PYRC - ECOLI - GREMLIN Contacts

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PYRC - Dihydroorotase

UniProt:	P05020	Sequences: MTAPSQVLKIRRPDDWHLHLRDGDMLKTVVPYTSEIYGRAIVMPNLAPPVTTVEAAVAYRQRILDAVPAGHDFTPLMTCYLTDSLDPNELERGFNEGVFTAAKLYPANATTNSSHGVTSIDAIMPVLERMEKIGMPLLVHGEVTHADIDIFDREARFIESVMEPLRQRLTALKVVFEHITTKDAADYVRDGNERLAATITPQHLMFNRNHMLVGGVRPHLYCLPILKRNIHQQALRELVASGFNRVFLGTDSAPHARHRKESSCGCAGCFNAPTALGSYATVFEEMNALQHFEAFCSVNGPQFYGLPVNDTFIELVREEQQVAESIALTDDTLVPFLAGETVRWSVKQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10806
Length:	348 (328)
Sequences:	7288 (4437)
Seq/√Len:	245.0

ECOLI - PYRC ALLB PHYDA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
291_H	294_A	3.746	1.00
319_E	340_E	3.545	1.00
229_N	233_Q	3.203	1.00
229_N	232_Q	3.107	1.00
34_S	73_F	2.949	1.00
324_E	337_L	2.897	1.00
182_K	230_I	2.896	1.00
192_N	245_R	2.818	1.00
199_I	203_H	2.779	1.00
158_I	184_A	2.769	1.00
299_N	302_Q	2.764	1.00
124_M	169_L	2.681	1.00
20_L	29_V	2.517	1.00
322_V	341_T	2.506	1.00
323_A	326_I	2.499	1.00
4_P	315_L	2.455	1.00
288_A	291_H	2.370	1.00
7_V	315_L	2.322	1.00
9_K	315_L	2.317	1.00
129_R	132_K	2.295	1.00
294_A	299_N	2.270	1.00
204_L	235_L	2.216	1.00
320_Q	344_W	2.170	1.00
35_E	328_L	2.162	1.00
155_A	183_D	2.147	1.00
12_R	38_G	2.122	1.00
39_R	76_L	2.120	1.00
189_R	241_S	2.100	1.00
207_N	229_N	2.067	1.00
175_V	196_A	2.045	1.00
162_M	187_Y	2.028	1.00
319_E	342_V	2.025	1.00
200_T	203_H	2.009	1.00
321_Q	340_E	2.003	1.00
189_R	243_F	1.884	1.00
179_I	188_V	1.883	1.00
222_C	269_C	1.848	1.00
162_M	195_L	1.843	1.00
282_V	286_M	1.838	1.00
37_Y	275_A	1.818	1.00
27_K	31_P	1.795	1.00
279_Y	292_F	1.777	1.00
151_F	183_D	1.772	1.00
130_M	137_L	1.763	1.00
8_L	289_L	1.756	1.00
247_F	303_F	1.752	1.00
16_W	247_F	1.746	1.00
10_I	316_V	1.742	1.00
291_H	295_F	1.733	1.00
138_L	177_E	1.732	1.00
127_L	172_L	1.705	1.00
182_K	234_A	1.702	1.00
188_V	197_A	1.695	1.00
13_P	276_L	1.691	1.00
323_A	337_L	1.678	1.00
206_F	278_S	1.666	1.00
318_E	344_W	1.665	1.00
197_A	244_N	1.652	1.00
89_E	92_R	1.649	1.00
228_R	231_H	1.645	1.00
279_Y	296_C	1.643	1.00
181_T	184_A	1.615	1.00
24_D	29_V	1.605	1.00
16_W	304_Y	1.593	1.00
298_V	302_Q	1.576	1.00
10_I	293_E	1.574	1.00
25_M	330_D	1.562	1.00
285_E	342_V	1.544	1.00
207_N	210_H	1.534	1.00
205_M	278_S	1.532	1.00
134_G	305_G	1.522	1.00
307_P	310_D	1.511	1.00
143_V	156_R	1.506	1.00
250_T	275_A	1.506	1.00
194_R	303_F	1.471	1.00
31_P	328_L	1.465	1.00
50_V	56_A	1.453	1.00
185_A	238_L	1.447	1.00
