OPUBA - BACSU - GREMLIN Contacts

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OPUBA - Choline transport ATP-binding protein OpuBA

UniProt:	Q45460	Sequences: MLTLENVSKTYKGGKKAVNNVNLKIAKGEFICFIGPSGCGKTTTMKMINRLIEPSAGKIFIDGENIMDQDPVELRRKIGYVIQQIGLFPHMTIQQNISLVPKLLKWPEQQRKERARELLKLVDMGPEYVDRYPHELSGGQQQRIGVLRALAAEPPLILMDEPFGALDPITRDSLQEEFKKLQKTLHKTIVFVTHDMDEAIKLADRIVILKAGEIVQVGTPDDILRNPADEFVEEFIGKERLIQSSSPDVERVDQIMNTQPVTITADKTLSEAIQLMRQERVDSLLVVNDERVLQGYVDVEIIDQCRKKANLVSEVLHEDIYTVLGGTLLRDTVRKILKRGVKYVPVVDEDRRLIGIVTRASLVDIVYDSLWGEEKQLAALS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	381 (301)
Sequences:	6664 (5656)
Seq/√Len:	326.0

ECOLI - PROV POTG POTA MALK METN CYSA UGPC FBPC YCJV YDCT YHES RBSA YADG YEHX DPPF UUP MODC DPPD GSIA ARAG SAPD OPPF OPPD DDPD MACB DDPF CYDC MDLB MDLA FEPC MSBA CYDD MLAF LSRA YTFR SAPF YOJI TAUB ETTA HISP NIKE YECC FECE FHUC LPTB GLNQ PHNC SSUB YPHE YHDZ GLTL SUFC LIVG PHNK FTSE PSTB XYLG ZNUC ARTP MODF ALSA LIVF THIQ LOLD BTUD FETA MGLA YBBA NIKD PHNL YDDA YEJF CCMA YNJD YBHF YBIT
BACSU - OPUBA OPUCA OPUAA YVRA METN YURJ MSMX OPPD YDIF TAGH DPPD YKFD YFIL APPD APPF YHCH YVFR YDBJ YHAQ YXLF YFMR RBSA YCBN YHEH OPPF SUNT YFIC ECFA1 YFIB YKNV YGAD YUSV BMRA YTRB YKNU FHUC YFMF YWJA YFMM YHEI YKPA TCYN YCLP YKOD YLMA CYDD SUFC CYDC ECSA YVCR BCEA YXDL YTLC SKFE ECFA2 FTSE GLNQ PSTB1 YXEO TCYC ARTM NATA ALBC YJKB PSTB2 SSUB MNTB YVRO YTHP YKNY EXPZ YCLH ZNUC YYBJ YHCG YUFO YTRE YYDI
HALSA - Q9HMW0 BTUDA Q9HMX3 Q9HHQ5 Q9HR06 Q9HNZ9 Q9HMX2 Q9HMT3 Q9HRJ6 Q9HMU8 Q9HMG1 PSTB2 Q9HRH8 Q9HSQ7 PHNC Q9HHM2 Q9HMG6 Q9HNY3 Q9HRV7 Q9HRZ9 Y2317 Y1631 PSTB1 Q9HR96 Q9HHR7 Q9HS04 Q9HT03 Q9HR21 Q9HQA8 Q9HMC1 Q9HMW1
SULSO - Q97UF2 Q97YY4 Q97UJ9 Q97UY8 Q7LX64 Q97UH3 Q97VF5 Q97ZC0 Q97VC1 Q97YP3 Q97VH6 Q97VK8 Q97VK9 Q97YP7 Q97VF4 Q97YP8 Q97UD4 Q97YK2 Q97X18 Q97YQ7 Q980W0 Q97Z03 Q97U54 PSTB Q97V01 Q97UH4 Y1893 Q97W42 Q97V00 Q7LY07 Y2030 Q7LXM4 Q97VM2 Q97VY4 Q97UG5 Q7LX80 Q97Z56 Q97YP4 Q97Z96 Q97UC2 Q980K5 Q97ZU0 Q980E6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
6_N	20_N	5.160	1.00
4_L	7_V	3.855	1.00
200_I	221_D	3.807	1.00
5_E	58_K	3.760	1.00
16_K	19_N	3.334	1.00
29_E	205_R	3.265	1.00
90_H	134_H	3.182	1.00
45_M	192_V	3.135	1.00
9_K	47_M	3.014	1.00
91_M	99_L	2.811	1.00
9_K	55_S	2.709	1.00
7_V	54_P	2.472	1.00
19_N	213_E	2.460	1.00
308_K	311_L	2.367	1.00
289_D	315_V	2.347	1.00
10_T	55_S	2.295	1.00
25_I	31_I	2.293	1.00
3_T	24_K	2.234	1.00
88_F	91_M	2.107	1.00
6_N	22_N	2.104	1.00
8_S	56_A	2.084	1.00
4_L	23_L	2.062	1.00
45_M	158_L	2.037	1.00
315_V	319_D	2.035	1.00
311_L	315_V	2.023	1.00
