GLDA - ECOLI - GREMLIN Contacts

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GLDA - Glycerol dehydrogenase

UniProt:	P0A9S5	Sequences: MDRIIQSPGKYIQGADVINRLGEYLKPLAERWLVVGDKFVLGFAQSTVEKSFKDAGLVVEIAPFGGECSQNEIDRLRGIAETAQCGAILGIGGGKTLDTAKALAHFMGVPVAIAPTIASTDAPCSALSVIYTDEGEFDRYLLLPNNPNMVIVDTKIVAGAPARLLAAGIGDALATWFEARACSRSGATTMAGGKCTQAALALAELCYNTLLEEGEKAMLAAEQHVVTPALERVIEANTYLSGVGFESGGLAAAHAVHNGLTAIPDAHHYYHGEKVAFGTLTQLVLENAPVEEIETVAALSHAVGLPITLAQLDIKEDVPAKMRIVAEAACAEGETIHNMPGGATPDQVYAALLVADQYGQRFLQEWE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11904
Length:	367 (323)
Sequences:	13909 (9679)
Seq/√Len:	538.6

ECOLI - GLDA FUCO ADH2 EUTG YQHD YBDH ADHE
BACSU - GBSB YUGJ YUGK G1PDH
HALSA - Q9HHR2 Q9HNB5 G1PDH
SULSO - G1PDH Q97VW4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
327_E	345_P	3.455	1.00
323_R	349_Y	3.309	1.00
284_V	297_A	3.041	1.00
215_E	302_A	3.006	1.00
78_G	82_T	2.869	1.00
76_L	103_L	2.612	1.00
71_N	133_D	2.577	1.00
15_A	155_K	2.555	1.00
88_I	100_A	2.472	1.00
216_K	227_T	2.454	1.00
46_S	50_K	2.450	1.00
344_T	347_Q	2.409	1.00
32_W	87_A	2.373	1.00
220_A	227_T	2.363	1.00
20_R	23_E	2.330	1.00
316_E	353_L	2.300	1.00
163_R	273_E	2.280	1.00
349_Y	353_L	2.218	1.00
31_R	58_V	2.193	1.00
162_A	166_A	2.188	1.00
16_D	155_K	2.145	1.00
110_P	148_N	2.122	1.00
158_A	228_P	2.096	1.00
256_V	352_L	2.056	1.00
322_M	349_Y	2.047	1.00
213_E	233_V	2.034	1.00
90_G	100_A	1.992	1.00
77_R	106_F	1.982	1.00
49_E	53_K	1.963	1.00
79_I	83_A	1.948	1.00
315_K	321_K	1.937	1.00
315_K	320_A	1.888	1.00
39_F	43_F	1.886	1.00
63_P	75_R	1.876	1.00
19_N	47_T	1.873	1.00
345_P	349_Y	1.871	1.00
17_V	20_R	1.866	1.00
46_S	49_E	1.843	1.00
215_E	219_L	1.836	1.00
298_A	302_A	1.834	1.00
60_E	83_A	1.824	1.00
97_L	113_I	1.815	1.00
205_L	208_N	1.789	1.00
72_E	75_R	1.781	1.00
167_A	273_E	1.780	1.00
257_H	274_K	1.775	1.00
152_V	235_E	1.774	1.00
79_I	82_T	1.752	1.00
176_W	206_C	1.718	1.00
53_K	59_V	1.709	1.00
80_A	107_M	1.685	1.00
326_A	349_Y	1.676	1.00
30_E	86_G	1.673	1.00
286_E	339_M	1.649	1.00
301_H	307_I	1.649	1.00
80_A	109_V	1.636	1.00
65_G	72_E	1.625	1.00
321_K	324_I	1.613	1.00
325_V	352_L	1.585	1.00
308_T	311_Q	1.578	1.00
24_Y	27_P	1.560	1.00
33_L	80_A	1.551	1.00
188_T	295_T	1.539	1.00
80_A	85_C	1.533	1.00
323_R	345_P	1.529	1.00
22_G	51_S	1.512	1.00
263_I	324_I	1.512	1.00
326_A	345_P	1.486	1.00
33_L	79_I	1.485	1.00
283_L	296_V	1.478	1.00
324_I	328_A	1.478	1.00
294_E	298_A	1.475	1.00
41_L	62_A	1.462	1.00
