YURR - BACSU - GREMLIN Contacts

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YURR - Uncharacterized oxidoreductase YurR

UniProt:	O32159	Sequences: MKSYIIVGAGILGASTAYHLAKTGARVTVIDRKEPGQATDAAAGIVCPWLSQRRNQDWYQLAKGGARYYKDLIHQLEKDGESDTGYKRVGAISIHTDASKLDKMEERAYKRREDAPEIGDITRLSASETKKLFPILADGYESVHISGAARVNGRALCRSLLSAAEKRGATVIKGNASLLFENGTVTGVQTDTKQFAADAVIVTAGAWANEILKPLGIHFQVSFQKAQIMHFEMTDADTGSWPVVMPPSDQYILSFDNGRIVAGATHENDAGLDDLRVTAGGQHEVLSKALAVAPGLADAAAVETRVGFRPFTPGFLPVVGAVPNVQGLYAANGLGASGLTMGPFLGAELAKLVLGKQTELDLSPYDPAGALA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	372 (342)
Sequences:	26155 (18755)
Seq/√Len:	1014.2

ECOLI - PUUB LHGO MTOX DADA MNMC GLPA GLPD MQO
BACSU - YURR GLOX YHFW GLPD
HALSA - Q9HSD9 Q9HNS4
SULSO - Q980U0 Q97VT4 Q97ZD5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
164_A	169_A	5.083	1.00
5_I	188_V	3.322	1.00
3_S	198_D	3.106	1.00
5_I	197_A	3.011	1.00
32_R	176_A	2.908	1.00
176_A	191_D	2.887	1.00
70_K	88_R	2.879	1.00
28_T	172_I	2.871	1.00
232_E	300_A	2.688	1.00
179_L	189_Q	2.658	1.00
3_S	26_R	2.647	1.00
125_S	128_E	2.622	1.00
4_Y	20_L	2.513	1.00
25_A	354_L	2.482	1.00
5_I	30_I	2.395	1.00
21_A	167_R	2.391	1.00
64_G	347_A	2.379	1.00
22_K	75_Q	2.378	1.00
30_I	195_F	2.242	1.00
21_A	169_A	2.180	1.00
26_R	170_T	2.146	1.00
19_H	347_A	2.106	1.00
120_D	147_G	2.105	1.00
4_Y	25_A	2.099	1.00
128_E	131_K	2.092	1.00
199_A	329_Y	2.085	1.00
122_T	128_E	2.060	1.00
16_T	201_I	2.048	1.00
129_T	142_S	2.020	1.00
226_A	309_R	1.984	1.00
23_T	354_L	1.967	1.00
18_Y	163_A	1.952	1.00
14_A	157_C	1.942	1.00
122_T	146_S	1.938	1.00
351_K	356_K	1.914	1.00
334_L	345_L	1.909	1.00
14_A	161_L	1.907	1.00
331_A	345_L	1.905	1.00
71_D	75_Q	1.901	1.00
5_I	195_F	1.859	1.00
85_G	155_A	1.846	1.00
23_T	356_K	1.837	1.00
283_H	287_S	1.830	1.00
105_E	123_R	1.810	1.00
331_A	349_L	1.797	1.00
187_G	196_A	1.793	1.00
109_Y	113_E	1.790	1.00
68_Y	347_A	1.780	1.00
22_K	167_R	1.773	1.00
19_H	346_G	1.740	1.00
18_Y	22_K	1.736	1.00
21_A	164_A	1.717	1.00
35_P	173_K	1.710	1.00
163_A	166_K	1.710	1.00
329_Y	353_V	1.708	1.00
329_Y	349_L	1.696	1.00
208_A	332_N	1.654	1.00
187_G	194_Q	1.627	1.00
126_A	130_K	1.621	1.00
163_A	167_R	1.618	1.00
178_L	191_D	1.613	1.00
201_I	353_V	1.611	1.00
105_E	109_Y	1.590	1.00
109_Y	112_R	1.583	1.00
68_Y	71_D	1.583	1.00
108_A	112_R	1.583	1.00
19_H	23_T	1.563	1.00
162_S	165_E	1.549	1.00
12_L	331_A	1.548	1.00
162_S	166_K	1.543	1.00
12_L	334_L	1.534	1.00
202_V	208_A	1.530	1.00
34_E	174_G	1.526	1.00
178_L	189_Q	1.503	1.00
152_N	155_A	1.498	1.00
232_E	302_V	1.487	1.00
161_L	165_E	1.487	1.00
199_A	353_V	1.485	1.00
