ODPB - BACSU - GREMLIN Contacts

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ODPB - Pyruvate dehydrogenase E1 component subunit beta

UniProt:	P21882	Sequences: MAQMTMIQAITDALRTELKNDENVLVFGEDVGVNGGVFRATEGLQKEFGEDRVFDTPLAESGIGGLALGLGLNGFRPVMEIQFFGFVYEVMDSVSGQMARMRYRSGGRWTSPVTIRSPFGGGVHTPELHADSLEGLVAQQPGIKVVIPSTPYDAKGLLISAIRDNDPVVFLEHMKLYRSFRQEVPEEEYTIELGKADVKREGTDLSIITYGAMVHESLKAADELEKDGISAEVVDLRTVSPLDIDTIIASVEKTGRAIVVQEAQKQAGIAANVVAEINDRAILSLEAPVLRVAAPDTVFPFSQAESVWLPNHKDVLETARKVLEF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	325 (300)
Sequences:	13970 (8083)
Seq/√Len:	466.7

ECOLI - DXS TKT1 TKT2
BACSU - ODPB ACOB ODBB DXS TKT
HALSA - Q9HN76
SULSO - Q97Y22 Q97YF5 Q980J2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
227_D	320_R	4.492	1.00
19_K	47_E	3.603	1.00
223_E	316_L	3.230	1.00
311_N	314_D	2.875	1.00
205_L	319_A	2.790	1.00
196_A	246_T	2.771	1.00
67_A	79_M	2.724	1.00
218_L	233_V	2.396	1.00
15_R	47_E	2.334	1.00
200_R	221_A	2.313	1.00
200_R	222_D	2.209	1.00
221_A	233_V	2.145	1.00
223_E	312_H	2.119	1.00
203_T	230_S	2.112	1.00
219_K	312_H	2.093	1.00
146_V	157_L	2.092	1.00
15_R	48_F	2.081	1.00
290_L	321_K	2.034	1.00
312_H	316_L	2.029	1.00
244_I	276_E	2.021	1.00
206_S	254_T	1.988	1.00
205_L	231_A	1.959	1.00
306_S	311_N	1.939	1.00
76_R	110_T	1.886	1.00
248_I	276_E	1.876	1.00
70_L	75_F	1.859	1.00
279_D	291_R	1.856	1.00
216_E	312_H	1.836	1.00
223_E	226_K	1.825	1.00
290_L	318_T	1.811	1.00
204_D	230_S	1.737	1.00
225_E	230_S	1.733	1.00
204_D	255_G	1.732	1.00
217_S	260_V	1.726	1.00
19_K	48_F	1.726	1.00
68_L	98_M	1.720	1.00
232_E	253_K	1.718	1.00
64_G	98_M	1.703	1.00
232_E	250_S	1.680	1.00
135_G	263_A	1.676	1.00
200_R	225_E	1.657	1.00
102_R	142_G	1.651	1.00
232_E	254_T	1.644	1.00
271_A	275_A	1.636	1.00
209_T	217_S	1.620	1.00
207_I	217_S	1.619	1.00
265_K	293_A	1.614	1.00
198_V	232_E	1.596	1.00
316_L	320_R	1.596	1.00
223_E	313_K	1.588	1.00
248_I	280_R	1.584	1.00
317_E	321_K	1.577	1.00
143_I	169_V	1.571	1.00
144_K	164_D	1.567	1.00
16_T	155_K	1.546	1.00
244_I	280_R	1.540	1.00
201_E	232_E	1.531	1.00
138_A	272_N	1.522	1.00
98_M	113_V	1.519	1.00
25_L	70_L	1.516	1.00
219_K	222_D	1.515	1.00
112_P	161_A	1.513	1.00
144_K	166_D	1.495	1.00
274_V	289_V	1.495	1.00
78_V	162_I	1.491	1.00
17_E	159_I	1.485	1.00
249_A	254_T	1.483	1.00