186_D	190_D	1.440	1.00
221_Y	265_G	1.423	1.00
237_E	241_S	1.413	1.00
159_E	165_L	1.410	1.00
281_T	285_E	1.403	1.00
52_T	55_A	1.403	1.00
207_N	232_Q	1.401	1.00
239_V	295_F	1.399	1.00
91_E	129_R	1.391	1.00
270_F	331_D	1.388	1.00
293_E	297_S	1.387	1.00
182_K	186_D	1.386	1.00
7_V	317_R	1.383	1.00
20_L	40_A	1.380	1.00
159_E	187_Y	1.368	1.00
20_L	30_V	1.365	1.00
129_R	133_I	1.364	1.00
41_I	78_T	1.360	1.00
78_T	111_T	1.337	1.00
248_L	279_Y	1.331	1.00
119_S	122_A	1.329	1.00
110_T	135_M	1.303	1.00
294_A	298_V	1.302	1.00
30_V	71_H	1.292	1.00
9_K	313_I	1.291	1.00
14_D	301_P	1.290	1.00
208_R	228_R	1.283	1.00
81_L	126_V	1.275	1.00
257_R	261_E	1.265	1.00
190_D	193_E	1.261	1.00
161_V	174_V	1.251	1.00
130_M	135_M	1.250	1.00
281_T	342_V	1.232	1.00
124_M	170_T	1.226	1.00
322_V	327_A	1.224	1.00
4_P	9_K	1.223	1.00
183_D	231_H	1.220	1.00
236_R	282_V	1.209	1.00
283_F	286_M	1.208	1.00
134_G	173_K	1.207	1.00
97_G	135_M	1.201	1.00
165_L	168_R	1.197	1.00
83_D	89_E	1.192	1.00
10_I	314_E	1.192	1.00
41_I	76_L	1.191	1.00
237_E	240_A	1.189	1.00
275_A	296_C	1.187	1.00
136_P	173_K	1.181	1.00
283_F	287_N	1.178	1.00
25_M	28_T	1.173	1.00
276_L	280_A	1.167	1.00
92_R	95_N	1.165	1.00
173_K	305_G	1.164	1.00
281_T	339_G	1.163	1.00
124_M	128_E	1.161	1.00
233_Q	237_E	1.159	1.00
199_I	235_L	1.153	1.00
13_P	296_C	1.148	1.00
62_R	65_D	1.148	1.00
210_H	220_L	1.138	1.00
16_W	300_G	1.135	1.00
302_Q	308_V	1.133	1.00
248_L	295_F	1.126	1.00
274_T	322_V	1.122	1.00
41_I	304_Y	1.121	1.00
13_P	37_Y	1.114	1.00
53_V	57_V	1.098	1.00
167_Q	174_V	1.096	1.00
292_F	296_C	1.092	1.00
178_H	251_D	1.084	1.00
209_N	229_N	1.083	1.00
277_G	320_Q	1.077	1.00
206_F	220_L	1.064	1.00
10_I	13_P	1.053	1.00
176_F	179_I	1.053	1.00
151_F	155_A	1.052	1.00
120_I	143_V	1.052	1.00
151_F	228_R	1.048	1.00
125_P	128_E	1.046	1.00
186_D	189_R	1.044	1.00
68_P	71_H	1.042	1.00
297_S	300_G	1.029	1.00
152_D	169_L	1.027	1.00
201_P	271_N	1.018	1.00
167_Q	194_R	1.017	1.00
140_H	178_H	1.008	1.00
205_M	282_V	1.006	1.00
206_F	226_L	1.004	1.00
20_L	42_V	1.004	1.00
284_E	287_N	1.003	1.00
171_A	194_R	1.003	1.00
280_A	289_L	1.002	1.00
187_Y	190_D	1.000	1.00
127_L	137_L	0.999	1.00
14_D	39_R	0.997	1.00
30_V	72_D	0.993	1.00
23_G	255_H	0.992	1.00
25_M	69_A	0.991	1.00
173_K	194_R	0.990	1.00
162_M	191_G	0.985	1.00
158_I	176_F	0.985	1.00
240_A	291_H	0.979	1.00
123_I	139_V	0.967	1.00
120_I	160_S	0.966	1.00
27_K	72_D	0.966	1.00
49_P	80_Y	0.958	1.00
91_E	133_I	0.958	1.00
259_R	266_C	0.956	1.00
32_Y	270_F	0.956	1.00
79_C	96_E	0.952	1.00
