YBDR - ECOLI - GREMLIN Contacts

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YBDR - Uncharacterized zinc-type alcohol dehydrogenase-like protein YbdR

UniProt:	P77316	Sequences: MKALTYHGPHHVQVENVPDPGVEQADDIILRITATAICGSDLHLYRGKIPQVKHGDIFGHEFMGEVVETGKDVKNLQKGDRVVIPFVIACGDCFFCRLQQYAACENTNAGKGAALNKKQIPAPAALFGYSHLYGGVPGGQAEYVRVPKGNVGPFKVPPLLSDDKALFLSDILPTAWQAAKNAQIQQGSSVAVYGAGPVGLLTIACARLLGAEQIFVVDHHPYRLHFAADRYGAIPINFDEDSDPAQSIIEQTAGHRGVDAVIDAVGFEAKGSTTETVLTNLKLEGSSGKALRQCIAAVRRGGIVSVPGVYAGFIHGFLFGDAFDKGLSFKMGQTHVHAWLGELLPLIEKGLLKPEEIVTHYMPFEEAARGYEIFEKREEECRKVILVPGAQSAEAAQKAVSGLVNAMPGGTI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13537
Length:	412 (336)
Sequences:	30925 (20196)
Seq/√Len:	1101.8

ECOLI - YBDR YGGP FRMA YDJL GATD RSPB YPHC YJJN YAHK ADHP TDH YDJJ AHR IDND QOR1 YCJQ ACUI CURA
BACSU - ADHB YYCR YJMD DHSO TDH BDHA ADHA YOGA YHFP YFMJ
HALSA - Q9HMB6 Q9HP38 GLCDH Q9HR85 Q9HQS8
SULSO - Q97YT7 ADH Q97ZV3 Q7LXK1 Q97VV5 Q97XR4 Q97V32 Q97VW0 Q97YM2 Q97WA1 Q97TZ4 GLCD2 GLCD1 GLCD3 Q97W06 Q97VB8 Q97UW5

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_T	65_E	3.122	1.00
366_E	369_R	3.093	1.00
33_T	162_D	3.063	1.00
31_R	67_V	2.987	1.00
189_S	213_Q	2.802	1.00
7_H	15_E	2.665	1.00
29_I	67_V	2.613	1.00
80_D	155_K	2.502	1.00
7_H	13_Q	2.485	1.00
247_S	250_E	2.453	1.00
163_D	361_Y	2.452	1.00
207_R	234_I	2.439	1.00
62_F	139_G	2.432	1.00
161_S	164_K	2.373	1.00
361_Y	387_V	2.362	1.00
25_A	71_K	2.340	1.00
362_M	373_I	2.293	1.00
26_D	72_D	2.285	1.00
46_R	375_E	2.277	1.00
363_P	366_E	2.258	1.00
224_L	228_A	2.252	1.00
372_E	376_K	2.230	1.00
31_R	65_E	2.206	1.00
25_A	72_D	2.201	1.00
360_H	373_I	2.191	1.00
31_R	143_Y	2.190	1.00
159_L	348_E	2.143	1.00
213_Q	235_P	2.130	1.00
77_Q	80_D	2.122	1.00
19_D	143_Y	2.111	1.00
75_N	148_K	2.107	1.00
303_I	328_S	2.089	1.00
190_V	206_A	2.060	1.00
345_P	349_K	2.049	1.00
185_Q	188_S	2.036	1.00
5_T	15_E	2.020	1.00
23_E	27_D	2.013	1.00
191_A	258_V	2.009	1.00
81_R	162_D	1.972	1.00
21_G	68_E	1.962	1.00
225_H	230_R	1.960	1.00
195_A	216_V	1.897	1.00
298_V	304_V	1.866	1.00
221_P	225_H	1.865	1.00
303_I	330_K	1.858	1.00
67_V	143_Y	1.830	1.00
225_H	228_A	1.829	1.00
29_I	145_R	1.827	1.00
226_F	230_R	1.762	1.00
156_V	165_A	1.757	1.00
224_L	236_I	1.751	1.00
62_F	84_I	1.739	1.00
191_A	217_V	1.738	1.00
81_R	156_V	1.726	1.00
235_P	251_Q	1.703	1.00
4_L	367_A	1.696	1.00
259_D	299_R	1.680	1.00
69_T	78_K	1.679	1.00
298_V	327_L	1.651	1.00
203_I	233_A	1.648	1.00
369_R	372_E	1.646	1.00
261_V	298_V	1.646	1.00
373_I	378_E	1.637	1.00
362_M	370_G	1.635	1.00
369_R	373_I	1.624	1.00
213_Q	234_I	1.622	1.00
68_E	78_K	1.612	1.00
