Q97YF5 - SULSO - GREMLIN Contacts

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Q97YF5 - Pyruvate dehydrogenase, beta subunit (Lipoamide). (PdhB-1)

UniProt:	Q97YF5	Sequences: MKIRGIAQAIAEGIRQEMERNDRIVVLGEDVTYWGAVFGFTMGLFDKFGRKRVIDTPITEQTFMGISVGAASSGLHPVVSLMFVDFLGAGFDQMFNHMAKNYYMSGGQYPMPITVITAIGGGYGDSSQHSQVLYSLFAHLPGFKVIVPSTPYDAKGLTIKALRDNNPVIIFGHKLLTGLPFLPFEGNEEEVPEEPYEIEFGKAAIRKEGTDLTIISAGLMVHRSLKAAEMLQKEGISAEVIDVRTFVPLDEETIIKSARKTGRVLIVDEDYMSYGVTGEIAFRIQSKALKDLKVPISRLAVPDVPIPFSEPLENAVIPNVNTIYSEAKKLIQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	332 (300)
Sequences:	13993 (8150)
Seq/√Len:	470.6

ECOLI - DXS TKT1 TKT2
BACSU - ODBB ODPB ACOB DXS TKT
HALSA - Q9HN76
SULSO - Q97YF5 Q97Y22 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
234_E	328_K	4.558	1.00
19_E	47_K	3.673	1.00
230_M	324_Y	3.284	1.00
319_N	322_T	2.902	1.00
212_L	327_A	2.799	1.00
67_S	79_V	2.780	1.00
203_A	253_T	2.766	1.00
225_L	240_V	2.413	1.00
207_K	228_A	2.403	1.00
15_R	47_K	2.323	1.00
207_K	229_E	2.236	1.00
15_R	48_F	2.211	1.00
230_M	320_V	2.180	1.00
228_A	240_V	2.167	1.00
210_T	237_S	2.136	1.00
146_I	157_L	2.127	1.00
226_K	320_V	2.117	1.00
297_S	329_K	2.087	1.00
320_V	324_Y	2.076	1.00
251_E	283_R	2.029	1.00
213_T	261_T	1.991	1.00
212_L	238_A	1.976	1.00
314_N	319_N	1.946	1.00
255_I	283_R	1.916	1.00
70_A	75_L	1.901	1.00
76_H	110_P	1.881	1.00
223_R	320_V	1.837	1.00
230_M	233_K	1.822	1.00
297_S	326_E	1.788	1.00
211_D	237_S	1.769	1.00
224_S	267_V	1.762	1.00
239_E	260_K	1.734	1.00
19_E	48_F	1.733	1.00
232_Q	237_S	1.732	1.00
64_M	98_M	1.714	1.00
239_E	257_S	1.701	1.00
135_S	270_D	1.700	1.00
68_V	98_M	1.685	1.00
207_K	232_Q	1.673	1.00
286_S	298_R	1.669	1.00
255_I	287_K	1.663	1.00
278_G	282_F	1.660	1.00
214_I	224_S	1.645	1.00
108_Q	142_G	1.637	1.00
216_S	224_S	1.625	1.00
230_M	321_N	1.623	1.00
324_Y	328_K	1.622	1.00
211_D	262_G	1.618	1.00
239_E	261_T	1.618	1.00
272_M	300_A	1.607	1.00
138_A	279_E	1.592	1.00
144_K	164_D	1.590	1.00
251_E	287_K	1.582	1.00
205_I	239_E	1.577	1.00
143_F	169_I	1.567	1.00
311_P	314_N	1.556	1.00
226_K	229_E	1.553	1.00
16_Q	155_K	1.549	1.00
78_V	162_L	1.541	1.00
325_S	329_K	1.535	1.00
144_K	166_N	1.534	1.00
281_A	296_I	1.528	1.00
256_K	261_T	1.523	1.00
25_V	70_A	1.519	1.00
112_P	161_A	1.511	1.00
17_E	159_I	1.500	1.00
208_E	239_E	1.497	1.00