32_C	203_A	2.021	1.00
47_M	54_P	1.955	1.00
313_S	317_H	1.952	1.00
289_D	292_V	1.937	1.00
8_S	20_N	1.884	1.00
32_C	199_A	1.868	1.00
31_I	207_V	1.839	1.00
282_D	285_L	1.787	1.00
47_M	59_I	1.786	1.00
4_L	48_I	1.716	1.00
265_A	268_T	1.687	1.00
318_E	322_T	1.673	1.00
131_R	135_E	1.666	1.00
273_I	277_R	1.659	1.00
9_K	52_I	1.653	1.00
26_A	29_E	1.651	1.00
307_K	310_N	1.647	1.00
314_E	318_E	1.640	1.00
219_T	222_D	1.629	1.00
49_N	158_L	1.628	1.00
79_G	154_P	1.619	1.00
272_A	276_M	1.611	1.00
263_I	266_D	1.607	1.00
271_E	275_L	1.591	1.00
91_M	95_Q	1.580	1.00
296_Y	299_V	1.575	1.00
7_V	47_M	1.568	1.00
292_V	296_Y	1.559	1.00
23_L	207_V	1.554	1.00
256_M	259_Q	1.538	1.00
96_N	133_P	1.507	1.00
268_T	272_A	1.498	1.00
133_P	144_I	1.491	1.00
278_Q	282_D	1.490	1.00
319_D	322_T	1.488	1.00
94_Q	98_S	1.485	1.00
317_H	321_Y	1.483	1.00
92_T	95_Q	1.482	1.00
262_T	265_A	1.475	1.00
218_G	222_D	1.474	1.00
261_V	265_A	1.472	1.00
282_D	322_T	1.471	1.00
128_Y	131_R	1.462	1.00
10_T	16_K	1.460	1.00
3_T	60_F	1.432	1.00
274_Q	277_R	1.420	1.00
96_N	148_R	1.399	1.00
269_L	272_A	1.392	1.00
210_K	213_E	1.388	1.00
179_K	201_K	1.381	1.00
46_K	52_I	1.377	1.00
270_S	274_Q	1.367	1.00
310_N	314_E	1.336	1.00
284_L	288_N	1.328	1.00
107_P	110_Q	1.321	1.00
36_P	39_C	1.320	1.00
283_S	287_V	1.319	1.00
89_P	134_H	1.310	1.00
46_K	51_L	1.310	1.00
237_G	240_R	1.305	1.00
11_Y	17_A	1.294	1.00
290_E	319_D	1.292	1.00
116_R	126_P	1.286	1.00
305_C	308_K	1.283	1.00
232_V	235_F	1.272	1.00
91_M	96_N	1.266	1.00
18_V	47_M	1.262	1.00
253_D	256_M	1.250	1.00
87_L	96_N	1.247	1.00
191_F	203_A	1.246	1.00
315_V	318_E	1.242	1.00
178_F	189_I	1.237	1.00
282_D	286_V	1.237	1.00
317_H	320_I	1.233	1.00
258_T	262_T	1.233	1.00
318_E	321_Y	1.227	1.00
47_M	55_S	1.227	1.00
5_E	60_F	1.219	1.00
257_N	260_P	1.219	1.00
281_V	284_L	1.210	1.00
205_R	216_Q	1.209	1.00
312_V	315_V	1.205	1.00
275_L	279_E	1.203	1.00
63_G	76_R	1.197	1.00
8_S	16_K	1.188	1.00
294_Q	320_I	1.182	1.00
301_I	304_Q	1.178	1.00
93_I	144_I	1.166	1.00
314_E	317_H	1.166	1.00
264_T	268_T	1.166	1.00
285_L	289_D	1.152	1.00
5_E	22_N	1.138	1.00
253_D	257_N	1.137	1.00
199_A	203_A	1.135	1.00
31_I	190_V	1.133	1.00
270_S	273_I	1.123	1.00
114_R	117_E	1.121	1.00
258_T	261_V	1.121	1.00
28_G	188_T	1.116	1.00
18_V	21_V	1.115	1.00
311_L	314_E	1.113	1.00
307_K	311_L	1.111	1.00
132_Y	135_E	1.106	1.00
95_Q	98_S	1.106	1.00
13_G	16_K	1.103	1.00
158_L	190_V	1.103	1.00
303_D	309_A	1.097	1.00
181_L	187_K	1.092	1.00
29_E	204_D	1.092	1.00
113_E	117_E	1.089	1.00
225_R	228_A	1.086	1.00
269_L	273_I	1.086	1.00
232_V	236_I	1.084	1.00