368_A	372_E	1.596	1.00
63_M	162_D	1.596	1.00
180_K	342_E	1.570	1.00
215_F	258_V	1.559	1.00
221_P	238_F	1.558	1.00
218_D	224_L	1.557	1.00
29_I	143_Y	1.543	1.00
22_V	29_I	1.528	1.00
242_S	247_S	1.521	1.00
2_K	365_E	1.515	1.00
76_L	155_K	1.499	1.00
66_V	76_L	1.496	1.00
93_C	96_C	1.494	1.00
2_K	16_N	1.490	1.00
345_P	348_E	1.489	1.00
32_I	62_F	1.481	1.00
163_D	387_V	1.478	1.00
172_L	201_L	1.470	1.00
26_D	147_P	1.466	1.00
65_E	162_D	1.465	1.00
243_D	246_Q	1.460	1.00
70_G	73_V	1.453	1.00
65_E	81_R	1.442	1.00
261_V	294_C	1.438	1.00
81_R	158_P	1.424	1.00
219_H	239_D	1.424	1.00
27_D	145_R	1.421	1.00
29_I	68_E	1.414	1.00
27_D	147_P	1.409	1.00
247_S	251_Q	1.405	1.00
228_A	236_I	1.393	1.00
34_A	163_D	1.387	1.00
22_V	145_R	1.369	1.00
76_L	80_D	1.364	1.00
19_D	29_I	1.359	1.00
3_A	17_V	1.357	1.00
28_I	151_V	1.356	1.00
246_Q	250_E	1.350	1.00
34_A	387_V	1.350	1.00
189_S	215_F	1.337	1.00
202_T	262_I	1.329	1.00
203_I	216_V	1.329	1.00
296_A	321_D	1.328	1.00
26_D	148_K	1.310	1.00
298_V	302_G	1.308	1.00
193_Y	294_C	1.299	1.00
221_P	224_L	1.294	1.00
181_N	328_S	1.293	1.00
8_G	11_H	1.290	1.00
90_C	93_C	1.273	1.00
241_D	247_S	1.271	1.00
265_V	290_A	1.267	1.00
188_S	303_I	1.267	1.00
4_L	14_V	1.257	1.00
208_L	351_L	1.252	1.00
94_F	299_R	1.249	1.00
156_V	162_D	1.229	1.00
90_C	96_C	1.229	1.00
180_K	339_W	1.227	1.00
93_C	104_C	1.223	1.00
182_A	260_A	1.221	1.00
32_I	144_V	1.207	1.00
2_K	142_E	1.203	1.00
28_I	76_L	1.188	1.00
292_R	296_A	1.184	1.00
22_V	27_D	1.162	1.00
7_H	11_H	1.155	1.00
164_K	353_K	1.152	1.00
96_C	104_C	1.151	1.00
363_P	387_V	1.140	1.00
364_F	388_P	1.136	1.00
175_A	202_T	1.133	1.00
30_L	82_V	1.128	1.00
92_D	106_N	1.127	1.00
5_T	17_V	1.126	1.00
140_Q	371_Y	1.125	1.00
195_A	218_D	1.124	1.00
105_E	300_R	1.123	1.00
208_L	346_L	1.113	1.00
193_Y	217_V	1.112	1.00
219_H	240_E	1.109	1.00
188_S	260_A	1.105	1.00
34_A	162_D	1.102	1.00
189_S	259_D	1.091	1.00
184_I	211_A	1.090	1.00
216_V	227_A	1.087	1.00
182_A	305_S	1.081	1.00
160_L	165_A	1.079	1.00
221_P	241_D	1.077	1.00
224_L	238_F	1.076	1.00
359_T	373_I	1.076	1.00
67_V	78_K	1.073	1.00
191_A	297_A	1.072	1.00
37_I	370_G	1.071	1.00
204_A	353_K	1.066	1.00
35_T	139_G	1.063	1.00
372_E	375_E	1.063	1.00
188_S	259_D	1.063	1.00
217_V	239_D	1.062	1.00
30_L	64_G	1.054	1.00
17_V	57_I	1.046	1.00
92_D	97_R	1.044	1.00
313_F	316_G	1.042	1.00
184_I	188_S	1.042	1.00
367_A	386_L	1.039	1.00
238_F	241_D	1.036	1.00
222_Y	225_H	1.029	1.00
168_L	347_I	1.028	1.00
100_Q	301_G	1.028	1.00
4_L	364_F	1.022	1.00
90_C	104_C	1.015	1.00
228_A	235_P	1.015	1.00
341_G	345_P	1.012	1.00
177_Q	339_W	1.011	1.00
322_A	329_F	1.011	1.00
140_Q	367_A	1.007	1.00