223_R	226_K	1.479	1.00
138_A	282_F	1.467	1.00
161_A	168_V	1.451	1.00
64_M	113_I	1.445	1.00
8_Q	36_A	1.429	1.00
216_S	221_V	1.423	1.00
215_I	243_V	1.414	1.00
229_E	233_K	1.414	1.00
222_H	226_K	1.409	1.00
326_E	329_K	1.407	1.00
265_L	330_L	1.405	1.00
223_R	323_I	1.376	1.00
64_M	79_V	1.376	1.00
13_G	155_K	1.362	1.00
314_N	321_N	1.355	1.00
322_T	326_E	1.348	1.00
241_I	253_T	1.347	1.00
137_F	169_I	1.344	1.00
227_A	324_Y	1.341	1.00
214_I	327_A	1.339	1.00
21_N	76_H	1.331	1.00
230_M	234_E	1.330	1.00
203_A	243_V	1.318	1.00
13_G	159_I	1.310	1.00
17_E	163_R	1.300	1.00
18_M	44_L	1.291	1.00
159_I	163_R	1.289	1.00
250_D	283_R	1.288	1.00
204_A	242_D	1.286	1.00
110_P	166_N	1.273	1.00
98_M	113_I	1.271	1.00
144_K	245_T	1.264	1.00
273_S	303_D	1.257	1.00
83_F	86_F	1.257	1.00
205_I	208_E	1.254	1.00
14_I	78_V	1.254	1.00
243_V	276_V	1.249	1.00
17_E	24_I	1.246	1.00
153_D	242_D	1.241	1.00
76_H	112_P	1.239	1.00
64_M	90_G	1.232	1.00
8_Q	12_E	1.230	1.00
241_I	257_S	1.229	1.00
229_E	232_Q	1.228	1.00
160_K	200_F	1.227	1.00
94_M	143_F	1.224	1.00
27_L	67_S	1.218	1.00
149_S	221_V	1.217	1.00
146_I	245_T	1.214	1.00
249_L	254_I	1.206	1.00
265_L	327_A	1.206	1.00
94_M	115_V	1.204	1.00
199_E	202_K	1.203	1.00
281_A	285_Q	1.200	1.00
17_E	162_L	1.179	1.00
213_T	257_S	1.174	1.00
27_L	56_T	1.167	1.00
153_D	244_R	1.166	1.00
23_R	75_L	1.164	1.00
256_K	260_K	1.155	1.00
215_I	264_V	1.154	1.00
268_D	277_T	1.152	1.00
43_G	46_D	1.146	1.00
110_P	165_N	1.137	1.00
252_E	256_K	1.130	1.00
25_V	75_L	1.123	1.00
26_V	41_T	1.119	1.00
255_I	288_A	1.116	1.00
149_S	242_D	1.111	1.00
12_E	155_K	1.106	1.00
214_I	238_A	1.097	1.00
238_A	327_A	1.095	1.00
255_I	259_R	1.094	1.00
297_S	330_L	1.092	1.00
206_R	221_V	1.087	1.00
146_I	168_V	1.083	1.00
264_V	284_I	1.079	1.00
115_V	169_I	1.067	1.00
16_Q	159_I	1.057	1.00
322_T	325_S	1.056	1.00
9_A	151_P	1.055	1.00
202_K	252_E	1.054	1.00
17_E	20_R	1.054	1.00
12_E	16_Q	1.053	1.00
71_A	77_P	1.051	1.00
13_G	16_Q	1.049	1.00
203_A	241_I	1.048	1.00
12_E	43_G	1.047	1.00
135_S	139_H	1.044	1.00
85_D	133_L	1.041	1.00
21_N	24_I	1.041	1.00
267_V	323_I	1.037	1.00
283_R	287_K	1.036	1.00
220_M	223_R	1.033	1.00
258_A	284_I	1.032	1.00
285_Q	296_I	1.030	1.00
91_F	136_L	1.030	1.00
247_V	303_D	1.022	1.00
251_E	255_I	1.018	1.00
209_G	237_S	1.016	1.00
207_K	237_S	1.015	1.00
