91_M	99_L	1.342	1.00
295_E	298_N	1.334	1.00
12_P	38_D	1.322	1.00
149_T	152_D	1.289	1.00
14_F	245_E	1.287	1.00
303_T	312_L	1.277	1.00
303_T	308_E	1.275	1.00
117_S	176_R	1.272	1.00
141_S	168_N	1.264	1.00
41_F	170_S	1.264	1.00
155_R	195_L	1.263	1.00
17_A	232_G	1.248	1.00
146_L	185_H	1.241	1.00
159_T	163_K	1.233	1.00
159_T	195_L	1.228	1.00
14_F	229_I	1.220	1.00
120_I	144_T	1.201	1.00
263_D	267_E	1.197	1.00
150_D	178_E	1.196	1.00
260_L	264_L	1.195	1.00
173_L	189_I	1.195	1.00
157_W	161_I	1.190	1.00
158_L	192_I	1.189	1.00
130_I	164_Q	1.187	1.00
154_W	192_I	1.187	1.00
255_L	259_R	1.186	1.00
39_V	98_G	1.185	1.00
217_G	245_E	1.180	1.00
29_H	264_L	1.177	1.00
81_P	125_V	1.167	1.00
50_Y	90_G	1.162	1.00
29_H	33_E	1.159	1.00
142_V	166_I	1.156	1.00
156_E	160_H	1.156	1.00
214_R	244_K	1.150	1.00
250_S	253_E	1.136	1.00
185_H	188_L	1.133	1.00
15_V	39_V	1.132	1.00
220_L	226_V	1.115	1.00
59_V	62_R	1.111	1.00
186_W	220_L	1.110	1.00
258_L	283_F	1.109	1.00
195_L	199_V	1.108	1.00
120_I	157_W	1.105	1.00
146_L	173_L	1.104	1.00
32_S	69_E	1.103	1.00
41_F	73_V	1.098	1.00
119_L	129_L	1.098	1.00
231_I	245_E	1.093	1.00
84_F	129_L	1.090	1.00
268_Y	274_R	1.083	1.00
34_A	257_L	1.081	1.00
253_E	256_D	1.073	1.00
126_A	161_I	1.069	1.00
26_V	268_Y	1.064	1.00
56_K	59_V	1.059	1.00
89_I	93_E	1.057	1.00
25_V	29_H	1.054	1.00
193_K	205_L	1.052	1.00
29_H	66_T	1.051	1.00
130_I	161_I	1.046	1.00
48_E	52_H	1.046	1.00
154_W	199_V	1.046	1.00
160_H	164_Q	1.043	1.00
199_V	205_L	1.041	1.00
303_T	309_V	1.039	1.00
304_K	308_E	1.037	1.00
273_A	277_K	1.030	1.00
16_L	235_I	1.029	1.00
16_L	31_V	1.027	1.00
29_H	68_D	1.025	1.00
295_E	299_Q	1.022	1.00
123_P	156_E	1.020	1.00
307_D	311_A	1.015	1.00
47_S	87_M	1.014	1.00
220_L	224_Y	1.010	1.00
287_L	293_A	1.010	1.00
211_I	217_G	1.009	1.00
85_R	89_I	1.006	1.00
130_I	142_V	0.990	1.00
261_H	283_F	0.986	1.00
240_F	254_L	0.982	1.00
254_L	290_F	0.974	1.00
60_R	63_L	0.966	1.00
144_T	157_W	0.962	1.00
235_I	241_A	0.959	1.00
269_S	278_P	0.953	1.00
149_T	177_A	0.951	1.00
82_E	132_A	0.940	1.00
32_S	71_P	0.939	1.00
170_S	230_M	0.935	1.00
277_K	280_P	0.933	1.00
162_L	199_V	0.933	1.00
171_I	205_L	0.931	1.00
114_G	118_G	0.930	1.00
26_V	264_L	0.930	1.00
34_A	243_E	0.929	1.00
191_E	195_L	0.922	1.00
270_K	275_P	0.917	1.00
210_D	233_R	0.916	1.00
166_I	169_L	0.915	1.00
64_T	94_L	0.911	1.00
214_R	218_L	0.911	1.00
89_I	92_A	0.911	1.00
306_T	310_R	0.910	1.00
235_I	242_F	0.908	0.99
124_A	127_A	0.902	0.99
25_V	64_T	0.902	0.99
51_C	86_K	0.899	0.99
299_Q	303_T	0.898	0.99
88_S	133_A	0.892	0.99
161_I	166_I	0.892	0.99
262_L	266_D	0.882	0.99
131_Q	163_K	0.881	0.99
22_V	285_I	0.881	0.99
234_G	238_N	0.879	0.99
85_R	132_A	0.878	0.99
81_P	128_E	0.877	0.99
261_H	279_L	0.874	0.99
107_V	110_V	0.874	0.99
264_L	267_E	0.874	0.99
73_V	141_S	0.870	0.99
155_R	191_E	0.870	0.99
15_V	41_F	0.869	0.99
178_E	182_V	0.863	0.99
259_R	263_D	0.859	0.99
261_H	265_H	0.859	0.99
59_V	63_L	0.858	0.99