316_L	319_D	1.079	1.00
265_A	269_L	1.078	1.00
303_D	306_R	1.076	1.00
100_V	148_R	1.076	1.00
171_R	195_D	1.075	1.00
290_E	294_Q	1.072	1.00
6_N	56_A	1.068	1.00
90_H	132_Y	1.067	1.00
293_L	297_V	1.067	1.00
267_K	270_S	1.065	1.00
316_L	320_I	1.064	1.00
254_Q	257_N	1.064	1.00
302_I	309_A	1.063	1.00
275_L	278_Q	1.063	1.00
308_K	312_V	1.062	1.00
260_P	263_I	1.046	1.00
92_T	96_N	1.045	1.00
176_E	180_K	1.040	1.00
292_V	295_G	1.038	1.00
276_M	279_E	1.030	1.00
279_E	283_S	1.026	1.00
112_K	115_A	1.013	1.00
271_E	274_Q	1.008	1.00
118_L	147_L	1.008	1.00
253_D	259_Q	1.007	1.00
4_L	59_I	1.005	1.00
8_S	19_N	1.003	1.00
262_T	266_D	0.997	1.00
222_D	226_N	0.996	1.00
235_F	238_K	0.995	1.00
208_I	227_P	0.995	1.00
257_N	261_V	0.992	1.00
110_Q	113_E	0.991	1.00
284_L	287_V	0.987	1.00
25_I	188_T	0.987	1.00
108_E	111_R	0.982	1.00
277_R	281_V	0.980	1.00
191_F	202_L	0.980	1.00
88_F	96_N	0.976	1.00
208_I	223_I	0.975	1.00
265_A	270_S	0.972	1.00
313_S	316_L	0.968	1.00
270_S	276_M	0.960	1.00
231_F	234_E	0.957	1.00
191_F	199_A	0.954	1.00
39_C	209_L	0.953	1.00
81_V	149_A	0.953	1.00
79_G	149_A	0.940	1.00
313_S	320_I	0.939	1.00
210_K	214_I	0.938	1.00
294_Q	298_D	0.936	1.00
291_R	295_G	0.934	1.00
93_I	133_P	0.932	1.00
293_L	296_Y	0.930	1.00
64_E	76_R	0.928	1.00
193_T	199_A	0.927	1.00
93_I	99_L	0.925	1.00
267_K	274_Q	0.924	1.00
220_P	224_L	0.924	1.00
293_L	312_V	0.923	1.00
118_L	151_A	0.914	1.00
107_P	112_K	0.912	1.00
81_V	142_Q	0.910	1.00
231_F	235_F	0.907	1.00
101_P	104_L	0.907	1.00
269_L	274_Q	0.906	1.00
274_Q	278_Q	0.906	1.00
305_C	309_A	0.903	1.00
238_K	242_I	0.898	1.00
286_V	290_E	0.898	1.00
251_R	254_Q	0.892	1.00
10_T	14_G	0.891	1.00
306_R	309_A	0.891	1.00
310_N	313_S	0.886	1.00
221_D	225_R	0.885	1.00
49_N	80_Y	0.875	1.00
305_C	312_V	0.871	1.00
252_V	256_M	0.871	1.00
291_R	294_Q	0.871	1.00
9_K	18_V	0.871	1.00
272_A	275_L	0.871	1.00
9_K	43_T	0.858	1.00
258_T	263_I	0.847	1.00
276_M	280_R	0.846	1.00
51_L	86_G	0.845	1.00
295_G	298_D	0.844	1.00
34_I	208_I	0.844	1.00
111_R	114_R	0.842	1.00
263_I	269_L	0.838	1.00
213_E	217_V	0.836	1.00
7_V	59_I	0.832	1.00
264_T	267_K	0.829	1.00
178_F	202_L	0.820	1.00
297_V	302_I	0.816	1.00
197_D	201_K	0.815	1.00
260_P	264_T	0.812	1.00
98_S	115_A	0.810	1.00
77_K	152_A	0.807	1.00
272_A	280_R	0.805	1.00
266_D	269_L	0.802	1.00
168_P	172_D	0.802	1.00
154_P	181_L	0.801	1.00
54_P	59_I	0.801	1.00
223_I	227_P	0.800	1.00
209_L	214_I	0.800	1.00
219_T	223_I	0.799	1.00
289_D	296_Y	0.799	1.00
279_E	282_D	0.798	1.00
193_T	198_E	0.798	1.00
233_E	237_G	0.796	1.00
301_I	305_C	0.791	1.00
192_V	195_D	0.791	1.00
