YFIM - BACSU - GREMLIN Contacts

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YFIM - Putative transport permease YfiM

UniProt:	P94441	Sequences: MKKSIWIAWKDVKIRITDRKGFMMLILMPLILTCILGAALGSVVDGGSRIDDIKVGYIQSDQSDTANMFTKDVLKKMKSIKVTKVGSKDKMKKLIDEKKIDVGIVIPNHWEAGKTSAVVNAAPDQTLKSSIIETAASSFIEQYKAVKEAASGSMDYISKTEAVKQGKLDPAQFAEKLAKTLEKETGDKLTIAEKSVGSKAVTSFQYYSAAMLCMFMLFHITVGAKSFLQEKDTETLARMLMTPAQKSVILFGKWLGTYLFAIIQFFIFLIVTINVFGVDWGGNLLLVSVLGLSYAAAVSGISMLLASCISDMKTADAIGGFGIQLLAVLGGSMLPLYQFPDVLQSVSKAVPNRWALDGFLSLMEGGGWADLQKPVLLFAAIGFCSLVIGIRRLHTR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	396 (350)
Sequences:	10850 (8951)
Seq/√Len:	478.5

ECOLI - YBHR YBHS YHHJ
BACSU - YFIM YFIN NATB YHAP YHGE
SULSO - Q97W41 Q7LY08 Q97WP5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
56_G	100_I	5.226	1.00
290_L	358_G	4.659	1.00
91_M	103_G	4.606	1.00
94_L	100_I	3.508	1.00
9_W	13_K	3.333	1.00
7_I	252_G	3.326	1.00
93_K	97_E	3.316	1.00
8_A	259_L	3.065	1.00
85_V	94_L	3.064	1.00
88_K	92_K	2.934	1.00
8_A	255_L	2.929	1.00
4_S	255_L	2.774	1.00
94_L	99_K	2.669	1.00
245_Q	248_V	2.528	1.00
11_D	253_K	2.489	1.00
296_A	382_G	2.484	1.00
92_K	96_D	2.431	1.00
372_Q	376_L	2.386	1.00
376_L	380_A	2.374	1.00
291_G	355_A	2.373	1.00
4_S	8_A	2.345	1.00
106_I	110_W	2.330	1.00
341_D	345_S	2.312	1.00
95_I	103_G	2.258	1.00
266_F	288_S	2.255	1.00
304_L	388_I	2.240	1.00
105_V	120_N	2.223	1.00
90_K	94_L	2.213	1.00
293_S	379_A	2.183	1.00
56_G	85_V	2.148	1.00
57_Y	70_T	2.094	1.00
270_I	274_N	2.036	1.00
60_S	88_K	1.971	1.00
300_G	382_G	1.949	1.00
88_K	105_V	1.935	1.00
60_S	105_V	1.928	1.00
86_G	90_K	1.919	1.00
380_A	384_C	1.909	1.00
13_K	16_I	1.905	1.00
367_G	370_D	1.895	1.00
381_I	385_S	1.887	1.00
5_I	9_W	1.857	1.00
297_A	382_G	1.850	1.00
294_Y	355_A	1.825	1.00
348_K	353_R	1.803	1.00
10_K	230_E	1.798	1.00
285_L	289_V	1.762	1.00
59_Q	66_A	1.758	1.00
12_V	263_I	1.758	1.00
54_K	81_K	1.745	1.00
347_S	353_R	1.735	1.00
58_I	91_M	1.723	1.00
348_K	354_W	1.720	1.00
54_K	83_T	1.712	1.00
357_D	374_P	1.694	1.00
59_Q	63_S	1.687	1.00
258_Y	296_A	1.686	1.00
258_Y	292_L	1.678	1.00
294_Y	298_V	1.651	1.00
52_D	81_K	1.650	1.00
61_D	111_E	1.648	1.00
286_L	362_L	1.637	1.00
63_S	66_A	1.621	1.00
144_K	147_K	1.617	1.00
89_D	92_K	1.607	1.00
265_F	291_G	1.590	1.00
29_P	39_A	1.587	1.00
93_K	96_D	1.583	1.00
137_S	140_I	1.555	1.00
59_Q	62_Q	1.550	1.00
230_E	253_K	1.547	1.00
90_K	93_K	1.537	1.00
16_I	19_R	1.535	1.00
293_S	382_G	1.524	1.00
100_I	103_G	1.512	1.00
102_V	132_I	1.506	1.00
307_S	392_R	1.506	1.00
72_D	146_V	1.505	1.00
336_L	347_S	1.474	1.00
