YVRN - BACSU - GREMLIN Contacts

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YVRN - Uncharacterized ABC transporter permease YvrN

UniProt:	P46324	Sequences: MLEHIRISFQSIFSHKLRSILTMLGVIIGIAAIIAIVSMLKGQSEQLKQSMIGMGNNAINVVYQPSGGEEESGGPQVSYASAPPVAEETVKAIKSDPMVKGLSLYYLSEGASVFHLTNVSYPQVYGVDDDYFDMFPIRITEGRKLTENDLNSTHQVVMINEAVRDELFPDGEALHKSIEMNGVPFKVVGVFKEKNQQESMFEGDYANPVLYVPKKVWPLIEGFDAPTQIAVQADSSEHIQEAGVMAADLLNQGLSEAELEKAEYSVMDLQEIAQEVESFNQSFALLLGGIASISLLVGGIGVMNIMLVSVTERTREIGIKKALGAKRRVILFQFLTEAVVLTSIGGILGVLAGFGIAKLLTVIFPMPFIVSIPAVVGALIFSMAVGIIFGLLPSIKASKLQPVDALRYE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	409 (359)
Sequences:	37489 (32144)
Seq/√Len:	1696.5

ECOLI - LOLE LOLC YBBP MACB FTSX
BACSU - YVRN YKNZ YCLI YTRF YXDM YVCS BCEB FTSX
HALSA - Q9HT02
SULSO - Q7LXM6 Q97XD5 Q97Z54

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
161_E	192_K	3.537	1.00
177_S	184_P	3.496	1.00
317_I	334_F	3.300	1.00
177_S	186_K	3.272	1.00
179_E	184_P	3.111	1.00
161_E	165_D	2.981	1.00
313_R	337_E	2.690	1.00
157_V	210_L	2.680	1.00
156_V	186_K	2.623	1.00
156_V	188_V	2.615	1.00
401_Q	404_D	2.571	1.00
138_R	192_K	2.506	1.00
164_R	190_V	2.459	1.00
158_M	189_G	2.438	1.00
173_A	176_K	2.424	1.00
172_E	176_K	2.420	1.00
86_A	89_T	2.411	1.00
321_K	327_R	2.350	1.00
13_F	16_K	2.315	1.00
346_G	379_L	2.293	1.00
243_G	247_A	2.290	1.00
326_K	329_V	2.275	1.00
391_L	395_I	2.204	1.00
238_H	241_E	2.196	1.00
159_I	164_R	2.152	1.00
90_V	94_K	2.149	1.00
395_I	399_K	2.131	1.00
91_K	94_K	2.091	1.00
338_A	390_G	2.091	1.00
157_V	185_F	2.061	1.00
155_Q	216_V	2.025	1.00
158_M	191_F	2.002	1.00
27_I	348_L	1.999	1.00
342_T	386_G	1.977	1.00
268_D	271_E	1.975	1.00
98_M	245_M	1.967	1.00
143_R	188_V	1.963	1.00
100_K	234_D	1.961	1.00
349_G	353_G	1.943	1.00
163_V	167_L	1.939	1.00
139_I	144_K	1.872	1.00
371_S	374_A	1.865	1.00
23_M	27_I	1.863	1.00
98_M	234_D	1.851	1.00
87_E	91_K	1.834	1.00
313_R	316_E	1.819	1.00
157_V	212_V	1.794	1.00
34_I	353_G	1.793	1.00
213_P	216_V	1.772	1.00
172_E	187_V	1.760	1.00
215_K	218_P	1.751	1.00
233_A	242_A	1.751	1.00
241_E	245_M	1.733	1.00
100_K	232_Q	1.720	1.00
91_K	95_S	1.715	1.00
159_I	163_V	1.703	1.00
185_F	216_V	1.701	1.00
212_V	217_W	1.698	1.00
331_L	395_I	1.690	1.00
92_A	95_S	1.686	1.00
141_E	172_E	1.676	1.00