295_G	299_V	0.790	1.00
156_L	190_V	0.789	1.00
221_D	224_L	0.786	1.00
254_Q	258_T	0.786	1.00
259_Q	263_I	0.785	1.00
288_N	291_R	0.780	1.00
93_I	136_L	0.778	1.00
116_R	129_V	0.778	1.00
300_E	303_D	0.775	1.00
281_V	285_L	0.774	1.00
288_N	292_V	0.769	1.00
280_R	284_L	0.767	1.00
280_R	283_S	0.763	1.00
290_E	320_I	0.761	1.00
110_Q	114_R	0.757	0.99
191_F	198_E	0.754	0.99
289_D	319_D	0.748	0.99
213_E	216_Q	0.747	0.99
233_E	236_I	0.737	0.99
266_D	270_S	0.736	0.99
224_L	227_P	0.735	0.99
25_I	190_V	0.734	0.99
286_V	289_D	0.733	0.99
302_I	308_K	0.733	0.99
303_D	307_K	0.729	0.99
92_T	132_Y	0.727	0.99
133_P	141_Q	0.724	0.99
99_L	104_L	0.722	0.99
299_V	302_I	0.722	0.99
116_R	120_K	0.722	0.99
249_V	252_V	0.719	0.99
302_I	305_C	0.718	0.99
297_V	313_S	0.715	0.99
27_K	155_P	0.715	0.99
220_P	223_I	0.715	0.99
107_P	111_R	0.709	0.99
214_I	217_V	0.697	0.99
99_L	103_L	0.691	0.99
224_L	228_A	0.691	0.99
298_D	301_I	0.691	0.99
317_H	322_T	0.690	0.99
239_E	242_I	0.689	0.99
127_E	130_D	0.688	0.99
294_Q	316_L	0.687	0.99
96_N	99_L	0.687	0.99
309_A	313_S	0.683	0.99
117_E	121_L	0.682	0.99
256_M	260_P	0.680	0.99
245_S	248_D	0.678	0.99
268_T	275_L	0.678	0.99
255_I	259_Q	0.672	0.99
94_Q	115_A	0.671	0.99
285_L	288_N	0.669	0.99
78_I	156_L	0.668	0.99
159_M	189_I	0.668	0.99
217_V	226_N	0.666	0.99
280_R	287_V	0.664	0.99
297_V	301_I	0.662	0.99
155_P	187_K	0.659	0.99
7_V	18_V	0.659	0.99
277_R	280_R	0.658	0.99
161_E	194_H	0.658	0.99
157_I	187_K	0.653	0.98
47_M	52_I	0.649	0.98
286_V	319_D	0.648	0.98
120_K	126_P	0.647	0.98
89_P	141_Q	0.645	0.98
306_R	310_N	0.642	0.98
11_Y	52_I	0.641	0.98
289_D	293_L	0.640	0.98
94_Q	129_V	0.639	0.98
97_I	100_V	0.638	0.98
254_Q	259_Q	0.637	0.98
273_I	297_V	0.636	0.98
122_V	147_L	0.632	0.98
2_L	156_L	0.627	0.98
265_A	273_I	0.626	0.98
267_K	281_V	0.624	0.98
237_G	241_L	0.622	0.98
25_I	156_L	0.619	0.98
99_L	102_K	0.617	0.98
138_G	143_R	0.613	0.98
263_I	270_S	0.613	0.98
300_E	305_C	0.612	0.98
2_L	61_I	0.612	0.98
309_A	312_V	0.609	0.98
273_I	276_M	0.608	0.98
11_Y	14_G	0.604	0.97
232_V	239_E	0.603	0.97
242_I	245_S	0.600	0.97
246_S	249_V	0.599	0.97
297_V	305_C	0.599	0.97
312_V	316_L	0.598	0.97
94_Q	130_D	0.597	0.97
108_E	112_K	0.596	0.97
296_Y	308_K	0.594	0.97
97_I	104_L	0.594	0.97
261_V	264_T	0.591	0.97
269_L	276_M	0.590	0.97
252_V	259_Q	0.586	0.97
308_K	315_V	0.586	0.97
109_Q	113_E	0.583	0.97
42_T	46_K	0.583	0.97
175_Q	198_E	0.582	0.97
62_D	76_R	0.582	0.97
98_S	102_K	0.581	0.97
227_P	233_E	0.581	0.97
299_V	303_D	0.578	0.97
290_E	297_V	0.577	0.97
275_L	283_S	0.576	0.97
175_Q	201_K	0.575	0.97
49_N	78_I	0.575	0.97