134_Y	217_A	1.014	1.00
281_A	298_R	1.013	1.00
20_R	159_I	1.009	1.00
205_I	241_I	0.999	1.00
18_M	24_I	0.998	1.00
205_I	253_T	0.996	1.00
265_L	268_D	0.994	1.00
307_P	315_A	0.993	1.00
144_K	168_V	0.993	1.00
282_F	298_R	0.990	1.00
234_E	324_Y	0.979	1.00
16_Q	20_R	0.978	1.00
67_S	111_M	0.977	1.00
84_V	171_F	0.967	1.00
61_Q	93_Q	0.962	1.00
15_R	19_E	0.957	1.00
257_S	260_K	0.946	1.00
135_S	274_Y	0.945	1.00
263_R	330_L	0.943	1.00
213_T	239_E	0.942	1.00
217_A	246_F	0.942	1.00
43_G	47_K	0.938	1.00
227_A	323_I	0.930	1.00
265_L	299_L	0.928	1.00
321_N	325_S	0.927	1.00
21_N	162_L	0.926	1.00
76_H	165_N	0.922	1.00
26_V	31_V	0.920	1.00
8_Q	11_A	0.917	1.00
266_I	277_T	0.916	1.00
149_S	204_A	0.912	1.00
16_Q	19_E	0.900	1.00
317_I	322_T	0.895	1.00
311_P	315_A	0.894	1.00
108_Q	166_N	0.891	1.00
56_T	66_I	0.886	1.00
213_T	241_I	0.883	1.00
32_T	53_V	0.882	1.00
63_F	79_V	0.880	1.00
134_Y	171_F	0.876	1.00
266_I	269_E	0.875	1.00
98_M	111_M	0.873	1.00
131_Q	301_V	0.871	1.00
304_V	315_A	0.868	1.00
231_L	327_A	0.864	1.00
8_Q	176_L	0.857	1.00
158_T	170_I	0.853	1.00
305_P	308_F	0.851	1.00
144_K	248_P	0.850	1.00
42_M	46_D	0.848	1.00
146_I	200_F	0.847	1.00
263_R	295_P	0.843	1.00
327_A	330_L	0.843	1.00
23_R	76_H	0.842	1.00
243_V	246_F	0.842	1.00
256_K	259_R	0.841	1.00
87_L	137_F	0.841	1.00
35_G	80_S	0.838	1.00
120_G	313_E	0.834	1.00
198_I	201_G	0.827	1.00
236_I	328_K	0.826	1.00
224_S	240_V	0.826	1.00
84_V	137_F	0.825	1.00
299_L	326_E	0.823	1.00
154_A	172_G	0.822	1.00
160_K	199_E	0.818	1.00
62_T	66_I	0.812	1.00
173_H	177_T	0.811	1.00
254_I	283_R	0.809	1.00
25_V	54_I	0.806	1.00
232_Q	238_A	0.803	1.00
190_E	193_E	0.802	1.00
212_L	265_L	0.802	1.00
134_Y	270_D	0.801	1.00
66_I	70_A	0.799	1.00
27_L	54_I	0.797	1.00
143_F	167_P	0.796	1.00
94_M	137_F	0.795	1.00
48_F	52_R	0.793	1.00
253_T	257_S	0.793	1.00
215_I	241_I	0.792	1.00
64_M	115_V	0.791	1.00
211_D	236_I	0.789	1.00
249_L	283_R	0.786	1.00
267_V	299_L	0.784	1.00
228_A	232_Q	0.778	1.00
123_Y	310_E	0.777	1.00
160_K	163_R	0.776	1.00
88_G	91_F	0.775	1.00
45_F	48_F	0.775	1.00
26_V	78_V	0.774	1.00
147_V	217_A	0.773	1.00
29_E	35_G	0.773	1.00
14_I	41_T	0.771	1.00
223_R	313_E	0.767	1.00
284_I	296_I	0.764	1.00
223_R	319_N	0.763	1.00
312_L	316_V	0.762	1.00
231_L	324_Y	0.761	1.00
13_G	17_E	0.759	1.00
138_A	246_F	0.758	1.00
13_G	158_T	0.757	1.00