78_T	138_L	0.951	1.00
191_G	195_L	0.951	1.00
33_T	40_A	0.949	1.00
280_A	284_E	0.942	1.00
232_Q	236_R	0.930	1.00
283_F	292_F	0.928	1.00
185_A	244_N	0.928	1.00
270_F	327_A	0.922	1.00
238_L	243_F	0.919	1.00
91_E	132_K	0.910	1.00
31_P	72_D	0.909	1.00
49_P	85_L	0.905	1.00
282_V	287_N	0.905	1.00
274_T	327_A	0.899	1.00
90_L	133_I	0.899	1.00
39_R	74_T	0.898	1.00
299_N	303_F	0.898	1.00
130_M	172_L	0.898	1.00
242_G	295_F	0.897	1.00
16_W	41_I	0.894	1.00
16_W	249_G	0.893	1.00
192_N	243_F	0.893	1.00
55_A	58_A	0.889	1.00
139_V	174_V	0.889	1.00
239_V	244_N	0.885	1.00
17_H	178_H	0.885	1.00
210_H	339_G	0.882	1.00
202_Q	222_C	0.881	1.00
196_A	303_F	0.877	0.99
177_E	198_T	0.870	0.99
27_K	69_A	0.867	0.99
34_S	72_D	0.866	0.99
23_G	259_R	0.865	0.99
51_T	55_A	0.862	0.99
20_L	272_A	0.857	0.99
54_E	58_A	0.855	0.99
218_P	265_G	0.854	0.99
276_L	316_V	0.853	0.99
234_A	238_L	0.851	0.99
12_R	311_T	0.849	0.99
74_T	308_V	0.848	0.99
202_Q	269_C	0.847	0.99
240_A	243_F	0.844	0.99
13_P	275_A	0.843	0.99
256_A	259_R	0.843	0.99
156_R	160_S	0.835	0.99
14_D	300_G	0.834	0.99
155_A	159_E	0.830	0.99
33_T	272_A	0.828	0.99
185_A	197_A	0.827	0.99
94_F	133_I	0.827	0.99
63_I	66_A	0.826	0.99
324_E	327_A	0.826	0.99
138_L	304_Y	0.820	0.99
121_D	125_P	0.820	0.99
185_A	235_L	0.818	0.99
236_R	287_N	0.817	0.99
21_R	255_H	0.817	0.99
280_A	316_V	0.813	0.99
294_A	302_Q	0.804	0.99
22_D	25_M	0.801	0.99
57_V	64_L	0.801	0.99
179_I	244_N	0.799	0.99
273_P	328_L	0.797	0.99
92_R	96_E	0.797	0.99
22_D	58_A	0.797	0.99
151_F	231_H	0.796	0.99
21_R	253_A	0.796	0.99
39_R	312_F	0.796	0.99
282_V	339_G	0.796	0.99
223_L	267_A	0.796	0.99
62_R	66_A	0.793	0.99
134_G	194_R	0.789	0.99
184_A	188_V	0.787	0.99
298_V	308_V	0.786	0.99
230_I	233_Q	0.786	0.99
204_L	279_Y	0.785	0.99
54_E	57_V	0.784	0.99
50_V	55_A	0.776	0.99
151_F	181_T	0.773	0.99
248_L	296_C	0.772	0.99
106_P	161_V	0.768	0.99
206_F	336_F	0.762	0.99
293_E	298_V	0.759	0.99
317_R	343_R	0.759	0.99
209_N	212_L	0.756	0.98
19_H	178_H	0.754	0.98
19_H	251_D	0.753	0.98
278_S	341_T	0.753	0.98
210_H	229_N	0.753	0.98
128_E	131_E	0.749	0.98
219_H	257_R	0.749	0.98
234_A	237_E	0.747	0.98
131_E	171_A	0.744	0.98
284_E	342_V	0.744	0.98
58_A	62_R	0.742	0.98
185_A	243_F	0.742	0.98
57_V	96_E	0.734	0.98
116_G	157_F	0.733	0.98
326_I	337_L	0.733	0.98
236_R	285_E	0.732	0.98
270_F	333_L	0.729	0.98
127_L	170_T	0.727	0.98
279_Y	283_F	0.727	0.98
22_D	62_R	0.725	0.98
88_N	129_R	0.725	0.98
182_K	237_E	0.725	0.98
30_V	40_A	0.724	0.98
276_L	313_I	0.722	0.98