244_V	247_A	1.650	1.00
127_V	131_Y	1.637	1.00
31_A	352_A	1.629	1.00
160_N	191_F	1.581	1.00
143_R	156_V	1.560	1.00
159_I	210_L	1.553	1.00
27_I	352_A	1.541	1.00
240_Q	243_G	1.540	1.00
162_A	193_E	1.536	1.00
45_E	49_Q	1.524	1.00
10_Q	13_F	1.516	1.00
23_M	345_G	1.507	1.00
159_I	187_V	1.506	1.00
157_V	178_I	1.504	1.00
174_L	190_V	1.502	1.00
239_I	243_G	1.499	1.00
329_V	332_F	1.489	1.00
214_K	218_P	1.482	1.00
345_G	349_G	1.468	1.00
88_E	92_A	1.464	1.00
153_T	156_V	1.448	1.00
11_S	337_E	1.446	1.00
328_R	332_F	1.440	1.00
355_G	359_L	1.429	1.00
144_K	158_M	1.426	1.00
89_T	92_A	1.426	1.00
179_E	182_G	1.414	1.00
158_M	188_V	1.413	1.00
18_R	312_E	1.413	1.00
30_I	349_G	1.403	1.00
162_A	165_D	1.400	1.00
92_A	96_D	1.392	1.00
327_R	398_S	1.385	1.00
212_V	216_V	1.382	1.00
317_I	330_I	1.382	1.00
372_I	376_V	1.380	1.00
235_S	238_H	1.379	1.00
244_V	248_D	1.376	1.00
140_T	161_E	1.374	1.00
240_Q	244_V	1.358	1.00
245_M	248_D	1.355	1.00
155_Q	183_V	1.355	1.00
342_T	346_G	1.354	1.00
26_V	345_G	1.352	1.00
314_T	405_A	1.344	1.00
145_L	188_V	1.326	1.00
41_K	371_S	1.323	1.00
389_F	393_P	1.321	1.00
394_S	398_S	1.318	1.00
373_P	377_G	1.318	1.00
351_L	355_G	1.305	1.00
12_I	19_S	1.301	1.00
98_M	242_A	1.284	1.00
318_G	405_A	1.280	1.00
96_D	245_M	1.271	1.00
325_A	329_V	1.270	1.00
376_V	380_I	1.266	1.00
101_G	232_Q	1.265	1.00
145_L	158_M	1.258	1.00
141_E	173_A	1.244	1.00
288_G	292_S	1.238	1.00
27_I	31_A	1.236	1.00
8_S	336_T	1.226	1.00
318_G	322_A	1.222	1.00
355_G	358_K	1.219	1.00
88_E	91_K	1.215	1.00
347_I	351_L	1.215	1.00
316_E	320_K	1.212	1.00
38_S	357_A	1.211	1.00
159_I	190_V	1.210	1.00
140_T	192_K	1.203	1.00
353_G	357_A	1.199	1.00
168_F	172_E	1.193	1.00
396_K	399_K	1.190	1.00
58_A	62_V	1.188	1.00
85_V	89_T	1.186	1.00
31_A	356_I	1.181	1.00
31_A	353_G	1.180	1.00
139_I	189_G	1.177	1.00
160_N	208_P	1.174	1.00
160_N	163_V	1.174	1.00
31_A	349_G	1.170	1.00
34_I	378_A	1.161	1.00
174_L	188_V	1.153	1.00
359_L	362_V	1.149	1.00
132_F	144_K	1.138	1.00
167_L	172_E	1.132	1.00
332_F	336_T	1.132	1.00
314_T	400_L	1.127	1.00
285_L	289_G	1.123	1.00
99_V	102_L	1.118	1.00
55_G	58_A	1.117	1.00
233_A	239_I	1.113	1.00
320_K	333_Q	1.113	1.00
145_L	156_V	1.097	1.00
17_L	20_I	1.095	1.00
44_S	48_K	1.080	1.00
320_K	325_A	1.078	1.00
105_Y	228_Q	1.077	1.00
162_A	166_E	1.074	1.00