16_T	331_A	1.475	1.00
64_G	67_R	1.473	1.00
161_L	171_V	1.470	1.00
231_F	234_T	1.464	1.00
23_T	350_A	1.455	1.00
19_H	22_K	1.444	1.00
190_T	195_F	1.439	1.00
34_E	173_K	1.437	1.00
102_D	105_E	1.435	1.00
9_A	35_P	1.432	1.00
181_E	186_T	1.430	1.00
28_T	195_F	1.424	1.00
286_L	290_L	1.422	1.00
3_S	28_T	1.419	1.00
189_Q	194_Q	1.418	1.00
202_V	328_L	1.418	1.00
101_L	105_E	1.415	1.00
3_S	25_A	1.411	1.00
23_T	351_K	1.408	1.00
9_A	29_V	1.403	1.00
177_S	188_V	1.389	1.00
190_T	193_K	1.380	1.00
86_Y	149_A	1.371	1.00
35_P	161_L	1.370	1.00
202_V	330_A	1.367	1.00
69_Y	156_L	1.367	1.00
90_G	144_H	1.341	1.00
5_I	28_T	1.330	1.00
282_Q	304_T	1.330	1.00
124_L	128_E	1.320	1.00
67_R	71_D	1.317	1.00
20_L	350_A	1.314	1.00
172_I	175_N	1.312	1.00
11_I	342_G	1.312	1.00
7_V	204_A	1.302	1.00
101_L	141_E	1.291	1.00
4_Y	199_A	1.290	1.00
279_A	283_H	1.287	1.00
15_S	19_H	1.287	1.00
30_I	197_A	1.286	1.00
127_S	131_K	1.271	1.00
322_V	330_A	1.255	1.00
33_K	37_Q	1.254	1.00
122_T	144_H	1.254	1.00
197_A	200_V	1.250	1.00
70_K	74_H	1.242	1.00
347_A	351_K	1.240	1.00
329_Y	352_L	1.234	1.00
6_I	17_A	1.230	1.00
346_G	350_A	1.230	1.00
41_A	305_R	1.227	1.00
204_A	211_I	1.216	1.00
17_A	27_V	1.207	1.00
331_A	334_L	1.198	1.00
14_A	164_A	1.198	1.00
204_A	208_A	1.194	1.00
28_T	170_T	1.193	1.00
175_N	190_T	1.190	1.00
14_A	29_V	1.190	1.00
71_D	74_H	1.186	1.00
124_L	132_L	1.184	1.00
348_E	351_K	1.182	1.00
128_E	132_L	1.181	1.00
90_G	146_S	1.162	1.00
184_T	187_G	1.157	1.00
182_N	185_V	1.142	1.00
154_R	158_R	1.133	1.00
95_H	104_M	1.131	1.00
241_W	244_V	1.130	1.00
56_Q	60_Q	1.130	1.00
106_E	109_Y	1.128	1.00
273_D	276_R	1.127	1.00
98_A	102_D	1.124	1.00
185_V	196_A	1.124	1.00
18_Y	167_R	1.123	1.00
66_A	70_K	1.114	1.00
7_V	200_V	1.106	1.00
108_A	143_V	1.104	1.00
199_A	321_A	1.101	1.00
101_L	123_R	1.094	1.00
15_S	160_L	1.087	1.00
108_A	123_R	1.086	1.00
321_A	326_Q	1.086	1.00
262_A	289_A	1.085	1.00
182_N	187_G	1.080	1.00
30_I	172_I	1.078	1.00
9_A	31_D	1.074	1.00
16_T	203_T	1.049	1.00
17_A	29_V	1.045	1.00
138_D	141_E	1.045	1.00
63_K	67_R	1.030	1.00
29_V	171_V	1.020	1.00
211_I	214_P	1.018	1.00
319_V	345_L	1.017	1.00
210_E	213_K	1.013	1.00
72_L	76_L	1.012	1.00
288_K	291_A	1.011	1.00
122_T	132_L	1.011	1.00
65_G	69_Y	1.009	1.00
20_L	25_A	1.005	1.00
151_V	156_L	1.003	1.00
16_T	346_G	1.001	1.00
98_A	141_E	1.000	1.00
120_D	146_S	0.999	1.00
278_T	281_G	0.998	1.00
102_D	106_E	0.997	1.00
240_S	243_V	0.993	1.00
156_L	343_P	0.985	1.00
15_S	342_G	0.980	1.00
151_V	339_L	0.974	1.00
132_L	144_H	0.968	1.00
259_R	302_V	0.960	1.00
180_F	200_V	0.958	1.00
202_V	212_L	0.956	1.00
15_S	346_G	0.955	1.00
159_S	163_A	0.953	1.00