68_M	71_K	1.472	1.00
387_V	391_R	1.434	1.00
71_K	75_K	1.424	1.00
361_S	366_G	1.421	1.00
261_A	295_A	1.412	1.00
133_E	137_S	1.389	1.00
290_L	362_L	1.387	1.00
202_T	205_Q	1.385	1.00
290_L	375_V	1.385	1.00
311_D	314_T	1.382	1.00
13_K	17_T	1.381	1.00
350_V	353_R	1.367	1.00
4_S	248_V	1.361	1.00
304_L	389_G	1.356	1.00
65_T	111_E	1.349	1.00
366_G	370_D	1.346	1.00
228_L	231_K	1.345	1.00
8_A	252_G	1.344	1.00
142_Q	146_V	1.341	1.00
342_V	345_S	1.333	1.00
293_S	375_V	1.333	1.00
301_I	322_G	1.324	1.00
341_D	344_Q	1.317	1.00
377_L	381_I	1.316	1.00
283_N	286_L	1.311	1.00
317_A	320_G	1.292	1.00
66_A	111_E	1.292	1.00
217_L	221_T	1.284	1.00
297_A	385_S	1.275	1.00
109_H	112_A	1.269	1.00
373_K	377_L	1.265	1.00
60_S	108_N	1.250	1.00
304_L	392_R	1.246	1.00
95_I	100_I	1.240	1.00
375_V	379_A	1.240	1.00
92_K	120_N	1.239	1.00
73_V	136_A	1.234	1.00
105_V	118_V	1.234	1.00
63_S	111_E	1.232	1.00
344_Q	348_K	1.228	1.00
345_S	349_A	1.226	1.00
250_L	390_I	1.223	1.00
88_K	103_G	1.221	1.00
297_A	378_F	1.217	1.00
377_L	380_A	1.216	1.00
137_S	141_E	1.212	1.00
85_V	100_I	1.209	1.00
270_I	273_I	1.203	1.00
185_T	188_K	1.201	1.00
259_L	263_I	1.201	1.00
81_K	84_K	1.190	1.00
262_I	292_L	1.179	1.00
18_D	21_G	1.177	1.00
5_I	8_A	1.174	1.00
353_R	357_D	1.171	1.00
4_S	252_G	1.160	1.00
361_S	364_E	1.160	1.00
331_G	335_P	1.157	1.00
345_S	348_K	1.153	1.00
61_D	109_H	1.152	1.00
140_I	144_K	1.151	1.00
104_I	119_V	1.151	1.00
247_S	251_F	1.151	1.00
12_V	259_L	1.143	1.00
271_V	275_V	1.143	1.00
140_I	143_Y	1.138	1.00
29_P	32_L	1.137	1.00
342_V	346_V	1.137	1.00
89_D	93_K	1.137	1.00
217_L	220_I	1.136	1.00
324_Q	327_A	1.133	1.00
30_L	34_C	1.133	1.00
247_S	390_I	1.130	1.00
7_I	244_A	1.118	1.00
230_E	235_T	1.118	1.00
54_K	101_D	1.109	1.00
269_L	291_G	1.094	1.00
297_A	381_I	1.087	1.00
321_F	325_L	1.083	1.00
4_S	251_F	1.074	1.00
354_W	374_P	1.069	1.00
136_A	139_F	1.068	1.00
66_A	106_I	1.067	1.00
144_K	148_E	1.064	1.00
135_A	140_I	1.046	1.00
141_E	145_A	1.045	1.00
287_V	359_F	1.044	1.00
143_Y	147_K	1.044	1.00
252_G	256_G	1.036	1.00
56_G	94_L	1.032	1.00
354_W	377_L	1.027	1.00
58_I	103_G	1.022	1.00
295_A	299_S	1.022	1.00
119_V	122_A	1.021	1.00
248_V	252_G	1.014	1.00
224_A	315_A	1.010	1.00
228_L	315_A	1.009	1.00
12_V	256_G	1.007	1.00
340_P	344_Q	1.006	1.00
354_W	357_D	1.005	1.00
8_A	256_G	0.994	1.00
302_S	306_A	0.990	1.00
23_M	27_L	0.988	1.00
258_Y	299_S	0.978	1.00
235_T	238_R	0.974	1.00
355_A	358_G	0.972	1.00
210_A	213_C	0.967	1.00
304_L	385_S	0.966	1.00
336_L	339_F	0.962	1.00
187_D	191_I	0.955	1.00
141_E	144_K	0.951	1.00
323_I	327_A	0.948	1.00