18_L	272_A	0.720	0.98
211_M	220_L	0.720	0.98
152_D	156_R	0.719	0.98
334_V	337_L	0.717	0.98
231_H	234_A	0.716	0.98
262_S	266_C	0.715	0.98
236_R	283_F	0.715	0.98
154_E	184_A	0.714	0.98
93_G	110_T	0.714	0.98
327_A	337_L	0.712	0.98
284_E	292_F	0.710	0.98
121_D	124_M	0.709	0.98
247_F	304_Y	0.709	0.98
74_T	312_F	0.706	0.98
18_L	37_Y	0.705	0.98
141_G	157_F	0.701	0.98
32_Y	273_P	0.701	0.98
103_K	178_H	0.699	0.97
276_L	314_E	0.698	0.97
233_Q	236_R	0.695	0.97
320_Q	345_S	0.691	0.97
276_L	292_F	0.689	0.97
139_V	176_F	0.685	0.97
137_L	172_L	0.684	0.97
45_N	48_P	0.683	0.97
189_R	237_E	0.682	0.97
155_A	181_T	0.681	0.97
11_R	298_V	0.681	0.97
156_R	159_E	0.680	0.97
65_D	69_A	0.679	0.97
185_A	189_R	0.678	0.97
167_Q	172_L	0.673	0.97
53_V	92_R	0.672	0.97
197_A	245_R	0.672	0.97
236_R	286_M	0.671	0.97
124_M	152_D	0.671	0.97
35_E	273_P	0.664	0.97
91_E	96_E	0.663	0.97
131_E	169_L	0.660	0.96
2_T	315_L	0.660	0.96
139_V	161_V	0.660	0.96
19_H	43_M	0.659	0.96
94_F	135_M	0.657	0.96
158_I	179_I	0.657	0.96
269_C	335_P	0.656	0.96
221_Y	267_A	0.655	0.96
105_Y	108_N	0.652	0.96
277_G	344_W	0.649	0.96
8_L	316_V	0.646	0.96
318_E	345_S	0.646	0.96
39_R	301_P	0.645	0.96
319_E	343_R	0.645	0.96
179_I	184_A	0.644	0.96
182_K	231_H	0.644	0.96
179_I	197_A	0.641	0.96
275_A	279_Y	0.640	0.96
271_N	274_T	0.639	0.96
94_F	129_R	0.639	0.96
219_H	261_E	0.635	0.96
206_F	335_P	0.635	0.96
17_H	251_D	0.634	0.96
178_H	253_A	0.630	0.95
34_S	71_H	0.627	0.95
222_C	267_A	0.626	0.95
85_L	115_H	0.624	0.95
79_C	93_G	0.619	0.95
189_R	193_E	0.617	0.95
166_R	170_T	0.617	0.95
196_A	245_R	0.616	0.95
219_H	333_L	0.614	0.95
104_L	126_V	0.613	0.95
83_D	118_T	0.612	0.95
159_E	190_D	0.612	0.95
127_L	174_V	0.611	0.95
283_F	289_L	0.610	0.95
23_G	256_A	0.609	0.95
82_T	122_A	0.608	0.94
120_I	156_R	0.608	0.94
16_W	175_V	0.608	0.94
276_L	296_C	0.608	0.94
201_P	274_T	0.606	0.94
274_T	277_G	0.606	0.94
186_D	234_A	0.602	0.94
165_L	169_L	0.601	0.94
320_Q	341_T	0.601	0.94
143_V	160_S	0.600	0.94
64_L	68_P	0.598	0.94
217_R	220_L	0.598	0.94
122_A	125_P	0.597	0.94
316_V	345_S	0.596	0.94
44_P	85_L	0.596	0.94
71_H	75_P	0.595	0.94
105_Y	109_A	0.595	0.94
327_A	332_T	0.594	0.94
30_V	75_P	0.594	0.94
51_T	82_T	0.594	0.94
239_V	248_L	0.594	0.94
325_S	337_L	0.593	0.94
32_Y	272_A	0.592	0.94
280_A	343_R	0.590	0.94
80_Y	85_L	0.590	0.94
108_N	112_N	0.589	0.93
17_H	43_M	0.589	0.93
199_I	204_L	0.589	0.93
201_P	279_Y	0.588	0.93
280_A	292_F	0.586	0.93
93_G	97_G	0.586	0.93
327_A	334_V	0.586	0.93
127_L	167_Q	0.585	0.93