76_L	163_A	0.951	1.00
287_S	290_L	0.946	1.00
30_I	190_T	0.946	1.00
64_G	344_F	0.943	1.00
25_A	199_A	0.942	1.00
30_I	177_S	0.938	1.00
185_V	198_D	0.938	1.00
64_G	68_Y	0.934	1.00
82_S	159_S	0.933	1.00
6_I	16_T	0.933	1.00
287_S	291_A	0.932	1.00
186_T	328_L	0.932	1.00
199_A	327_G	0.931	1.00
184_T	326_Q	0.929	1.00
112_R	121_I	0.928	1.00
92_I	129_T	0.927	1.00
186_T	327_G	0.923	1.00
36_G	157_C	0.922	1.00
203_T	331_A	0.921	1.00
97_D	100_K	0.920	1.00
251_Y	254_S	0.916	1.00
14_A	171_V	0.915	1.00
27_V	169_A	0.911	1.00
282_Q	286_L	0.907	1.00
179_L	214_P	0.904	1.00
17_A	169_A	0.904	1.00
224_Q	311_F	0.898	1.00
65_G	68_Y	0.895	1.00
199_A	202_V	0.891	1.00
69_Y	342_G	0.891	1.00
159_S	162_S	0.891	1.00
350_A	353_V	0.890	1.00
156_L	339_L	0.889	1.00
73_I	84_T	0.878	1.00
23_T	347_A	0.876	1.00
88_R	147_G	0.876	1.00
83_D	155_A	0.867	1.00
58_W	62_A	0.860	1.00
250_Q	254_S	0.858	1.00
227_Q	267_E	0.858	1.00
32_R	175_N	0.853	1.00
87_K	150_R	0.851	1.00
290_L	297_A	0.851	1.00
284_E	288_K	0.851	1.00
321_A	352_L	0.848	1.00
35_P	171_V	0.848	1.00
23_T	355_G	0.847	1.00
239_G	242_P	0.847	1.00
321_A	329_Y	0.846	1.00
232_E	259_R	0.844	1.00
312_T	333_G	0.844	1.00
242_P	245_M	0.843	1.00
186_T	200_V	0.841	1.00
230_H	261_V	0.840	1.00
69_Y	73_I	0.838	1.00
172_I	195_F	0.838	1.00
175_N	191_D	0.835	1.00
4_Y	201_I	0.833	1.00
85_G	152_N	0.833	1.00
17_A	164_A	0.829	1.00
250_Q	253_L	0.828	1.00
181_E	185_V	0.827	1.00
230_H	303_E	0.824	1.00
44_G	153_G	0.821	1.00
225_K	267_E	0.820	1.00
19_H	68_Y	0.814	1.00
155_A	158_R	0.813	1.00
231_F	262_A	0.805	1.00
124_L	129_T	0.803	1.00
11_I	39_T	0.803	1.00
115_A	120_D	0.802	1.00
164_A	168_G	0.800	1.00
62_A	66_A	0.798	1.00
175_N	192_T	0.798	1.00
284_E	287_S	0.796	1.00
41_A	307_G	0.795	1.00
229_M	301_A	0.794	1.00
29_V	169_A	0.792	1.00
156_L	160_L	0.792	1.00
18_Y	160_L	0.789	1.00
221_V	310_P	0.787	1.00
47_C	337_S	0.785	1.00
200_V	327_G	0.783	1.00
337_S	340_T	0.779	1.00
38_A	206_A	0.777	1.00
11_I	157_C	0.777	1.00
127_S	130_K	0.777	1.00
180_F	188_V	0.771	1.00
95_H	101_L	0.769	1.00
239_G	243_V	0.767	1.00
175_N	195_F	0.763	1.00
319_V	323_P	0.760	1.00
15_S	156_L	0.753	1.00
212_L	330_A	0.748	1.00
104_M	108_A	0.747	1.00
225_K	306_V	0.744	1.00
69_Y	343_P	0.743	1.00
130_K	137_A	0.742	1.00
39_T	42_A	0.742	1.00
164_A	171_V	0.740	1.00
290_L	298_D	0.736	1.00
16_T	349_L	0.735	1.00
65_G	344_F	0.735	1.00
157_C	161_L	0.731	1.00
319_V	349_L	0.730	1.00
92_I	142_S	0.730	1.00
20_L	353_V	0.729	1.00
16_T	353_V	0.726	1.00
47_C	340_T	0.718	1.00
267_E	281_G	0.717	1.00
230_H	259_R	0.715	1.00
231_F	301_A	0.714	1.00
92_I	124_L	0.712	1.00
325_V	328_L	0.711	1.00