29_G	291_A	1.071	1.00
45_E	369_I	1.067	1.00
19_S	341_L	1.063	1.00
243_G	268_D	1.056	1.00
245_M	249_L	1.054	1.00
395_I	398_S	1.053	1.00
373_P	376_V	1.053	1.00
274_Q	278_S	1.052	1.00
41_K	44_S	1.048	1.00
306_M	338_A	1.047	1.00
143_R	146_T	1.046	1.00
50_S	53_G	1.044	1.00
44_S	284_A	1.042	1.00
229_I	233_A	1.039	1.00
45_E	48_K	1.036	1.00
23_M	348_L	1.028	1.00
87_E	90_V	1.028	1.00
49_Q	52_I	1.027	1.00
49_Q	53_G	1.024	1.00
216_V	219_L	1.023	1.00
233_A	236_S	1.023	1.00
342_T	382_S	1.021	1.00
369_I	372_I	1.016	1.00
299_G	389_F	1.013	1.00
161_E	193_E	1.009	1.00
101_G	134_M	1.008	1.00
348_L	351_L	1.008	1.00
168_F	173_A	1.000	1.00
23_M	344_I	0.987	1.00
20_I	24_L	0.977	1.00
217_W	221_E	0.973	1.00
294_S	301_G	0.967	1.00
346_G	382_S	0.966	1.00
241_E	244_V	0.964	1.00
27_I	30_I	0.960	1.00
41_K	374_A	0.959	1.00
15_H	312_E	0.958	1.00
370_V	375_V	0.953	1.00
141_E	174_L	0.948	1.00
229_I	232_Q	0.948	1.00
400_L	404_D	0.947	1.00
103_S	128_D	0.946	1.00
338_A	342_T	0.944	1.00
89_T	93_I	0.940	1.00
154_H	215_K	0.934	1.00
101_G	133_D	0.930	1.00
9_F	13_F	0.930	1.00
234_D	237_E	0.925	1.00
314_T	318_G	0.923	1.00
261_K	264_Y	0.922	1.00
331_L	391_L	0.922	1.00
41_K	45_E	0.920	1.00
90_V	104_L	0.920	1.00
394_S	397_A	0.919	1.00
130_D	133_D	0.919	1.00
15_H	18_R	0.919	1.00
299_G	385_V	0.915	1.00
350_V	375_V	0.913	1.00
277_E	281_Q	0.911	1.00
94_K	102_L	0.907	1.00
160_N	207_N	0.905	1.00
106_Y	217_W	0.903	1.00
303_M	307_L	0.899	1.00
27_I	345_G	0.898	1.00
90_V	102_L	0.897	1.00
325_A	330_I	0.889	1.00
38_S	42_G	0.888	1.00
154_H	213_P	0.886	1.00
392_L	395_I	0.886	1.00
281_Q	285_L	0.885	1.00
26_V	30_I	0.882	1.00
237_E	241_E	0.879	1.00
313_R	334_F	0.878	1.00
339_V	387_I	0.876	1.00
54_M	58_A	0.870	1.00
396_K	400_L	0.868	1.00
327_R	399_K	0.867	1.00
380_I	384_A	0.862	1.00
382_S	386_G	0.861	1.00
111_A	124_V	0.859	1.00
321_K	402_P	0.858	1.00
400_L	405_A	0.855	1.00
92_A	249_L	0.853	1.00
246_A	249_L	0.853	1.00
93_I	246_A	0.850	1.00
141_E	190_V	0.850	1.00
48_K	52_I	0.848	1.00
358_K	362_V	0.846	1.00
124_V	212_V	0.846	1.00
168_F	176_K	0.845	1.00
56_N	59_I	0.839	1.00
278_S	281_Q	0.834	1.00
327_R	331_L	0.830	1.00
265_S	268_D	0.829	1.00
133_D	144_K	0.829	1.00
128_D	131_Y	0.828	1.00
237_E	242_A	0.827	1.00
377_G	380_I	0.825	1.00
402_P	405_A	0.824	1.00
93_I	96_D	0.822	1.00
104_L	128_D	0.818	1.00