216_E	219_K	1.482	1.00
161_A	168_V	1.471	1.00
64_G	113_V	1.446	1.00
209_T	214_V	1.442	1.00
318_T	321_K	1.418	1.00
138_A	275_A	1.408	1.00
215_H	219_K	1.405	1.00
208_I	236_L	1.383	1.00
220_A	316_L	1.378	1.00
196_A	236_L	1.367	1.00
64_G	79_M	1.366	1.00
222_D	226_K	1.364	1.00
216_E	315_V	1.357	1.00
207_I	319_A	1.355	1.00
314_D	318_T	1.351	1.00
137_V	169_V	1.350	1.00
21_D	76_R	1.343	1.00
306_S	313_K	1.342	1.00
192_E	195_K	1.341	1.00
13_A	155_K	1.340	1.00
258_I	322_V	1.337	1.00
234_V	246_T	1.327	1.00
223_E	227_D	1.320	1.00
13_A	159_I	1.299	1.00
197_D	235_D	1.294	1.00
144_K	238_T	1.278	1.00
17_E	163_R	1.276	1.00
18_L	44_L	1.273	1.00
243_D	276_E	1.270	1.00
76_R	112_P	1.268	1.00
159_I	163_R	1.266	1.00
110_T	166_D	1.265	1.00
17_E	24_V	1.258	1.00
64_G	90_V	1.250	1.00
153_D	235_D	1.249	1.00
27_F	67_A	1.240	1.00
14_L	78_V	1.239	1.00
277_I	289_V	1.226	1.00
146_V	238_T	1.215	1.00
8_Q	12_D	1.212	1.00
236_L	269_I	1.209	1.00
23_N	75_F	1.203	1.00
43_G	46_K	1.202	1.00
160_S	193_L	1.201	1.00
94_V	143_I	1.199	1.00
222_D	225_E	1.190	1.00
198_V	201_E	1.187	1.00
110_T	165_N	1.185	1.00
274_V	278_N	1.184	1.00
206_S	250_S	1.183	1.00
249_A	253_K	1.181	1.00
94_V	115_I	1.180	1.00
258_I	319_A	1.179	1.00
234_V	250_S	1.178	1.00
17_E	162_I	1.177	1.00
149_S	214_V	1.177	1.00
153_D	237_R	1.173	1.00
27_F	56_T	1.168	1.00
102_R	166_D	1.165	1.00
242_L	247_I	1.160	1.00
261_Q	270_A	1.151	1.00
248_I	281_A	1.138	1.00
149_S	235_D	1.135	1.00
208_I	257_A	1.133	1.00
245_D	249_A	1.131	1.00
26_V	41_T	1.126	1.00
199_K	214_V	1.126	1.00
207_I	231_A	1.125	1.00
12_D	155_K	1.118	1.00
248_I	252_E	1.115	1.00
25_L	75_F	1.105	1.00
202_G	230_S	1.088	1.00
135_G	139_Q	1.087	1.00
231_A	319_A	1.081	1.00
17_E	20_N	1.081	1.00
146_V	168_V	1.080	1.00
115_I	169_V	1.074	1.00
13_A	16_T	1.066	1.00
116_R	172_E	1.066	1.00
9_A	151_P	1.061	1.00
71_G	77_P	1.059	1.00
91_M	136_L	1.057	1.00
21_D	24_V	1.057	1.00
16_T	159_I	1.057	1.00
213_M	216_E	1.057	1.00
314_D	317_E	1.049	1.00
198_V	246_T	1.047	1.00
275_A	291_R	1.044	1.00
274_V	291_R	1.041	1.00
244_I	248_I	1.040	1.00
195_K	245_D	1.040	1.00
240_S	296_D	1.039	1.00
12_D	43_G	1.032	1.00
200_R	230_S	1.030	1.00
290_L	322_V	1.027	1.00
196_A	234_V	1.024	1.00
12_D	16_T	1.024	1.00
300_P	307_V	1.019	1.00
269_I	273_V	1.018	1.00
20_N	159_I	1.018	1.00
257_A	277_I	1.016	1.00
198_V	234_V	1.013	1.00