142_Q	147_K	0.947	1.00
361_S	374_P	0.947	1.00
209_A	213_C	0.944	1.00
213_C	216_M	0.942	1.00
300_G	386_L	0.939	1.00
55_V	104_I	0.933	1.00
379_A	383_F	0.930	1.00
286_L	289_V	0.923	1.00
75_K	78_K	0.920	1.00
262_I	266_F	0.915	1.00
300_G	385_S	0.911	1.00
75_K	82_V	0.908	1.00
384_C	388_I	0.902	1.00
208_S	211_M	0.899	1.00
186_G	189_L	0.896	1.00
339_F	344_Q	0.896	1.00
207_Y	211_M	0.895	1.00
239_M	249_I	0.891	1.00
76_K	79_S	0.888	1.00
240_L	249_I	0.887	1.00
254_W	299_S	0.882	1.00
130_S	133_E	0.880	1.00
68_M	72_D	0.878	1.00
190_T	193_E	0.877	1.00
6_W	9_W	0.876	1.00
12_V	16_I	0.876	1.00
143_Y	146_V	0.873	1.00
277_G	280_W	0.872	1.00
228_L	232_D	0.868	1.00
36_L	40_L	0.868	1.00
369_A	373_K	0.868	1.00
88_K	91_M	0.867	1.00
29_P	34_C	0.866	1.00
142_Q	145_A	0.865	1.00
91_M	94_L	0.864	1.00
59_Q	67_N	0.859	1.00
139_F	143_Y	0.857	1.00
212_L	220_I	0.854	1.00
103_G	120_N	0.854	1.00
35_I	39_A	0.854	1.00
67_N	71_K	0.847	1.00
10_K	13_K	0.844	1.00
213_C	355_A	0.842	1.00
58_I	85_V	0.842	1.00
373_K	376_L	0.840	1.00
368_W	372_Q	0.839	1.00
107_P	118_V	0.833	1.00
365_G	368_W	0.831	1.00
59_Q	106_I	0.829	1.00
309_I	318_I	0.829	1.00
59_Q	70_T	0.823	1.00
188_K	193_E	0.822	1.00
34_C	271_V	0.821	1.00
187_D	190_T	0.820	1.00
134_T	137_S	0.819	1.00
328_V	334_L	0.818	1.00
11_D	256_G	0.816	1.00
62_Q	108_N	0.815	1.00
131_I	135_A	0.815	1.00
55_V	102_V	0.815	1.00
117_A	120_N	0.815	1.00
382_G	386_L	0.814	1.00
309_I	314_T	0.805	1.00
277_G	281_G	0.805	1.00
122_A	125_Q	0.805	1.00
320_G	324_Q	0.805	1.00
189_L	192_A	0.805	1.00
104_I	117_A	0.803	1.00
211_M	214_M	0.799	1.00
145_A	149_A	0.790	1.00
266_F	284_L	0.789	1.00
213_C	352_N	0.787	1.00
188_K	194_K	0.786	1.00
285_L	288_S	0.775	1.00
132_I	135_A	0.774	1.00
371_L	375_V	0.771	1.00
361_S	370_D	0.771	1.00
314_T	321_F	0.770	1.00
191_I	195_S	0.770	1.00
348_K	351_P	0.768	1.00
34_C	38_A	0.763	1.00
203_S	206_Y	0.761	1.00
146_V	149_A	0.761	1.00
10_K	14_I	0.760	1.00
284_L	288_S	0.757	1.00
15_R	260_F	0.756	1.00
357_D	361_S	0.755	1.00
232_D	312_M	0.750	1.00
36_L	39_A	0.748	1.00
14_I	230_E	0.746	1.00
56_G	103_G	0.745	1.00
118_V	121_A	0.743	1.00
69_F	140_I	0.742	1.00
326_L	350_V	0.742	1.00
386_L	390_I	0.742	1.00
33_T	272_T	0.740	1.00
307_S	389_G	0.740	1.00
211_M	215_F	0.739	1.00
29_P	35_I	0.738	1.00
69_F	106_I	0.738	1.00
61_D	106_I	0.737	1.00
85_V	91_M	0.734	1.00
145_A	148_E	0.729	1.00
78_K	81_K	0.729	1.00
222_V	225_K	0.725	1.00
255_L	259_L	0.724	1.00
385_S	389_G	0.723	1.00
138_S	142_Q	0.723	1.00
293_S	378_F	0.719	1.00
15_R	25_L	0.715	1.00
192_A	195_S	0.715	1.00
358_G	362_L	0.711	1.00
286_L	375_V	0.710	1.00