142_E	223_L	0.584	0.93
40_A	73_F	0.582	0.93
38_G	312_F	0.579	0.93
302_Q	310_D	0.576	0.93
131_E	170_T	0.575	0.93
45_N	80_Y	0.572	0.92
167_Q	170_T	0.571	0.92
277_G	341_T	0.570	0.92
11_R	310_D	0.570	0.92
247_F	295_F	0.569	0.92
78_T	177_E	0.566	0.92
274_T	336_F	0.565	0.92
295_F	299_N	0.564	0.92
175_V	303_F	0.563	0.92
302_Q	307_P	0.563	0.92
149_D	267_A	0.561	0.92
262_S	265_G	0.560	0.92
41_I	138_L	0.559	0.92
79_C	91_E	0.558	0.92
51_T	80_Y	0.558	0.92
166_R	195_L	0.557	0.91
83_D	86_D	0.556	0.91
17_H	198_T	0.555	0.91
28_T	330_D	0.555	0.91
314_E	345_S	0.554	0.91
11_R	293_E	0.554	0.91
201_P	249_G	0.554	0.91
41_I	306_L	0.553	0.91
183_D	186_D	0.551	0.91
258_H	261_E	0.551	0.91
199_I	239_V	0.550	0.91
84_S	87_P	0.549	0.91
106_P	109_A	0.549	0.91
21_R	45_N	0.549	0.91
30_V	73_F	0.548	0.91
91_E	95_N	0.547	0.91
45_N	255_H	0.547	0.91
182_K	238_L	0.547	0.91
205_M	339_G	0.546	0.91
88_N	92_R	0.546	0.91
133_I	136_P	0.545	0.91
65_D	68_P	0.543	0.90
276_L	289_L	0.542	0.90
200_T	249_G	0.541	0.90
309_N	312_F	0.540	0.90
222_C	226_L	0.538	0.90
53_V	89_E	0.538	0.90
19_H	253_A	0.538	0.90
283_F	288_A	0.535	0.90
56_A	77_M	0.534	0.90
218_P	261_E	0.534	0.90
277_G	345_S	0.534	0.90
32_Y	36_I	0.533	0.90
162_M	168_R	0.532	0.90
105_Y	110_T	0.531	0.89
166_R	187_Y	0.528	0.89
176_F	188_V	0.527	0.89
14_D	308_V	0.526	0.89
131_E	172_L	0.524	0.89
322_V	334_V	0.523	0.89
219_H	337_L	0.522	0.89
341_T	344_W	0.519	0.88
189_R	234_A	0.517	0.88
26_L	71_H	0.516	0.88
127_L	130_M	0.516	0.88
117_V	123_I	0.515	0.88
202_Q	251_D	0.514	0.88
38_G	311_T	0.513	0.88
104_L	123_I	0.513	0.88
125_P	129_R	0.513	0.88
141_G	176_F	0.512	0.88
123_I	161_V	0.511	0.88
18_L	252_S	0.510	0.87
140_H	251_D	0.510	0.87
36_I	277_G	0.509	0.87
4_P	313_I	0.508	0.87
281_T	341_T	0.507	0.87
6_Q	317_R	0.506	0.87
282_V	285_E	0.505	0.87
327_A	331_D	0.504	0.87
301_P	308_V	0.503	0.87
18_L	40_A	0.503	0.87
274_T	334_V	0.502	0.87
318_E	321_Q	0.501	0.87
155_A	187_Y	0.501	0.87
52_T	89_E	0.500	0.86

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
2z26A	2	0.9655	100	0.35	Contact Map
4lfyA	2	0.9713	100	0.355	Contact Map
3dc8A	3	0.9598	100	0.45	Contact Map
2ftyA	3	0.9626	100	0.452	Contact Map
3pnuA	2	0.9454	100	0.457	Contact Map
4lcqA	3	0.9655	100	0.462	Contact Map
4c6eA	2	0.9023	100	0.465	Contact Map
2ftwA	3	0.9655	100	0.478	Contact Map
3e74A	3	0.9397	100	0.479	Contact Map
3griA	1	0.9483	100	0.489	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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