212_L	215_L	0.710	1.00
7_V	202_V	0.708	1.00
177_S	180_F	0.705	1.00
252_I	255_F	0.704	1.00
19_H	350_A	0.704	1.00
312_T	335_G	0.702	1.00
320_G	323_P	0.702	1.00
312_T	318_V	0.700	1.00
32_R	207_W	0.699	1.00
165_E	171_V	0.697	1.00
15_S	343_P	0.696	1.00
322_V	325_V	0.696	1.00
21_A	26_R	0.695	1.00
73_I	76_L	0.695	1.00
29_V	161_L	0.694	1.00
238_T	242_P	0.693	1.00
11_I	339_L	0.693	1.00
223_F	308_F	0.689	1.00
185_V	200_V	0.689	1.00
57_D	62_A	0.687	1.00
22_K	163_A	0.685	1.00
108_A	121_I	0.683	1.00
207_W	210_E	0.682	1.00
350_A	354_L	0.680	1.00
111_R	116_P	0.679	1.00
129_T	143_V	0.679	1.00
198_D	327_G	0.679	1.00
238_T	241_W	0.679	1.00
110_K	113_E	0.677	1.00
126_A	129_T	0.677	1.00
286_L	304_T	0.677	1.00
176_A	179_L	0.673	1.00
60_Q	63_K	0.673	1.00
91_A	148_A	0.672	1.00
103_K	106_E	0.670	1.00
62_A	65_G	0.669	1.00
46_V	86_Y	0.667	1.00
201_I	349_L	0.667	1.00
39_T	157_C	0.665	1.00
321_A	327_G	0.665	1.00
213_K	218_H	0.664	1.00
69_Y	72_L	0.661	1.00
3_S	196_A	0.660	1.00
32_R	37_Q	0.657	1.00
334_L	342_G	0.656	1.00
26_R	198_D	0.649	1.00
251_Y	263_G	0.648	1.00
178_L	190_T	0.648	1.00
145_I	148_A	0.646	1.00
229_M	285_V	0.645	1.00
3_S	197_A	0.642	1.00
5_I	200_V	0.641	1.00
344_F	347_A	0.641	1.00
265_T	309_R	0.640	1.00
165_E	170_T	0.640	1.00
18_Y	164_A	0.640	1.00
174_G	192_T	0.639	1.00
283_H	286_L	0.633	1.00
245_M	248_S	0.632	1.00
180_F	186_T	0.629	1.00
29_V	164_A	0.629	1.00
12_L	345_L	0.628	1.00
226_A	265_T	0.626	1.00
92_I	144_H	0.622	1.00
228_I	305_R	0.621	1.00
351_K	355_G	0.621	1.00
270_A	273_D	0.619	1.00
241_W	245_M	0.618	1.00
59_Y	63_K	0.618	1.00
155_A	159_S	0.617	1.00
82_S	85_G	0.617	1.00
190_T	194_Q	0.615	1.00
31_D	173_K	0.614	1.00
69_Y	76_L	0.614	1.00
112_R	120_D	0.613	1.00
161_L	173_K	0.610	1.00
53_R	56_Q	0.608	1.00
68_Y	343_P	0.608	1.00
280_G	283_H	0.608	1.00
105_E	108_A	0.608	1.00
160_L	342_G	0.607	1.00
290_L	296_L	0.606	1.00
288_K	292_V	0.605	1.00
67_R	70_K	0.600	1.00
106_E	110_K	0.599	1.00
266_H	336_A	0.599	1.00
28_T	197_A	0.598	1.00
62_A	68_Y	0.597	1.00
317_P	320_G	0.596	1.00
310_P	334_L	0.595	1.00
158_R	162_S	0.595	1.00
240_S	244_V	0.594	1.00
265_T	281_G	0.594	1.00
181_E	184_T	0.591	1.00
181_E	325_V	0.588	1.00
60_Q	64_G	0.588	1.00
344_F	348_E	0.587	1.00
191_D	194_Q	0.587	1.00
143_V	146_S	0.587	1.00
111_R	121_I	0.585	1.00
342_G	346_G	0.585	1.00
125_S	131_K	0.584	1.00
186_T	189_Q	0.584	1.00
31_D	34_E	0.583	1.00
62_A	69_Y	0.582	1.00
244_V	247_P	0.581	1.00
238_T	244_V	0.580	1.00
19_H	72_L	0.579	1.00
320_G	330_A	0.578	1.00
43_A	251_Y	0.577	1.00
62_A	341_M	0.576	1.00
239_G	244_V	0.575	1.00
206_A	308_F	0.575	1.00
224_Q	266_H	0.574	1.00