244_A	249_I	0.709	1.00
332_S	356_L	0.708	1.00
254_W	296_A	0.707	1.00
69_F	110_W	0.707	1.00
224_A	228_L	0.704	1.00
68_M	146_V	0.701	1.00
378_F	381_I	0.700	1.00
134_T	138_S	0.699	1.00
216_M	220_I	0.699	1.00
279_D	282_G	0.699	1.00
230_E	234_E	0.696	1.00
385_S	388_I	0.694	1.00
136_A	140_I	0.692	1.00
304_L	308_C	0.692	1.00
191_I	194_K	0.691	1.00
32_L	40_L	0.690	1.00
269_L	287_V	0.689	1.00
305_L	309_I	0.688	1.00
229_Q	233_T	0.688	1.00
65_T	68_M	0.686	1.00
354_W	358_G	0.685	1.00
30_L	33_T	0.685	1.00
67_N	70_T	0.684	1.00
218_F	221_T	0.684	1.00
76_K	80_I	0.683	1.00
354_W	362_L	0.681	1.00
188_K	191_I	0.681	1.00
85_V	90_K	0.681	1.00
286_L	371_L	0.680	1.00
374_P	377_L	0.680	1.00
376_L	379_A	0.678	1.00
8_A	12_V	0.678	1.00
339_F	342_V	0.677	1.00
302_S	319_G	0.677	1.00
382_G	385_S	0.676	1.00
134_T	141_E	0.676	1.00
379_A	382_G	0.676	1.00
347_S	350_V	0.675	1.00
28_M	32_L	0.675	1.00
368_W	371_L	0.674	1.00
352_N	356_L	0.672	1.00
77_M	80_I	0.669	1.00
130_S	134_T	0.668	1.00
132_I	139_F	0.667	1.00
35_I	38_A	0.666	1.00
264_Q	267_I	0.666	1.00
184_E	187_D	0.663	1.00
65_T	70_T	0.661	1.00
203_S	207_Y	0.661	1.00
358_G	374_P	0.658	1.00
182_E	188_K	0.656	1.00
327_A	330_G	0.654	1.00
223_G	227_F	0.652	1.00
138_S	141_E	0.651	1.00
7_I	249_I	0.651	1.00
127_L	130_S	0.651	1.00
253_K	257_T	0.650	1.00
77_M	82_V	0.650	1.00
33_T	39_A	0.649	1.00
351_P	354_W	0.647	1.00
358_G	378_F	0.646	1.00
353_R	356_L	0.645	1.00
336_L	344_Q	0.644	1.00
225_K	306_A	0.642	1.00
366_G	371_L	0.641	1.00
98_K	122_A	0.640	1.00
61_D	66_A	0.639	1.00
269_L	284_L	0.638	1.00
324_Q	328_V	0.638	1.00
66_A	70_T	0.636	1.00
336_L	353_R	0.636	1.00
223_G	226_S	0.635	1.00
365_G	370_D	0.635	1.00
238_R	242_T	0.633	1.00
94_L	97_E	0.633	1.00
19_R	22_F	0.632	1.00
250_L	303_M	0.632	1.00
15_R	256_G	0.632	1.00
239_M	242_T	0.632	1.00
31_I	35_I	0.628	1.00
331_G	336_L	0.627	1.00
186_G	190_T	0.623	0.99
236_L	249_I	0.623	0.99
304_L	307_S	0.620	0.99
55_V	58_I	0.620	0.99
50_I	53_I	0.620	0.99
188_K	195_S	0.618	0.99
388_I	391_R	0.617	0.99
254_W	300_G	0.616	0.99
317_A	321_F	0.616	0.99
318_I	322_G	0.614	0.99
30_L	35_I	0.610	0.99
24_M	29_P	0.609	0.99
308_C	392_R	0.609	0.99
371_L	374_P	0.608	0.99
101_D	122_A	0.608	0.99
305_L	318_I	0.607	0.99
91_M	95_I	0.606	0.99
190_T	195_S	0.605	0.99
340_P	343_L	0.604	0.99
235_T	243_P	0.602	0.99
350_V	354_W	0.601	0.99
229_Q	232_D	0.601	0.99
217_L	298_V	0.598	0.99
305_L	319_G	0.597	0.99
131_I	140_I	0.596	0.99
231_K	234_E	0.596	0.99
37_G	276_F	0.595	0.99
62_Q	66_A	0.595	0.99
133_E	136_A	0.594	0.99
95_I	98_K	0.594	0.99
135_A	139_F	0.594	0.99