144_K	200_F	0.757	1.00
159_I	195_P	0.754	1.00
314_N	322_T	0.750	1.00
99_A	305_P	0.748	1.00
226_K	230_M	0.748	1.00
216_S	220_M	0.747	1.00
97_H	113_I	0.739	1.00
264_V	268_D	0.737	1.00
112_P	168_V	0.736	1.00
246_F	250_D	0.729	1.00
208_E	260_K	0.728	1.00
116_I	172_G	0.727	1.00
301_V	316_V	0.726	1.00
11_A	15_R	0.726	1.00
10_I	80_S	0.726	1.00
65_G	93_Q	0.724	1.00
191_V	194_E	0.723	1.00
99_A	140_L	0.719	1.00
87_L	117_T	0.718	1.00
29_E	63_F	0.718	1.00
304_V	316_V	0.717	1.00
133_L	171_F	0.717	1.00
71_A	111_M	0.717	1.00
45_F	53_V	0.716	1.00
44_L	53_V	0.714	1.00
156_G	159_I	0.714	1.00
144_K	247_V	0.714	1.00
189_E	192_P	0.711	1.00
227_A	267_V	0.709	1.00
298_R	326_E	0.709	1.00
136_L	140_L	0.707	1.00
100_K	126_S	0.705	1.00
265_L	297_S	0.702	1.00
325_S	328_K	0.702	1.00
254_I	284_I	0.697	1.00
207_K	225_L	0.697	1.00
27_L	66_I	0.697	1.00
152_Y	192_P	0.692	1.00
150_T	206_R	0.692	1.00
250_D	278_G	0.685	1.00
285_Q	288_A	0.683	1.00
201_G	204_A	0.679	1.00
27_L	63_F	0.676	1.00
94_M	113_I	0.676	1.00
213_T	260_K	0.672	1.00
257_S	261_T	0.672	1.00
98_M	167_P	0.670	1.00
276_V	280_I	0.670	1.00
326_E	330_L	0.669	1.00
178_G	222_H	0.669	1.00
160_K	197_E	0.667	1.00
126_S	129_H	0.667	1.00
138_A	274_Y	0.666	1.00
79_V	113_I	0.665	1.00
268_D	275_G	0.664	1.00
157_L	244_R	0.664	1.00
206_R	225_L	0.658	1.00
134_Y	145_V	0.656	1.00
87_L	115_V	0.656	1.00
146_I	160_K	0.655	1.00
9_A	13_G	0.654	1.00
227_A	327_A	0.651	1.00
217_A	243_V	0.650	1.00
150_T	189_E	0.646	1.00
43_G	55_D	0.642	1.00
22_D	52_R	0.642	1.00
272_M	286_S	0.640	1.00
262_G	265_L	0.640	1.00
302_P	316_V	0.639	1.00
72_S	109_Y	0.638	1.00
304_V	307_P	0.638	1.00
205_I	256_K	0.637	1.00
309_S	312_L	0.634	1.00
279_E	282_F	0.632	1.00
71_A	109_Y	0.632	1.00
258_A	264_V	0.632	1.00
145_V	169_I	0.632	1.00
208_E	256_K	0.630	1.00
266_I	296_I	0.629	0.99
163_R	195_P	0.626	0.99
44_L	48_F	0.623	0.99
156_G	160_K	0.621	0.99
146_I	161_A	0.620	0.99
67_S	80_S	0.619	0.99
120_G	312_L	0.619	0.99
264_V	267_V	0.618	0.99
274_Y	278_G	0.617	0.99
140_L	143_F	0.614	0.99
251_E	286_S	0.612	0.99
277_T	300_A	0.610	0.99
32_T	45_F	0.607	0.99
78_V	158_T	0.606	0.99
24_I	162_L	0.605	0.99
108_Q	165_N	0.604	0.99
152_Y	156_G	0.604	0.99
84_V	133_L	0.603	0.99
92_D	96_N	0.599	0.99
54_I	66_I	0.599	0.99
24_I	78_V	0.596	0.99
318_P	322_T	0.595	0.99
211_D	238_A	0.592	0.99