213_E	216_K	1.450	1.00
70_Q	74_D	1.443	1.00
290_V	294_E	1.440	1.00
216_K	220_A	1.435	1.00
35_V	100_A	1.433	1.00
246_E	249_G	1.426	1.00
227_T	230_L	1.422	1.00
60_E	79_I	1.420	1.00
350_A	353_L	1.418	1.00
173_L	207_Y	1.415	1.00
73_I	99_T	1.413	1.00
37_D	40_V	1.411	1.00
75_R	78_G	1.398	1.00
32_W	89_L	1.379	1.00
132_T	135_G	1.375	1.00
165_L	231_E	1.372	1.00
155_K	158_A	1.358	1.00
50_K	54_D	1.337	1.00
112_A	149_M	1.331	1.00
73_I	130_I	1.323	1.00
33_L	85_C	1.321	1.00
277_F	312_L	1.320	1.00
47_T	155_K	1.319	1.00
172_A	210_L	1.302	1.00
49_E	59_V	1.289	1.00
71_N	74_D	1.285	1.00
24_Y	149_M	1.277	1.00
14_G	20_R	1.267	1.00
15_A	158_A	1.257	1.00
297_A	301_H	1.254	1.00
347_Q	350_A	1.248	1.00
88_I	104_A	1.247	1.00
269_Y	274_K	1.246	1.00
97_L	122_A	1.245	1.00
215_E	218_M	1.239	1.00
295_T	298_A	1.239	1.00
170_G	300_S	1.238	1.00
229_A	233_V	1.237	1.00
50_K	53_K	1.227	1.00
157_V	235_E	1.218	1.00
26_K	55_A	1.216	1.00
157_V	231_E	1.216	1.00
38_K	63_P	1.215	1.00
31_R	60_E	1.205	1.00
346_D	349_Y	1.205	1.00
90_G	111_V	1.190	1.00
35_V	103_L	1.189	1.00
219_L	302_A	1.189	1.00
38_K	62_A	1.189	1.00
10_K	24_Y	1.187	1.00
167_A	270_Y	1.184	1.00
11_Y	239_Y	1.184	1.00
48_V	91_I	1.184	1.00
74_D	78_G	1.181	1.00
324_I	327_E	1.171	1.00
87_A	112_A	1.165	1.00
169_I	214_G	1.162	1.00
161_P	164_L	1.157	1.00
73_I	103_L	1.152	1.00
256_V	278_G	1.150	1.00
214_G	218_M	1.148	1.00
25_L	87_A	1.138	1.00
105_H	143_L	1.137	1.00
18_I	47_T	1.136	1.00
38_K	42_G	1.129	1.00
170_G	305_L	1.129	1.00
322_M	353_L	1.123	1.00
31_R	83_A	1.120	1.00
21_L	48_V	1.116	1.00
12_I	24_Y	1.110	1.00
211_L	214_G	1.108	1.00
15_A	228_P	1.106	1.00
127_L	142_L	1.105	1.00
73_I	77_R	1.102	1.00
80_A	88_I	1.100	1.00
77_R	81_E	1.100	1.00
169_I	234_I	1.099	1.00
327_E	331_A	1.092	1.00
252_A	343_A	1.092	1.00
14_G	17_V	1.088	1.00
346_D	350_A	1.081	1.00
18_I	156_I	1.080	1.00
65_G	69_S	1.072	1.00
16_D	19_N	1.068	1.00
39_F	42_G	1.067	1.00
15_A	232_R	1.064	1.00
280_L	297_A	1.060	1.00
216_K	229_A	1.050	1.00
18_I	114_A	1.043	1.00
284_V	290_V	1.034	1.00
40_V	43_F	1.024	1.00
19_N	51_S	1.024	1.00
213_E	217_A	1.019	1.00
17_V	151_I	1.018	1.00
160_A	164_L	1.013	1.00
34_V	49_E	1.013	1.00
269_Y	277_F	1.009	1.00
205_L	209_T	1.007	1.00
47_T	50_K	1.002	1.00
35_V	64_F	1.002	1.00
20_R	24_Y	1.001	1.00
252_A	279_T	0.998	1.00
263_I	328_A	0.997	1.00
216_K	219_L	0.994	1.00
201_A	205_L	0.991	1.00
285_L	347_Q	0.990	1.00
217_A	220_A	0.990	1.00
214_G	217_A	0.981	1.00
75_R	79_I	0.980	1.00
298_A	301_H	0.980	1.00