193_T	196_M	0.574	0.97
145_G	150_L	0.572	0.97
257_N	263_I	0.571	0.97
268_T	276_M	0.571	0.97
10_T	56_A	0.570	0.96
250_E	255_I	0.568	0.96
101_P	151_A	0.567	0.96
267_K	271_E	0.565	0.96
50_R	61_I	0.565	0.96
302_I	310_N	0.562	0.96
164_G	196_M	0.561	0.96
305_C	320_I	0.561	0.96
312_V	319_D	0.560	0.96
210_K	215_V	0.559	0.96
181_L	189_I	0.557	0.96
234_E	241_L	0.557	0.96
165_A	171_R	0.556	0.96
287_V	290_E	0.554	0.96
95_Q	130_D	0.554	0.96
266_D	272_A	0.553	0.96
21_V	207_V	0.552	0.96
304_Q	307_K	0.552	0.96
97_I	151_A	0.551	0.96
256_M	262_T	0.550	0.96
92_T	130_D	0.549	0.96
94_Q	99_L	0.549	0.96
115_A	151_A	0.549	0.96
238_K	241_L	0.547	0.96
94_Q	97_I	0.547	0.96
34_I	223_I	0.546	0.96
220_P	232_V	0.545	0.95
235_F	239_E	0.545	0.95
119_L	122_V	0.544	0.95
218_G	223_I	0.543	0.95
290_E	293_L	0.543	0.95
263_I	271_E	0.542	0.95
195_D	198_E	0.541	0.95
62_D	155_P	0.540	0.95
287_V	291_R	0.539	0.95
17_A	39_C	0.539	0.95
280_R	286_V	0.537	0.95
199_A	202_L	0.536	0.95
313_S	321_Y	0.536	0.95
34_I	217_V	0.535	0.95
305_C	310_N	0.535	0.95
266_D	271_E	0.534	0.95
31_I	205_R	0.533	0.95
205_R	217_V	0.533	0.95
41_K	161_E	0.533	0.95
236_I	240_R	0.533	0.95
313_S	322_T	0.532	0.95
273_I	279_E	0.532	0.95
293_L	298_D	0.532	0.95
261_V	269_L	0.531	0.95
44_T	209_L	0.531	0.95
100_V	152_A	0.530	0.95
253_D	258_T	0.529	0.95
261_V	268_T	0.528	0.95
212_G	216_Q	0.524	0.94
297_V	303_D	0.524	0.94
255_I	258_T	0.524	0.94
267_K	273_I	0.524	0.94
234_E	237_G	0.521	0.94
259_Q	262_T	0.520	0.94
175_Q	197_D	0.520	0.94
37_S	164_G	0.517	0.94
248_D	252_V	0.517	0.94
46_K	80_Y	0.517	0.94
298_D	303_D	0.516	0.94
47_M	53_E	0.515	0.94
50_R	53_E	0.514	0.94
263_I	268_T	0.513	0.94
34_I	206_I	0.513	0.94
44_T	48_I	0.512	0.94
313_S	319_D	0.511	0.94
254_Q	263_I	0.510	0.94
33_F	44_T	0.508	0.93
304_Q	320_I	0.507	0.93
166_L	174_L	0.507	0.93
21_V	214_I	0.507	0.93
109_Q	112_K	0.506	0.93
48_I	190_V	0.505	0.93
100_V	103_L	0.504	0.93
120_K	125_G	0.504	0.93
97_I	102_K	0.502	0.93
81_V	145_G	0.502	0.93
82_I	85_I	0.502	0.93
11_Y	43_T	0.501	0.93
97_I	101_P	0.501	0.93
275_L	282_D	0.500	0.93

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
4f4cA	1	0.5827	100	0.281	Contact Map
3tuiC	2	0.8793	100	0.281	Contact Map
4ry2A	2	0.6168	100	0.282	Contact Map
4yerA	2	0.7428	100	0.292	Contact Map
4u00A	1	0.6247	100	0.298	Contact Map
4ymuJ	2	0.622	100	0.298	Contact Map
2oljA	2	0.622	100	0.299	Contact Map
4q9hA	1	0.6168	100	0.302	Contact Map
1vplA	2	0.622	100	0.303	Contact Map
1b0uA	2	0.6352	100	0.303	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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