10_I	158_T	0.590	0.99
95_F	140_L	0.589	0.99
202_K	250_D	0.588	0.99
265_L	269_E	0.581	0.99
11_A	36_A	0.580	0.99
266_I	280_I	0.580	0.99
138_A	276_V	0.578	0.99
88_G	133_L	0.577	0.99
263_R	266_I	0.577	0.99
302_P	305_P	0.576	0.99
138_A	145_V	0.575	0.99
272_M	298_R	0.573	0.99
151_P	189_E	0.573	0.99
262_G	293_K	0.573	0.99
305_P	309_S	0.572	0.99
161_A	170_I	0.572	0.99
268_D	271_Y	0.570	0.99
286_S	297_S	0.570	0.99
144_K	201_G	0.570	0.99
227_A	320_V	0.568	0.99
90_G	94_M	0.568	0.99
299_L	318_P	0.568	0.99
33_Y	55_D	0.568	0.99
201_G	245_T	0.567	0.99
91_F	139_H	0.567	0.99
208_E	237_S	0.566	0.99
15_R	53_V	0.565	0.99
266_I	298_R	0.564	0.99
147_V	218_G	0.562	0.99
205_I	257_S	0.558	0.99
265_L	326_E	0.558	0.99
220_M	267_V	0.555	0.99
264_V	296_I	0.554	0.99
59_T	62_T	0.554	0.99
313_E	318_P	0.554	0.99
64_M	81_L	0.551	0.99
302_P	322_T	0.550	0.99
70_A	77_P	0.549	0.99
221_V	240_V	0.548	0.99
216_S	243_V	0.547	0.99
173_H	219_L	0.545	0.99
42_M	48_F	0.545	0.99
156_G	195_P	0.545	0.99
277_T	298_R	0.544	0.99
231_L	238_A	0.543	0.99
213_T	263_R	0.541	0.98
99_A	143_F	0.540	0.98
155_K	159_I	0.536	0.98
164_D	168_V	0.536	0.98
278_G	298_R	0.535	0.98
156_G	197_E	0.533	0.98
149_S	153_D	0.532	0.98
131_Q	271_Y	0.532	0.98
135_S	271_Y	0.530	0.98
76_H	162_L	0.529	0.98
224_S	268_D	0.528	0.98
245_T	248_P	0.526	0.98
159_I	197_E	0.526	0.98
112_P	158_T	0.525	0.98
93_Q	97_H	0.525	0.98
279_E	298_R	0.524	0.98
88_G	136_L	0.524	0.98
5_G	8_Q	0.522	0.98
192_P	196_Y	0.522	0.98
246_F	276_V	0.521	0.98
112_P	170_I	0.521	0.98
231_L	236_I	0.519	0.98
228_A	238_A	0.519	0.98
203_A	250_D	0.519	0.98
18_M	53_V	0.518	0.98
306_I	316_V	0.518	0.98
211_D	263_R	0.513	0.98
219_L	223_R	0.506	0.98
164_D	200_F	0.506	0.98
213_T	264_V	0.506	0.98
288_A	293_K	0.505	0.98
214_I	267_V	0.503	0.98
18_M	48_F	0.500	0.97
15_R	18_M	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	0.9669	100	0.211	Contact Map
1umdB	2	0.9639	100	0.222	Contact Map
1ik6A	3	0.8373	100	0.225	Contact Map
2ozlB	2	0.9789	100	0.234	Contact Map
1qs0B	2	0.9849	100	0.239	Contact Map
2o1xA	2	0.9127	100	0.252	Contact Map
2bfdB	2	0.9669	100	0.258	Contact Map
4kxvA	2	0.9127	100	0.264	Contact Map
2o1sA	2	0.9036	100	0.264	Contact Map
1gpuA	2	0.8886	100	0.304	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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