35_T	140_Q	1.003	1.00
23_E	145_R	0.999	1.00
33_T	63_M	0.998	1.00
178_A	307_P	0.997	1.00
294_C	304_V	0.997	1.00
245_A	249_I	0.996	1.00
94_F	98_L	0.991	1.00
17_V	137_P	0.991	1.00
215_F	251_Q	0.991	1.00
74_K	148_K	0.989	1.00
245_A	296_A	0.988	1.00
14_V	365_E	0.987	1.00
215_F	235_P	0.985	1.00
56_D	137_P	0.979	1.00
33_T	81_R	0.978	1.00
243_D	247_S	0.972	1.00
301_G	326_G	0.970	1.00
215_F	237_N	0.962	1.00
342_E	345_P	0.957	1.00
362_M	366_E	0.956	1.00
45_Y	371_Y	0.952	1.00
19_D	68_E	0.946	1.00
31_R	142_E	0.945	1.00
157_P	348_E	0.943	1.00
94_F	105_E	0.937	1.00
193_Y	290_A	0.936	1.00
321_D	325_K	0.932	1.00
181_N	330_K	0.925	1.00
245_A	293_Q	0.924	1.00
203_I	214_I	0.922	1.00
205_C	343_L	0.921	1.00
175_A	205_C	0.920	1.00
337_H	341_G	0.916	1.00
216_V	233_A	0.915	1.00
34_A	385_I	0.912	1.00
206_A	211_A	0.911	1.00
69_T	77_Q	0.910	1.00
84_I	146_V	0.909	1.00
192_V	206_A	0.901	1.00
5_T	57_I	0.898	1.00
293_Q	296_A	0.894	1.00
346_L	351_L	0.893	1.00
306_V	329_F	0.893	1.00
69_T	73_V	0.893	1.00
95_F	105_E	0.879	1.00
248_I	258_V	0.878	1.00
267_F	290_A	0.872	1.00
140_Q	386_L	0.870	1.00
252_T	257_G	0.863	1.00
220_H	223_R	0.863	1.00
218_D	236_I	0.860	1.00
62_F	144_V	0.860	1.00
219_H	224_L	0.859	1.00
146_V	151_V	0.858	1.00
32_I	388_P	0.847	1.00
193_Y	261_V	0.847	1.00
362_M	384_V	0.844	1.00
362_M	386_L	0.842	1.00
172_L	343_L	0.836	1.00
38_C	60_H	0.833	1.00
261_V	304_V	0.830	1.00
358_V	361_Y	0.829	1.00
19_D	67_V	0.829	1.00
268_E	292_R	0.823	1.00
94_F	256_R	0.821	1.00
318_L	321_D	0.804	1.00
322_A	331_M	0.802	1.00
245_A	297_A	0.802	1.00
175_A	201_L	0.801	1.00
28_I	148_K	0.800	1.00
4_L	12_V	0.799	1.00
258_V	261_V	0.798	1.00
183_Q	328_S	0.796	1.00
195_A	203_I	0.796	1.00
184_I	260_A	0.794	1.00
263_D	266_G	0.794	1.00
338_A	342_E	0.792	1.00
103_A	326_G	0.791	1.00
342_E	346_L	0.788	1.00
177_Q	326_G	0.788	1.00
38_C	61_E	0.787	1.00
26_D	71_K	0.785	1.00
360_H	381_C	0.785	1.00
189_S	258_V	0.785	1.00
176_W	342_E	0.784	1.00
176_W	343_L	0.783	1.00
183_Q	330_K	0.782	1.00
45_Y	375_E	0.779	1.00
183_Q	303_I	0.778	1.00
215_F	248_I	0.778	1.00
373_I	384_V	0.775	1.00
3_A	57_I	0.774	1.00
154_F	341_G	0.765	1.00
95_F	100_Q	0.765	1.00
214_I	234_I	0.762	1.00
175_A	198_V	0.761	1.00
338_A	341_G	0.754	1.00
77_Q	155_K	0.753	1.00
190_V	211_A	0.751	1.00
206_A	214_I	0.751	1.00
226_F	381_C	0.744	1.00
91_G	149_G	0.741	1.00
207_R	214_I	0.740	1.00
4_L	368_A	0.737	1.00
23_E	26_D	0.737	1.00
34_A	388_P	0.736	1.00
22_V	70_G	0.734	1.00
322_A	327_L	0.730	1.00
180_K	209_L	0.728	1.00
94_F	259_D	0.727	1.00
346_L	350_G	0.726	1.00
309_V	323_F	0.725	1.00
76_L	151_V	0.722	1.00
192_V	216_V	0.722	1.00