191_I	194_G	1.007	1.00
132_S	294_A	1.001	1.00
67_A	111_S	1.001	1.00
260_V	315_V	0.993	1.00
85_G	134_E	0.991	1.00
18_L	24_V	0.989	1.00
276_E	280_R	0.988	1.00
251_V	277_I	0.987	1.00
61_S	93_S	0.986	1.00
84_F	171_L	0.985	1.00
16_T	20_N	0.972	1.00
294_A	308_W	0.971	1.00
210_Y	239_V	0.970	1.00
258_I	292_V	0.969	1.00
266_Q	296_D	0.960	1.00
250_S	253_K	0.957	1.00
227_D	316_L	0.953	1.00
8_Q	11_T	0.953	1.00
21_D	162_I	0.950	1.00
144_K	168_V	0.949	1.00
151_P	179_S	0.949	1.00
270_A	293_A	0.946	1.00
220_A	315_V	0.941	1.00
282_I	287_A	0.938	1.00
15_R	19_K	0.936	1.00
270_A	291_R	0.935	1.00
26_V	31_V	0.931	1.00
206_S	232_E	0.930	1.00
260_V	289_V	0.929	1.00
99_A	140_Q	0.926	1.00
309_L	314_D	0.922	1.00
278_N	289_V	0.922	1.00
259_V	270_A	0.920	1.00
87_V	115_I	0.919	1.00
76_R	165_N	0.912	1.00
38_F	41_T	0.912	1.00
313_K	317_E	0.903	1.00
16_T	19_K	0.903	1.00
206_S	234_V	0.901	1.00
256_R	322_V	0.899	1.00
149_S	197_D	0.897	1.00
146_V	193_L	0.895	1.00
297_T	307_V	0.888	1.00
258_I	261_Q	0.887	1.00
98_M	111_S	0.887	1.00
135_G	267_A	0.887	1.00
8_Q	176_L	0.886	1.00
43_G	47_E	0.882	1.00
63_I	79_M	0.877	1.00
56_T	66_L	0.873	1.00
288_P	321_K	0.873	1.00
224_L	319_A	0.871	1.00
32_G	53_V	0.867	1.00
217_S	233_V	0.860	1.00
42_E	46_K	0.859	1.00
256_R	288_P	0.857	1.00
23_N	76_R	0.849	1.00
158_L	170_F	0.847	1.00
184_V	187_E	0.846	1.00
121_G	305_E	0.838	1.00
249_A	252_E	0.833	1.00
144_K	241_P	0.832	1.00
205_L	258_I	0.831	1.00
64_G	115_I	0.830	1.00
94_V	137_V	0.830	1.00
178_R	215_H	0.829	1.00
100_R	127_E	0.825	1.00
66_L	70_L	0.821	1.00
138_A	239_V	0.819	1.00
319_A	322_V	0.818	1.00
303_Q	306_S	0.816	1.00
25_L	54_F	0.815	1.00
229_I	320_R	0.813	1.00
143_I	167_P	0.813	1.00
160_S	192_E	0.811	1.00
87_V	137_V	0.811	1.00
216_E	311_N	0.810	1.00
27_F	54_F	0.809	1.00
45_Q	48_F	0.808	1.00
154_A	172_E	0.804	1.00
259_V	262_E	0.803	1.00
62_G	66_L	0.802	1.00
224_L	316_L	0.800	1.00
217_S	261_Q	0.800	1.00
147_I	210_Y	0.796	1.00
236_L	239_V	0.796	1.00
87_V	117_S	0.791	1.00
13_A	17_E	0.790	1.00
242_L	276_E	0.783	1.00
194_G	197_D	0.783	1.00
98_M	167_P	0.782	1.00
29_E	39_R	0.781	1.00
247_I	276_E	0.780	1.00
88_Y	91_M	0.779	1.00
209_T	213_M	0.777	1.00
26_V	78_V	0.777	1.00
201_E	253_K	0.775	1.00
84_F	137_V	0.773	1.00
221_A	225_E	0.772	1.00
243_D	275_A	0.770	1.00
208_I	234_V	0.764	1.00
306_S	314_D	0.758	1.00