331_A	346_G	0.572	1.00
129_T	132_L	0.572	1.00
68_Y	72_L	0.571	1.00
68_Y	344_F	0.568	1.00
121_I	145_I	0.567	1.00
21_A	27_V	0.567	1.00
30_I	175_N	0.566	1.00
123_R	143_V	0.566	1.00
220_Q	313_P	0.565	1.00
242_P	247_P	0.563	1.00
343_P	346_G	0.562	1.00
180_F	215_L	0.560	1.00
181_E	327_G	0.559	1.00
61_L	65_G	0.559	1.00
229_M	282_Q	0.558	1.00
61_L	348_E	0.557	1.00
188_V	200_V	0.557	1.00
46_V	151_V	0.556	1.00
56_Q	113_E	0.554	1.00
63_K	66_A	0.554	1.00
208_A	221_V	0.553	1.00
3_S	195_F	0.551	1.00
125_S	129_T	0.550	1.00
6_I	27_V	0.550	1.00
334_L	338_G	0.550	1.00
110_K	114_D	0.548	1.00
187_G	200_V	0.546	1.00
232_E	235_D	0.546	1.00
227_Q	306_V	0.544	1.00
48_P	145_I	0.544	1.00
88_R	149_A	0.544	1.00
5_I	198_D	0.542	1.00
309_R	334_L	0.541	1.00
181_E	187_G	0.539	1.00
129_T	139_G	0.537	1.00
57_D	60_Q	0.536	1.00
201_I	329_Y	0.535	1.00
135_I	295_G	0.535	1.00
250_Q	255_F	0.534	1.00
294_P	297_A	0.533	1.00
351_K	357_Q	0.532	1.00
242_P	246_P	0.532	1.00
296_L	299_A	0.532	1.00
42_A	339_L	0.531	1.00
84_T	159_S	0.529	1.00
25_A	353_V	0.526	1.00
164_A	167_R	0.526	1.00
130_K	138_D	0.525	1.00
46_V	340_T	0.524	1.00
175_N	193_K	0.524	1.00
349_L	352_L	0.524	1.00
261_V	265_T	0.524	1.00
186_T	325_V	0.523	1.00
254_S	258_G	0.523	1.00
227_Q	278_T	0.522	1.00
38_A	309_R	0.522	1.00
240_S	245_M	0.521	1.00
59_Y	62_A	0.519	1.00
45_I	148_A	0.519	1.00
9_A	161_L	0.518	1.00
277_V	304_T	0.516	1.00
58_W	337_S	0.515	1.00
311_F	336_A	0.515	1.00
289_A	293_A	0.514	1.00
7_V	177_S	0.514	1.00
286_L	301_A	0.513	1.00
107_R	110_K	0.513	1.00
221_V	332_N	0.512	1.00
182_N	196_A	0.512	1.00
189_Q	192_T	0.512	1.00
227_Q	281_G	0.511	1.00
180_F	328_L	0.510	1.00
133_F	136_L	0.510	1.00
111_R	114_D	0.509	1.00
31_D	171_V	0.509	1.00
153_G	339_L	0.508	1.00
92_I	132_L	0.507	1.00
71_D	347_A	0.506	1.00
11_I	156_L	0.505	1.00
43_A	253_L	0.505	1.00
18_Y	21_A	0.505	1.00
206_A	223_F	0.505	1.00
202_V	211_I	0.503	1.00
297_A	300_A	0.503	1.00
58_W	69_Y	0.503	1.00
252_I	256_D	0.502	1.00
187_G	190_T	0.502	1.00
65_G	72_L	0.502	1.00
286_L	298_D	0.501	1.00
38_A	310_P	0.501	1.00
124_L	142_S	0.500	1.00

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
4h1bA	1	0.9624	100	0.26	Contact Map
1y56B	1	0.9624	100	0.298	Contact Map
4x9mA	1	0.9785	100	0.303	Contact Map
3axbA	2	0.9597	100	0.306	Contact Map
1ryiA	4	0.9597	100	0.307	Contact Map
2gf3A	1	0.9677	100	0.311	Contact Map
2gagB	1	0.9651	100	0.313	Contact Map
3pvcA	1	0.9516	100	0.325	Contact Map
3ps9A	1	0.957	100	0.329	Contact Map
4rslA	1	0.9489	100	0.333	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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