246_Q	249_I	0.721	1.00
85_P	154_F	0.720	1.00
154_F	340_L	0.720	1.00
373_I	376_K	0.717	1.00
248_I	297_A	0.715	1.00
21_G	29_I	0.715	1.00
34_A	361_Y	0.714	1.00
81_R	159_L	0.711	1.00
95_F	300_R	0.711	1.00
192_V	202_T	0.706	1.00
2_K	14_V	0.701	1.00
80_D	158_P	0.700	1.00
292_R	316_G	0.699	1.00
22_V	68_E	0.698	1.00
30_L	84_I	0.697	1.00
108_N	136_V	0.694	1.00
235_P	247_S	0.692	1.00
36_A	61_E	0.691	1.00
37_I	140_Q	0.689	1.00
154_F	344_L	0.689	1.00
313_F	318_L	0.688	1.00
158_P	348_E	0.686	1.00
42_L	375_E	0.685	1.00
243_D	293_Q	0.684	1.00
63_M	166_L	0.684	1.00
260_A	305_S	0.684	1.00
26_D	70_G	0.683	1.00
14_V	364_F	0.682	1.00
195_A	227_A	0.681	1.00
211_A	214_I	0.678	1.00
26_D	149_G	0.678	1.00
73_V	148_K	0.676	1.00
168_L	344_L	0.674	1.00
300_R	325_K	0.673	1.00
40_S	60_H	0.673	1.00
11_H	368_A	0.672	1.00
168_L	343_L	0.671	1.00
244_P	293_Q	0.671	1.00
360_H	369_R	0.670	1.00
52_V	56_D	0.667	1.00
359_T	382_R	0.666	1.00
179_A	206_A	0.664	1.00
139_G	144_V	0.664	1.00
28_I	66_V	0.663	1.00
42_L	374_F	0.661	1.00
261_V	297_A	0.654	1.00
105_E	256_R	0.654	1.00
347_I	354_P	0.650	1.00
268_E	316_G	0.649	1.00
227_A	233_A	0.648	1.00
175_A	179_A	0.648	1.00
20_P	143_Y	0.642	1.00
35_T	388_P	0.640	1.00
63_M	81_R	0.637	1.00
207_R	233_A	0.630	1.00
204_A	231_Y	0.630	1.00
346_L	349_K	0.628	1.00
186_Q	209_L	0.627	1.00
127_F	130_S	0.626	1.00
305_S	330_K	0.625	1.00
10_H	372_E	0.625	1.00
292_R	321_D	0.625	1.00
374_F	384_V	0.625	1.00
88_I	150_N	0.623	1.00
179_A	205_C	0.622	1.00
263_D	304_V	0.622	1.00
95_F	98_L	0.621	1.00
218_D	227_A	0.617	1.00
173_P	335_H	0.616	1.00
53_K	56_D	0.614	1.00
176_W	346_L	0.613	1.00
260_A	303_I	0.613	1.00
190_V	260_A	0.613	1.00
265_V	308_G	0.612	1.00
218_D	239_D	0.609	1.00
126_L	130_S	0.608	1.00
191_A	248_I	0.606	1.00
321_D	324_D	0.606	1.00
37_I	374_F	0.605	1.00
321_D	327_L	0.605	1.00
192_V	203_I	0.605	1.00
20_P	145_R	0.605	1.00
244_P	248_I	0.602	1.00
60_H	170_D	0.593	1.00
237_N	247_S	0.593	1.00
269_A	293_Q	0.592	1.00
186_Q	210_G	0.591	1.00
202_T	264_A	0.591	1.00
202_T	307_P	0.590	1.00
371_Y	375_E	0.589	1.00
83_V	156_V	0.586	1.00
305_S	332_G	0.585	1.00
59_G	140_Q	0.585	1.00
223_R	381_C	0.584	1.00
75_N	155_K	0.583	1.00
34_A	63_M	0.580	1.00
237_N	244_P	0.579	1.00
358_V	385_I	0.578	1.00
204_A	352_L	0.577	1.00
230_R	353_K	0.576	1.00
370_G	386_L	0.576	1.00
38_C	41_D	0.574	1.00
69_T	80_D	0.572	1.00
160_L	347_I	0.571	1.00
384_V	387_V	0.571	1.00
28_I	69_T	0.570	1.00
380_E	384_V	0.570	1.00
209_L	342_E	0.569	1.00
237_N	251_Q	0.567	1.00
217_V	237_N	0.567	1.00
269_A	290_A	0.567	1.00
36_A	166_L	0.566	1.00
203_I	227_A	0.566	1.00
174_T	198_V	0.564	1.00
160_L	348_E	0.562	1.00