144_K	193_L	0.758	1.00
112_P	168_V	0.756	1.00
246_T	250_S	0.756	1.00
13_A	158_L	0.750	1.00
204_D	229_I	0.750	1.00
219_K	223_E	0.749	1.00
216_E	305_E	0.748	1.00
304_A	308_W	0.748	1.00
102_R	165_N	0.746	1.00
48_F	52_R	0.744	1.00
136_L	140_Q	0.743	1.00
94_V	113_V	0.742	1.00
156_G	159_I	0.741	1.00
71_G	111_S	0.740	1.00
159_I	188_E	0.738	1.00
288_P	318_T	0.737	1.00
225_E	231_A	0.737	1.00
258_I	290_L	0.733	1.00
183_E	186_E	0.729	1.00
318_T	322_V	0.724	1.00
85_G	131_D	0.723	1.00
138_A	267_A	0.722	1.00
45_Q	53_V	0.722	1.00
29_E	63_I	0.720	1.00
27_F	66_L	0.717	1.00
144_K	240_S	0.716	1.00
10_I	80_E	0.713	1.00
173_H	177_Y	0.712	1.00
160_S	163_R	0.711	1.00
239_V	243_D	0.711	1.00
150_T	199_K	0.710	1.00
250_S	254_T	0.709	1.00
200_R	218_L	0.707	1.00
27_F	63_I	0.706	1.00
67_A	80_E	0.704	1.00
160_S	190_T	0.700	1.00
11_T	15_R	0.698	1.00
44_L	53_V	0.697	1.00
152_Y	185_P	0.697	1.00
99_A	298_V	0.696	1.00
317_E	320_R	0.693	1.00
127_E	130_A	0.691	1.00
247_I	277_I	0.690	1.00
278_N	281_A	0.689	1.00
220_A	260_V	0.681	1.00
65_G	93_S	0.680	1.00
14_L	41_T	0.680	1.00
248_I	282_I	0.679	1.00
199_K	218_L	0.678	1.00
292_V	318_T	0.675	1.00
71_G	109_W	0.675	1.00
220_A	319_A	0.673	1.00
9_A	13_A	0.671	1.00
124_H	303_Q	0.668	1.00
72_L	109_W	0.668	1.00
301_F	305_E	0.665	1.00
206_S	253_K	0.664	1.00
157_L	237_R	0.663	1.00
146_V	160_S	0.660	1.00
79_M	113_V	0.660	1.00
210_Y	236_L	0.660	1.00
265_K	279_D	0.659	1.00
198_V	249_A	0.658	1.00
32_G	45_Q	0.657	1.00
272_N	275_A	0.654	1.00
140_Q	143_I	0.654	1.00
99_A	143_I	0.649	1.00
265_K	291_R	0.646	1.00
297_T	308_W	0.643	1.00
152_Y	156_G	0.642	1.00
204_D	231_A	0.640	1.00
295_P	308_W	0.637	1.00
83_F	125_T	0.636	1.00
95_S	140_Q	0.634	1.00
78_V	158_L	0.630	0.99
22_E	52_R	0.629	0.99
24_V	162_I	0.626	0.99
7_I	40_A	0.624	0.99
161_A	170_F	0.619	0.99
257_A	261_Q	0.615	0.99
183_E	187_E	0.614	0.99
266_Q	291_R	0.613	0.99
201_E	249_A	0.610	0.99
92_D	96_G	0.609	0.99
156_G	160_S	0.603	0.99
146_V	161_A	0.602	0.99
163_R	188_E	0.602	0.99
134_E	171_L	0.599	0.99
156_G	190_T	0.599	0.99
70_L	77_P	0.599	0.99
178_R	219_K	0.598	0.99
258_I	262_E	0.595	0.99
90_V	94_V	0.594	0.99
251_V	257_A	0.593	0.99
195_K	243_D	0.593	0.99
295_P	314_D	0.593	0.99
261_Q	268_G	0.593	0.99
152_Y	179_S	0.592	0.99
270_A	275_A	0.590	0.99
54_F	66_L	0.589	0.99
138_A	145_V	0.588	0.99