330_C	345_P	0.975	1.00
90_G	113_I	0.975	1.00
40_V	44_A	0.968	1.00
78_G	81_E	0.968	1.00
16_D	153_D	0.963	1.00
264_P	321_K	0.961	1.00
102_A	106_F	0.955	1.00
60_E	85_C	0.954	1.00
23_E	55_A	0.951	1.00
291_E	294_E	0.950	1.00
12_I	149_M	0.947	1.00
212_E	233_V	0.939	1.00
200_L	203_A	0.939	1.00
12_I	20_R	0.938	1.00
100_A	111_V	0.937	1.00
165_L	217_A	0.936	1.00
165_L	221_A	0.933	1.00
210_L	234_I	0.932	1.00
10_K	27_P	0.914	1.00
124_C	239_Y	0.914	1.00
162_A	218_M	0.913	1.00
118_A	165_L	0.911	1.00
217_A	221_A	0.911	1.00
204_E	208_N	0.911	1.00
328_A	331_A	0.909	1.00
256_V	348_V	0.908	1.00
285_L	341_G	0.907	1.00
323_R	327_E	0.906	1.00
40_V	45_Q	0.898	1.00
47_T	51_S	0.896	1.00
316_E	320_A	0.896	1.00
284_V	293_I	0.895	1.00
53_K	58_V	0.892	1.00
162_A	304_G	0.886	1.00
209_T	212_E	0.885	1.00
31_R	86_G	0.883	1.00
124_C	150_V	0.883	1.00
41_L	45_Q	0.882	1.00
208_N	212_E	0.881	1.00
25_L	112_A	0.879	1.00
253_A	279_T	0.879	1.00
71_N	75_R	0.878	1.00
34_V	59_V	0.876	1.00
70_Q	130_I	0.874	1.00
211_L	295_T	0.873	1.00
253_A	275_V	0.871	1.00
69_S	72_E	0.866	1.00
170_G	276_A	0.865	1.00
257_H	261_T	0.865	1.00
87_A	110_P	0.862	1.00
80_A	103_L	0.861	1.00
56_G	59_V	0.847	1.00
99_T	103_L	0.841	1.00
22_G	26_K	0.837	1.00
64_F	99_T	0.834	1.00
179_A	244_G	0.833	1.00
90_G	97_L	0.832	1.00
176_W	241_S	0.830	1.00
254_H	271_H	0.829	1.00
18_I	155_K	0.828	1.00
155_K	228_P	0.826	1.00
36_G	41_L	0.824	1.00
53_K	56_G	0.824	1.00
77_R	107_M	0.823	1.00
181_A	185_S	0.822	1.00
23_E	27_P	0.822	1.00
283_L	293_I	0.819	1.00
104_A	109_V	0.817	1.00
97_L	115_P	0.815	1.00
113_I	147_P	0.812	1.00
287_N	293_I	0.811	1.00
202_L	240_L	0.811	1.00
203_A	206_C	0.810	1.00
39_F	63_P	0.810	1.00
51_S	54_D	0.807	1.00
280_L	300_S	0.805	1.00
22_G	55_A	0.804	1.00
259_G	328_A	0.804	1.00
61_I	76_L	0.799	1.00
169_I	172_A	0.794	1.00
71_N	134_E	0.784	1.00
182_C	185_S	0.784	1.00
236_A	240_L	0.784	1.00
126_A	144_P	0.784	1.00
211_L	215_E	0.780	1.00
61_I	67_E	0.776	1.00
104_A	111_V	0.775	1.00
259_G	352_L	0.774	1.00
174_A	279_T	0.773	1.00
70_Q	133_D	0.771	1.00
19_N	155_K	0.769	1.00
212_E	216_K	0.768	1.00
31_R	84_Q	0.767	1.00
18_I	153_D	0.765	1.00
22_G	54_D	0.764	1.00
293_I	297_A	0.762	1.00
69_S	133_D	0.759	1.00
35_V	76_L	0.759	1.00
281_T	284_V	0.754	1.00
37_D	63_P	0.753	1.00
160_A	168_G	0.753	1.00
37_D	43_F	0.753	1.00
270_Y	273_E	0.751	1.00
58_V	83_A	0.751	1.00
41_L	46_S	0.750	1.00
74_D	77_R	0.750	1.00
287_N	290_V	0.748	1.00
24_Y	151_I	0.748	1.00
154_T	232_R	0.744	1.00