99_V	231_V	0.817	1.00
378_A	382_S	0.817	1.00
384_A	388_I	0.816	1.00
120_S	166_E	0.815	1.00
134_M	232_Q	0.813	1.00
30_I	382_S	0.812	1.00
11_S	313_R	0.812	1.00
242_A	246_A	0.812	1.00
126_G	217_W	0.810	1.00
60_N	63_Y	0.809	1.00
242_A	245_M	0.809	1.00
310_V	317_I	0.807	1.00
234_D	238_H	0.802	1.00
25_G	29_G	0.801	1.00
351_L	354_F	0.801	1.00
25_G	301_G	0.799	1.00
22_T	25_G	0.796	1.00
161_E	164_R	0.795	1.00
86_A	90_V	0.793	1.00
375_V	379_L	0.788	1.00
122_P	210_L	0.787	1.00
321_K	330_I	0.784	1.00
377_G	381_F	0.781	1.00
359_L	363_I	0.779	1.00
339_V	386_G	0.778	1.00
266_V	269_L	0.776	1.00
393_P	397_A	0.775	1.00
403_V	406_L	0.771	1.00
160_N	209_V	0.769	1.00
124_V	210_L	0.769	1.00
59_I	243_G	0.768	1.00
311_T	314_T	0.767	1.00
292_S	296_L	0.767	1.00
309_S	337_E	0.766	1.00
16_K	20_I	0.766	1.00
381_F	384_A	0.762	1.00
90_V	93_I	0.761	1.00
173_A	190_V	0.760	1.00
304_N	308_V	0.757	1.00
160_N	193_E	0.757	1.00
233_A	237_E	0.756	1.00
267_M	271_E	0.756	1.00
214_K	217_W	0.749	1.00
354_F	370_V	0.748	1.00
57_N	61_V	0.743	1.00
142_G	145_L	0.743	1.00
352_A	355_G	0.742	1.00
137_I	191_F	0.740	1.00
11_S	316_E	0.737	1.00
33_I	37_V	0.737	1.00
90_V	229_I	0.736	1.00
180_M	185_F	0.735	1.00
338_A	393_P	0.734	1.00
191_F	211_Y	0.734	1.00
242_A	249_L	0.733	1.00
291_A	295_L	0.732	1.00
247_A	266_V	0.731	1.00
208_P	211_Y	0.730	1.00
346_G	386_G	0.730	1.00
357_A	361_T	0.730	1.00
25_G	304_N	0.729	1.00
263_E	266_V	0.729	1.00
358_K	368_F	0.727	1.00
335_L	387_I	0.727	1.00
309_S	313_R	0.726	1.00
331_L	398_S	0.726	1.00
230_A	233_A	0.726	1.00
271_E	274_Q	0.725	1.00
191_F	195_N	0.725	1.00
102_L	105_Y	0.725	1.00
280_N	284_A	0.724	1.00
139_I	191_F	0.724	1.00
122_P	163_V	0.724	1.00
357_A	368_F	0.723	1.00
100_K	104_L	0.722	1.00
346_G	350_V	0.721	1.00
381_F	385_V	0.721	1.00
7_I	11_S	0.720	1.00
344_I	347_I	0.720	1.00
379_L	383_M	0.720	1.00
105_Y	108_S	0.719	1.00
270_Q	274_Q	0.718	1.00
346_G	383_M	0.718	1.00
159_I	178_I	0.716	1.00
35_A	356_I	0.711	1.00
374_A	377_G	0.710	1.00
174_L	189_G	0.708	1.00
159_I	172_E	0.706	1.00
46_Q	50_S	0.706	1.00
96_D	249_L	0.701	1.00
350_V	379_L	0.700	1.00
126_G	214_K	0.699	1.00
102_L	231_V	0.699	1.00
374_A	378_A	0.699	1.00
139_I	143_R	0.698	1.00
278_S	282_S	0.697	1.00
35_A	353_G	0.695	1.00
38_S	353_G	0.695	1.00
319_I	322_A	0.695	1.00