111_A	118_G	0.853	0.99
90_G	94_L	0.851	0.99
90_G	93_E	0.850	0.99
236_F	285_I	0.848	0.99
266_D	270_K	0.848	0.99
126_A	130_I	0.846	0.99
83_N	86_K	0.845	0.99
215_Q	218_L	0.842	0.99
252_K	256_D	0.842	0.99
281_R	285_I	0.841	0.99
91_M	96_F	0.839	0.99
86_K	90_G	0.837	0.99
256_D	260_L	0.836	0.99
251_S	254_L	0.835	0.99
30_V	264_L	0.834	0.99
168_N	204_L	0.834	0.99
211_I	229_I	0.831	0.99
16_L	23_T	0.830	0.99
100_D	170_S	0.827	0.99
98_G	141_S	0.818	0.99
155_R	158_L	0.817	0.99
243_E	247_K	0.811	0.99
155_R	199_V	0.805	0.99
121_C	149_T	0.803	0.99
307_D	310_R	0.800	0.99
297_R	301_M	0.799	0.99
14_F	242_F	0.798	0.99
13_F	38_D	0.796	0.99
104_G	208_N	0.791	0.99
294_S	298_N	0.786	0.99
33_E	264_L	0.785	0.99
221_A	226_V	0.785	0.99
64_T	67_E	0.784	0.99
266_D	310_R	0.783	0.98
287_L	296_L	0.778	0.98
31_V	36_R	0.778	0.98
31_V	235_I	0.778	0.98
249_H	253_E	0.778	0.98
51_C	83_N	0.777	0.98
254_L	258_L	0.775	0.98
65_F	72_I	0.774	0.98
65_F	69_E	0.771	0.98
108_P	112_G	0.769	0.98
240_F	249_H	0.769	0.98
169_L	203_T	0.767	0.98
268_Y	271_E	0.764	0.98
155_R	159_T	0.763	0.98
155_R	192_I	0.757	0.98
17_A	230_M	0.755	0.98
103_M	142_V	0.753	0.98
133_A	140_V	0.749	0.98
216_T	220_L	0.749	0.98
132_A	135_A	0.749	0.98
76_I	84_F	0.748	0.98
144_T	158_L	0.744	0.98
13_F	228_G	0.743	0.98
144_T	169_L	0.743	0.98
118_G	121_C	0.742	0.98
42_T	72_I	0.741	0.98
56_K	60_R	0.740	0.98
262_L	306_T	0.738	0.98
221_A	229_I	0.738	0.98
108_P	111_A	0.737	0.98
162_L	169_L	0.734	0.98
79_D	114_G	0.733	0.98
65_F	70_Q	0.731	0.98
20_E	44_F	0.726	0.98
32_S	40_F	0.720	0.97
95_G	138_L	0.716	0.97
212_P	232_G	0.715	0.97
81_P	129_L	0.714	0.97
85_R	136_G	0.712	0.97
50_Y	55_G	0.707	0.97
218_L	221_A	0.698	0.97
139_P	167_A	0.696	0.97
214_R	217_G	0.693	0.97
263_D	306_T	0.693	0.97
120_I	153_E	0.691	0.97
180_S	210_D	0.689	0.97
39_V	168_N	0.687	0.97
187_E	191_E	0.687	0.97
263_D	266_D	0.687	0.97
150_D	177_A	0.685	0.97
149_T	175_T	0.685	0.97
46_N	77_W	0.684	0.96
158_L	171_I	0.684	0.96
99_L	136_G	0.682	0.96
31_V	34_A	0.681	0.96
47_S	84_F	0.681	0.96
205_L	226_V	0.681	0.96
79_D	115_K	0.680	0.96
22_V	236_F	0.680	0.96
31_V	242_F	0.670	0.96
244_K	248_E	0.670	0.96
54_D	59_V	0.670	0.96
170_S	206_T	0.669	0.96
168_N	228_G	0.668	0.96
26_V	29_H	0.665	0.96
182_V	185_H	0.662	0.96
111_A	148_Y	0.660	0.96
14_F	246_P	0.658	0.96
120_I	126_A	0.657	0.96
88_S	99_L	0.655	0.96
33_E	68_D	0.652	0.95
199_V	202_D	0.650	0.95
47_S	83_N	0.650	0.95
159_T	199_V	0.646	0.95
269_S	275_P	0.644	0.95
154_W	188_L	0.642	0.95
266_D	306_T	0.641	0.95
293_A	297_R	0.641	0.95
238_N	241_A	0.641	0.95
189_I	205_L	0.640	0.95
56_K	62_R	0.638	0.95
103_M	161_I	0.636	0.95
46_N	49_S	0.636	0.95
276_Y	280_P	0.635	0.95
160_H	163_K	0.634	0.95
214_R	245_E	0.634	0.95
287_L	297_R	0.634	0.95
308_E	312_L	0.632	0.95
42_T	74_A	0.631	0.95
231_I	241_A	0.630	0.94
123_P	160_H	0.630	0.94
55_G	61_G	0.627	0.94
190_P	224_Y	0.626	0.94
274_R	278_P	0.625	0.94
61_G	64_T	0.625	0.94