207_Y	211_L	0.744	1.00
326_A	330_C	0.743	1.00
210_L	237_N	0.738	1.00
163_R	167_A	0.737	1.00
277_F	280_L	0.730	1.00
294_E	297_A	0.727	1.00
158_A	222_E	0.726	1.00
15_A	154_T	0.724	1.00
67_E	95_K	0.723	1.00
32_W	86_G	0.720	1.00
21_L	114_A	0.717	1.00
73_I	102_A	0.714	1.00
252_A	282_Q	0.713	1.00
36_G	96_T	0.713	1.00
320_A	323_R	0.712	1.00
330_C	348_V	0.711	1.00
209_T	213_E	0.711	1.00
166_A	218_M	0.710	1.00
78_G	134_E	0.707	1.00
73_I	106_F	0.706	1.00
76_L	99_T	0.706	1.00
307_I	311_Q	0.703	1.00
177_F	292_E	0.703	1.00
23_E	26_K	0.703	1.00
67_E	268_H	0.701	1.00
12_I	17_V	0.700	1.00
232_R	243_V	0.698	1.00
276_A	300_S	0.697	1.00
36_G	62_A	0.694	1.00
183_S	342_G	0.693	1.00
257_H	275_V	0.693	1.00
278_G	351_A	0.693	1.00
21_L	151_I	0.692	1.00
228_P	246_E	0.689	1.00
260_L	274_K	0.688	1.00
202_L	206_C	0.688	1.00
32_W	57_L	0.688	1.00
297_A	307_I	0.688	1.00
341_G	347_Q	0.686	1.00
18_I	48_V	0.684	1.00
213_E	230_L	0.680	1.00
185_S	189_T	0.677	1.00
41_L	44_A	0.677	1.00
258_N	332_E	0.676	1.00
296_V	300_S	0.674	1.00
19_N	54_D	0.673	1.00
325_V	329_A	0.672	1.00
285_L	343_A	0.670	1.00
206_C	209_T	0.668	1.00
88_I	109_V	0.666	1.00
24_Y	28_L	0.665	1.00
200_L	204_E	0.664	1.00
74_D	106_F	0.664	1.00
206_C	241_S	0.662	1.00
162_A	219_L	0.662	1.00
229_A	232_R	0.662	1.00
211_L	218_M	0.660	1.00
113_I	150_V	0.658	1.00
323_R	326_A	0.657	1.00
283_L	292_E	0.656	1.00
166_A	304_G	0.656	1.00
306_P	311_Q	0.655	1.00
218_M	304_G	0.655	1.00
216_K	230_L	0.655	1.00
73_I	129_V	0.649	1.00
343_A	347_Q	0.649	1.00
41_L	49_E	0.648	1.00
61_I	96_T	0.645	1.00
209_T	233_V	0.643	1.00
291_E	295_T	0.642	1.00
218_M	303_V	0.637	1.00
252_A	348_V	0.637	1.00
282_Q	286_E	0.636	1.00
207_Y	210_L	0.632	1.00
173_L	177_F	0.629	1.00
186_G	189_T	0.628	1.00
10_K	149_M	0.627	1.00
256_V	281_T	0.626	1.00
12_I	151_I	0.626	1.00
33_L	83_A	0.626	1.00
102_A	130_I	0.625	1.00
287_N	291_E	0.625	1.00
61_I	75_R	0.624	1.00
273_E	306_P	0.622	1.00
228_P	232_R	0.620	1.00
61_I	72_E	0.619	1.00
132_T	141_L	0.619	1.00
177_F	296_V	0.616	1.00
120_T	172_A	0.616	1.00
174_A	253_A	0.616	1.00
111_V	148_N	0.616	1.00
169_I	303_V	0.615	1.00
35_V	96_T	0.615	1.00
30_E	58_V	0.613	1.00
77_R	103_L	0.613	1.00
164_L	167_A	0.613	1.00
343_A	348_V	0.613	1.00
177_F	207_Y	0.612	1.00
173_L	303_V	0.609	1.00
22_G	25_L	0.607	1.00
90_G	96_T	0.607	1.00
166_A	305_L	0.602	1.00
105_H	145_N	0.601	1.00
162_A	221_A	0.600	1.00
221_A	230_L	0.597	1.00
44_A	159_G	0.595	1.00
177_F	184_R	0.594	1.00
300_S	307_I	0.593	1.00