301_G	304_N	0.694	1.00
318_G	402_P	0.692	1.00
392_L	396_K	0.692	1.00
390_G	394_S	0.691	1.00
338_A	386_G	0.691	1.00
114_F	179_E	0.689	1.00
303_M	389_F	0.689	1.00
298_G	301_G	0.689	1.00
178_I	185_F	0.688	1.00
105_Y	230_A	0.687	1.00
155_Q	186_K	0.687	1.00
123_Q	126_G	0.686	1.00
22_T	305_I	0.686	1.00
7_I	320_K	0.684	1.00
336_T	339_V	0.682	1.00
331_L	394_S	0.680	1.00
209_V	213_P	0.680	1.00
56_N	60_N	0.679	1.00
275_E	278_S	0.677	1.00
315_R	319_I	0.675	1.00
227_T	231_V	0.672	1.00
185_F	212_V	0.669	1.00
7_I	333_Q	0.668	1.00
139_I	158_M	0.667	1.00
158_M	211_Y	0.667	1.00
316_E	337_E	0.667	1.00
96_D	242_A	0.665	1.00
336_T	340_V	0.665	1.00
338_A	394_S	0.663	1.00
122_P	125_Y	0.663	1.00
113_V	122_P	0.662	1.00
94_K	101_G	0.661	1.00
101_G	130_D	0.660	1.00
100_K	103_S	0.659	1.00
260_E	263_E	0.659	1.00
141_E	164_R	0.658	1.00
282_S	286_L	0.656	1.00
319_I	323_L	0.653	1.00
175_H	186_K	0.650	1.00
140_T	191_F	0.650	1.00
305_I	309_S	0.650	1.00
354_F	358_K	0.648	1.00
183_V	219_L	0.646	1.00
62_V	267_M	0.644	1.00
172_E	178_I	0.640	1.00
393_P	398_S	0.639	1.00
306_M	309_S	0.636	1.00
139_I	145_L	0.635	1.00
337_E	340_V	0.633	1.00
8_S	333_Q	0.633	1.00
37_V	41_K	0.632	1.00
331_L	335_L	0.631	1.00
198_E	206_A	0.631	1.00
273_A	277_E	0.630	1.00
343_S	383_M	0.627	1.00
322_A	402_P	0.626	1.00
34_I	349_G	0.625	1.00
59_I	231_V	0.625	1.00
124_V	127_V	0.623	1.00
27_I	349_G	0.619	1.00
114_F	119_V	0.616	1.00
125_Y	211_Y	0.615	1.00
297_V	301_G	0.614	1.00
209_V	212_V	0.614	1.00
26_V	302_V	0.612	1.00
161_E	190_V	0.612	1.00
85_V	88_E	0.611	1.00
127_V	132_F	0.611	1.00
128_D	214_K	0.611	1.00
29_G	301_G	0.610	1.00
354_F	375_V	0.609	1.00
316_E	319_I	0.608	1.00
121_Y	124_V	0.607	1.00
306_M	390_G	0.607	1.00
115_H	118_N	0.606	1.00
17_L	21_L	0.604	1.00
316_E	333_Q	0.604	1.00
102_L	229_I	0.604	1.00
365_P	369_I	0.603	1.00
9_F	340_V	0.602	1.00
134_M	137_I	0.601	1.00
284_A	288_G	0.601	1.00
46_Q	49_Q	0.598	1.00
21_L	25_G	0.596	1.00
140_T	190_V	0.595	1.00
342_T	390_G	0.594	1.00
114_F	117_T	0.594	1.00
40_L	284_A	0.593	1.00
243_G	271_E	0.592	1.00
310_V	334_F	0.591	1.00
233_A	238_H	0.588	1.00
310_V	397_A	0.587	1.00
44_S	47_L	0.586	1.00
97_P	100_K	0.584	1.00
267_M	272_I	0.584	1.00
155_Q	185_F	0.584	1.00
154_H	216_V	0.581	1.00
164_R	173_A	0.581	1.00
111_A	115_H	0.580	1.00
58_A	64_Q	0.579	1.00