186_W	223_Q	0.624	0.94
36_R	40_F	0.622	0.94
260_L	263_D	0.621	0.94
85_R	133_A	0.619	0.94
231_I	235_I	0.617	0.94
158_L	169_L	0.616	0.94
122_R	128_E	0.615	0.94
65_F	97_K	0.615	0.94
120_I	154_W	0.612	0.94
15_V	168_N	0.608	0.93
114_G	125_V	0.607	0.93
309_V	312_L	0.605	0.93
15_V	170_S	0.604	0.93
25_V	66_T	0.602	0.93
166_I	203_T	0.599	0.93
14_F	217_G	0.598	0.93
299_Q	312_L	0.598	0.93
153_E	157_W	0.593	0.93
74_A	96_F	0.593	0.93
78_G	101_I	0.591	0.92
151_V	188_L	0.590	0.92
217_G	221_A	0.589	0.92
101_I	130_I	0.589	0.92
266_D	271_E	0.588	0.92
76_I	133_A	0.585	0.92
19_M	22_V	0.585	0.92
30_V	34_A	0.583	0.92
51_C	87_M	0.580	0.92
162_L	204_L	0.580	0.92
284_K	301_M	0.577	0.91
265_H	279_L	0.577	0.91
274_R	279_L	0.576	0.91
300_C	313_L	0.575	0.91
231_I	242_F	0.573	0.91
88_S	140_V	0.571	0.91
241_A	245_E	0.570	0.91
117_S	120_I	0.567	0.91
258_L	261_H	0.564	0.91
110_V	115_K	0.564	0.91
252_K	257_L	0.563	0.90
23_T	31_V	0.563	0.90
41_F	141_S	0.562	0.90
56_K	61_G	0.561	0.90
238_N	248_E	0.561	0.90
251_S	255_L	0.560	0.90
244_K	247_K	0.559	0.90
148_Y	176_R	0.556	0.90
296_L	299_Q	0.552	0.90
241_A	244_K	0.552	0.90
29_H	267_E	0.550	0.89
222_E	225_G	0.550	0.89
211_I	231_I	0.549	0.89
173_L	184_A	0.549	0.89
41_F	98_G	0.549	0.89
25_V	65_F	0.548	0.89
34_A	260_L	0.547	0.89
62_R	65_F	0.542	0.89
255_L	313_L	0.542	0.89
133_A	136_G	0.542	0.89
150_D	175_T	0.542	0.89
89_I	134_K	0.541	0.89
158_L	195_L	0.540	0.89
55_G	62_R	0.540	0.89
269_S	274_R	0.538	0.88
104_G	230_M	0.536	0.88
20_E	45_T	0.535	0.88
273_A	304_K	0.534	0.88
283_F	309_V	0.534	0.88
88_S	92_A	0.532	0.88
85_R	134_K	0.532	0.88
199_V	204_L	0.532	0.88
184_A	188_L	0.529	0.88
126_A	144_T	0.529	0.88
48_E	80_K	0.527	0.87
144_T	161_I	0.526	0.87
287_L	313_L	0.526	0.87
44_F	77_W	0.525	0.87
129_L	132_A	0.525	0.87
84_F	88_S	0.525	0.87
81_P	132_A	0.525	0.87
46_N	50_Y	0.525	0.87
73_V	168_N	0.522	0.87
81_P	133_A	0.521	0.87
280_P	304_K	0.521	0.87
299_Q	308_E	0.520	0.87
173_L	208_N	0.519	0.87
193_K	225_G	0.518	0.86
169_L	204_L	0.517	0.86
38_D	231_I	0.513	0.86
25_V	268_Y	0.512	0.86
153_E	156_E	0.511	0.86
14_F	38_D	0.510	0.86
30_V	261_H	0.510	0.86
107_V	179_M	0.509	0.86
56_K	94_L	0.509	0.86
261_H	282_F	0.507	0.85
72_I	97_K	0.507	0.85
65_F	74_A	0.504	0.85
64_T	268_Y	0.503	0.85
134_K	159_T	0.503	0.85
144_T	154_W	0.503	0.85
300_C	303_T	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
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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
4bfaA	1	0.9415	100	0.383	Contact Map
1vhnA	1	0.9108	100	0.384	Contact Map
3b0pA	1	0.9077	100	0.385	Contact Map
4xp7A	1	0.8985	100	0.423	Contact Map
1gteA	4	0.96	100	0.619	Contact Map
3sgzA	4	0.7723	100	0.645	Contact Map
3tjlA	2	0.8738	100	0.647	Contact Map
3l5aA	1	0.8492	100	0.652	Contact Map
1p4cA	3	0.7846	100	0.654	Contact Map
4gbuA	2	0.8523	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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