10_I	158_L	0.587	0.99
159_I	190_T	0.587	0.99
31_V	83_F	0.586	0.99
244_I	279_D	0.586	0.99
185_P	189_Y	0.585	0.99
255_G	286_E	0.585	0.99
43_G	55_D	0.582	0.99
145_V	169_V	0.579	0.99
59_A	62_G	0.579	0.99
24_V	78_V	0.579	0.99
91_M	139_Q	0.579	0.99
257_A	289_V	0.577	0.99
198_V	250_S	0.574	0.99
209_T	236_L	0.573	0.99
135_G	264_Q	0.572	0.99
259_V	289_V	0.570	0.99
101_M	109_W	0.570	0.99
214_V	233_V	0.570	0.99
292_V	310_P	0.570	0.99
138_A	269_I	0.568	0.99
255_G	258_I	0.568	0.99
18_L	53_V	0.566	0.99
303_Q	307_V	0.566	0.99
33_V	55_D	0.563	0.99
310_P	314_D	0.562	0.99
144_K	194_G	0.561	0.99
155_K	159_I	0.557	0.99
206_S	257_A	0.556	0.99
213_M	260_V	0.556	0.99
282_I	288_P	0.555	0.99
64_G	81_I	0.554	0.99
259_V	273_V	0.553	0.99
164_D	168_V	0.553	0.99
299_F	308_W	0.553	0.99
76_R	162_I	0.551	0.99
149_S	153_D	0.551	0.99
156_G	188_E	0.550	0.99
224_L	231_A	0.548	0.99
206_S	256_R	0.547	0.99
112_P	158_L	0.547	0.99
72_L	101_M	0.547	0.99
114_T	161_A	0.546	0.99
220_A	312_H	0.545	0.99
147_I	211_G	0.544	0.98
132_S	264_Q	0.543	0.98
112_P	170_F	0.543	0.98
271_A	291_R	0.541	0.98
238_T	241_P	0.541	0.98
202_G	225_E	0.541	0.98
147_I	212_A	0.540	0.98
268_G	271_A	0.539	0.98
212_A	216_E	0.539	0.98
173_H	212_A	0.539	0.98
194_G	238_T	0.538	0.98
121_G	304_A	0.534	0.98
45_Q	50_E	0.534	0.98
21_D	163_R	0.532	0.98
15_R	53_V	0.530	0.98
305_E	310_P	0.530	0.98
6_M	177_Y	0.530	0.98
309_L	318_T	0.529	0.98
313_K	316_L	0.528	0.98
272_N	291_R	0.527	0.98
279_D	290_L	0.527	0.98
88_Y	136_L	0.525	0.98
224_L	229_I	0.523	0.98
201_E	230_S	0.523	0.98
259_V	291_R	0.521	0.98
164_D	193_L	0.521	0.98
166_D	244_I	0.521	0.98
134_E	261_Q	0.521	0.98
221_A	231_A	0.511	0.98
157_L	168_V	0.509	0.98
144_K	244_I	0.507	0.98
152_Y	189_Y	0.507	0.98
239_V	269_I	0.501	0.97
207_I	258_I	0.500	0.97
137_V	143_I	0.500	0.97

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
1w85B	2	0.9877	100	0.211	Contact Map
1umdB	2	0.9846	100	0.222	Contact Map
1ik6A	3	0.8554	100	0.223	Contact Map
2ozlB	2	1	100	0.232	Contact Map
2bfdB	2	0.9938	100	0.248	Contact Map
1qs0B	2	0.9846	100	0.251	Contact Map
2o1xA	2	0.9262	100	0.257	Contact Map
4kxvA	2	0.9292	100	0.268	Contact Map
2o1sA	2	0.92	100	0.27	Contact Map
1gpuA	2	0.9077	100	0.314	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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