54_M	57_N	0.575	1.00
372_I	375_V	0.574	1.00
29_G	32_A	0.573	1.00
311_T	396_K	0.573	1.00
100_K	233_A	0.573	1.00
335_L	391_L	0.572	1.00
34_I	38_S	0.570	1.00
235_S	239_I	0.569	1.00
103_S	134_M	0.566	1.00
16_K	19_S	0.566	1.00
164_R	167_L	0.566	1.00
31_A	35_A	0.565	1.00
386_G	389_F	0.563	1.00
47_L	51_M	0.563	1.00
299_G	303_M	0.561	1.00
18_R	301_G	0.561	1.00
41_K	373_P	0.561	1.00
59_I	233_A	0.560	1.00
139_I	192_K	0.559	1.00
314_T	396_K	0.558	1.00
369_I	373_P	0.556	1.00
175_H	178_I	0.556	1.00
334_F	338_A	0.555	1.00
32_A	334_F	0.555	1.00
118_N	121_Y	0.555	1.00
157_V	187_V	0.554	1.00
194_K	197_Q	0.553	1.00
267_M	270_Q	0.553	1.00
226_P	229_I	0.551	1.00
142_G	189_G	0.551	1.00
286_L	290_I	0.550	1.00
135_F	138_R	0.550	1.00
386_G	390_G	0.548	1.00
206_A	209_V	0.548	1.00
385_V	389_F	0.547	1.00
302_V	342_T	0.546	1.00
143_R	147_E	0.545	1.00
60_N	267_M	0.545	1.00
243_G	266_V	0.545	1.00
96_D	99_V	0.543	1.00
43_Q	46_Q	0.543	1.00
156_V	213_P	0.542	1.00
11_S	15_H	0.542	1.00
22_T	26_V	0.542	1.00
187_V	190_V	0.541	1.00
94_K	97_P	0.540	1.00
127_V	211_Y	0.540	1.00
333_Q	336_T	0.539	1.00
57_N	60_N	0.538	1.00
195_N	207_N	0.537	1.00
294_S	298_G	0.537	1.00
133_D	136_P	0.533	1.00
228_Q	231_V	0.532	1.00
347_I	350_V	0.528	1.00
388_I	392_L	0.527	1.00
287_L	291_A	0.526	1.00
338_A	389_F	0.523	1.00
358_K	361_T	0.522	1.00
164_R	174_L	0.520	1.00
164_R	187_V	0.517	1.00
90_V	96_D	0.517	1.00
350_V	354_F	0.516	1.00
228_Q	232_Q	0.514	1.00
191_F	194_K	0.513	1.00
283_F	287_L	0.513	1.00
335_L	339_V	0.510	1.00
185_F	220_I	0.510	1.00
22_T	304_N	0.510	1.00
129_D	132_F	0.509	1.00
333_Q	337_E	0.506	1.00
174_L	187_V	0.505	1.00
173_A	187_V	0.504	1.00
135_F	230_A	0.504	1.00
321_K	405_A	0.504	1.00
103_S	106_Y	0.503	1.00
11_S	18_R	0.503	1.00
376_V	379_L	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
3ftjA	1	0.5183	99.6	0.682	Contact Map
3is6A	2	0.5355	99.2	0.745	Contact Map
4av3A	2	0.2641	35.8	0.935	Contact Map
3w9iA	3	0.8313	22.4	0.941	Contact Map
4dx5A	3	0.8337	17.7	0.944	Contact Map
4mt1A	3	0.8533	16.2	0.945	Contact Map
4k0jA	3	0.8289	14.5	0.946	Contact Map
4pl0A	2	0.2298	12.3	0.948	Contact Map
4a01A	2	0.3178	10.3	0.95	Contact Map
4gycB	2	0.1394	8.1	0.952	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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