214_G	220_A	0.593	1.00
47_T	156_I	0.591	1.00
276_A	305_L	0.588	0.99
69_S	268_H	0.588	0.99
48_V	51_S	0.588	0.99
213_E	229_A	0.586	0.99
301_H	311_Q	0.585	0.99
252_A	296_V	0.583	0.99
157_V	165_L	0.581	0.99
279_T	300_S	0.580	0.99
46_S	53_K	0.579	0.99
118_A	235_E	0.579	0.99
31_R	85_C	0.579	0.99
201_A	208_N	0.578	0.99
118_A	157_V	0.577	0.99
34_V	91_I	0.577	0.99
328_A	332_E	0.576	0.99
19_N	50_K	0.576	0.99
275_V	278_G	0.573	0.99
292_E	296_V	0.573	0.99
171_D	271_H	0.572	0.99
67_E	72_E	0.571	0.99
322_M	326_A	0.568	0.99
179_A	203_A	0.567	0.99
173_L	299_L	0.566	0.99
18_I	51_S	0.566	0.99
212_E	215_E	0.566	0.99
174_A	275_V	0.565	0.99
213_E	234_I	0.564	0.99
213_E	218_M	0.562	0.99
273_E	305_L	0.561	0.99
124_C	243_V	0.560	0.99
173_L	210_L	0.560	0.99
210_L	214_G	0.558	0.99
255_A	334_E	0.556	0.99
114_A	151_I	0.555	0.99
206_C	214_G	0.553	0.99
136_E	268_H	0.551	0.99
206_C	210_L	0.551	0.99
261_T	274_K	0.551	0.99
65_G	75_R	0.550	0.99
181_A	283_L	0.548	0.99
252_A	255_A	0.547	0.99
81_E	107_M	0.544	0.99
227_T	231_E	0.543	0.99
42_G	46_S	0.542	0.99
322_M	352_L	0.541	0.99
138_D	271_H	0.541	0.99
218_M	222_E	0.540	0.99
21_L	51_S	0.540	0.99
269_Y	273_E	0.540	0.99
239_Y	243_V	0.539	0.99
260_L	352_L	0.536	0.99
179_A	200_L	0.535	0.99
89_L	112_A	0.533	0.99
297_A	308_T	0.532	0.99
178_E	252_A	0.530	0.99
125_S	242_G	0.530	0.99
11_Y	150_V	0.529	0.99
310_A	316_E	0.525	0.99
163_R	270_Y	0.524	0.99
164_L	270_Y	0.524	0.99
166_A	169_I	0.523	0.99
285_L	351_A	0.523	0.99
39_F	67_E	0.521	0.99
176_W	203_A	0.519	0.99
8_P	146_N	0.519	0.99
102_A	128_S	0.519	0.99
285_L	344_T	0.517	0.99
329_A	352_L	0.516	0.99
102_A	141_L	0.512	0.99
206_C	217_A	0.512	0.99
301_H	304_G	0.510	0.99
258_N	334_E	0.510	0.99
180_R	204_E	0.509	0.99
14_G	154_T	0.507	0.99
105_H	141_L	0.507	0.99
260_L	269_Y	0.507	0.99
284_V	294_E	0.505	0.98
209_T	237_N	0.504	0.98
36_G	91_I	0.504	0.98
171_D	254_H	0.503	0.98
26_K	30_E	0.502	0.98
128_S	141_L	0.500	0.98

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
3ox4A	2	0.9128	100	0.142	Contact Map
1rrmA	2	0.9128	100	0.144	Contact Map
3bfjA	5	0.9101	100	0.149	Contact Map
4fr2A	2	0.9101	100	0.159	Contact Map
1vljA	2	0.9155	100	0.167	Contact Map
4mcaA	7	0.9973	100	0.168	Contact Map
3uhjA	5	0.9673	100	0.168	Contact Map
1jq5A	5	0.9891	100	0.177	Contact Map
3zdrA	2	0.921	100	0.179	Contact Map
1ta9A	5	0.9946	100	0.182	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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