171_I	201_L	0.562	1.00
178_A	262_I	0.561	1.00
69_T	76_L	0.560	1.00
350_G	353_K	0.560	1.00
258_V	297_A	0.560	1.00
91_G	96_C	0.559	1.00
200_L	382_R	0.558	1.00
38_C	170_D	0.558	1.00
269_A	292_R	0.557	1.00
12_V	371_Y	0.553	1.00
205_C	346_L	0.552	1.00
292_R	318_L	0.551	1.00
213_Q	251_Q	0.551	1.00
37_I	386_L	0.550	1.00
44_L	56_D	0.550	1.00
293_Q	297_A	0.550	1.00
176_W	205_C	0.549	1.00
222_Y	378_E	0.549	1.00
291_L	306_V	0.547	1.00
381_C	384_V	0.546	1.00
189_S	252_T	0.546	1.00
20_P	29_I	0.546	1.00
354_P	357_I	0.545	1.00
75_N	337_H	0.545	1.00
33_T	387_V	0.545	1.00
344_L	348_E	0.545	1.00
176_W	339_W	0.543	1.00
193_Y	297_A	0.541	1.00
39_G	43_H	0.540	1.00
249_I	257_G	0.538	1.00
155_K	158_P	0.534	1.00
264_A	307_P	0.533	1.00
42_L	46_R	0.532	1.00
193_Y	293_Q	0.532	1.00
40_S	43_H	0.532	1.00
256_R	299_R	0.531	1.00
94_F	97_R	0.530	1.00
10_H	45_Y	0.530	1.00
182_A	303_I	0.529	1.00
86_F	334_T	0.528	1.00
43_H	48_K	0.528	1.00
170_D	174_T	0.527	1.00
221_P	228_A	0.527	1.00
157_P	165_A	0.526	1.00
228_A	234_I	0.524	1.00
12_V	367_A	0.524	1.00
252_T	258_V	0.523	1.00
172_L	205_C	0.523	1.00
98_L	299_R	0.523	1.00
201_L	357_I	0.523	1.00
95_F	103_A	0.523	1.00
203_I	207_R	0.522	1.00
84_I	139_G	0.522	1.00
201_L	204_A	0.521	1.00
34_A	166_L	0.521	1.00
178_A	332_G	0.521	1.00
197_P	383_K	0.520	1.00
32_I	35_T	0.520	1.00
189_S	256_R	0.520	1.00
178_A	202_T	0.518	1.00
290_A	293_Q	0.517	1.00
263_D	308_G	0.515	1.00
291_L	319_F	0.515	1.00
83_V	344_L	0.515	1.00
100_Q	103_A	0.514	1.00
362_M	369_R	0.513	1.00
14_V	367_A	0.512	1.00
81_R	161_S	0.512	1.00
74_K	77_Q	0.512	1.00
190_V	262_I	0.510	1.00
3_A	141_A	0.509	1.00
63_M	165_A	0.509	1.00
173_P	339_W	0.509	1.00
219_H	238_F	0.509	1.00
208_L	352_L	0.509	1.00
200_L	226_F	0.509	1.00
218_D	223_R	0.508	1.00
201_L	205_C	0.508	1.00
28_I	73_V	0.507	1.00
242_S	246_Q	0.507	1.00
81_R	165_A	0.507	1.00
295_I	304_V	0.505	1.00
256_R	259_D	0.505	1.00
253_A	256_R	0.505	1.00
75_N	341_G	0.504	1.00
19_D	22_V	0.503	1.00
320_G	324_D	0.503	1.00
66_V	80_D	0.503	1.00
339_W	342_E	0.502	1.00
177_Q	332_G	0.502	1.00
183_Q	188_S	0.501	1.00
75_N	78_K	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
4cpdA	2	0.8374	100	0.256	Contact Map
3ukoA	4	0.8762	100	0.259	Contact Map
4ilkA	2	0.8107	100	0.26	Contact Map
4ej6A	1	0.8155	100	0.261	Contact Map
1cdoA	2	0.8689	100	0.265	Contact Map
1h2bA	4	0.8107	100	0.266	Contact Map
1f8fA	4	0.8544	100	0.269	Contact Map
1e3iA	2	0.8665	100	0.271	Contact Map
1rjwA	4	0.8155	100	0.271	Contact Map
2dq4A	4	0.8155	100	0.271	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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