372_Q	375_V	0.592	0.99
320_G	327_A	0.588	0.99
317_A	325_L	0.586	0.99
290_L	355_A	0.586	0.99
349_A	381_I	0.584	0.99
137_S	146_V	0.583	0.99
264_Q	268_F	0.581	0.99
231_K	236_L	0.581	0.99
59_Q	111_E	0.580	0.99
213_C	326_L	0.579	0.99
75_K	81_K	0.578	0.99
140_I	147_K	0.578	0.99
29_P	315_A	0.577	0.99
303_M	389_G	0.577	0.99
269_L	273_I	0.576	0.99
214_M	217_L	0.575	0.99
292_L	296_A	0.575	0.99
79_S	82_V	0.574	0.99
223_G	299_S	0.573	0.99
209_A	216_M	0.571	0.99
29_P	33_T	0.570	0.99
374_P	378_F	0.570	0.99
11_D	249_I	0.569	0.99
300_G	389_G	0.567	0.99
128_K	131_I	0.566	0.99
38_A	275_V	0.564	0.99
330_G	350_V	0.564	0.99
4_S	247_S	0.563	0.99
6_W	10_K	0.563	0.99
250_L	389_G	0.563	0.99
239_M	253_K	0.563	0.99
69_F	143_Y	0.561	0.99
72_D	75_K	0.560	0.99
210_A	333_M	0.560	0.99
125_Q	128_K	0.559	0.99
201_V	205_Q	0.559	0.99
374_P	381_I	0.558	0.99
319_G	323_I	0.558	0.99
354_W	381_I	0.557	0.99
210_A	215_F	0.556	0.99
27_L	32_L	0.556	0.99
388_I	392_R	0.555	0.99
193_E	196_V	0.553	0.99
314_T	317_A	0.553	0.99
222_V	226_S	0.553	0.99
288_S	291_G	0.552	0.99
369_A	372_Q	0.551	0.99
214_M	218_F	0.550	0.99
290_L	371_L	0.549	0.99
32_L	36_L	0.548	0.99
291_G	359_F	0.548	0.99
88_K	120_N	0.546	0.99
26_I	29_P	0.545	0.99
137_S	147_K	0.545	0.99
102_V	105_V	0.541	0.99
115_T	120_N	0.537	0.98
188_K	192_A	0.535	0.98
231_K	237_A	0.534	0.98
323_I	326_L	0.534	0.98
213_C	219_H	0.532	0.98
300_G	307_S	0.532	0.98
326_L	352_N	0.529	0.98
266_F	269_L	0.528	0.98
70_T	75_K	0.528	0.98
189_L	196_V	0.527	0.98
199_K	205_Q	0.527	0.98
265_F	269_L	0.526	0.98
288_S	292_L	0.526	0.98
33_T	36_L	0.525	0.98
88_K	118_V	0.523	0.98
184_E	190_T	0.523	0.98
58_I	105_V	0.521	0.98
11_D	15_R	0.521	0.98
76_K	82_V	0.520	0.98
301_I	385_S	0.519	0.98
127_L	134_T	0.519	0.98
24_M	40_L	0.518	0.98
31_I	34_C	0.518	0.98
213_C	330_G	0.518	0.98
236_L	250_L	0.517	0.98
183_K	186_G	0.516	0.98
32_L	39_A	0.515	0.98
107_P	116_S	0.515	0.98
358_G	361_S	0.514	0.98
51_D	57_Y	0.513	0.98
189_L	193_E	0.512	0.98
72_D	139_F	0.512	0.98
348_K	357_D	0.512	0.98
352_N	355_A	0.511	0.98
102_V	119_V	0.511	0.98
116_S	192_A	0.510	0.98
66_A	69_F	0.509	0.98
184_E	191_I	0.509	0.98
127_L	132_I	0.509	0.98
11_D	257_T	0.509	0.98
55_V	59_Q	0.507	0.98
280_W	287_V	0.507	0.98
325_L	328_V	0.506	0.98
334_L	338_Q	0.505	0.98
258_Y	262_I	0.505	0.98
228_L	234_E	0.505	0.98
318_I	326_L	0.505	0.98
69_F	73_V	0.503	0.98
322_G	326_L	0.503	0.98
254_W	303_M	0.503	0.98
29_P	36_L	0.502	0.98
38_A	41_G	0.502	0.98
298_V	302_S	0.501	0.98
263_I	266_F	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
3cniA	2	0.3409	99.2	0.771	Contact Map
2p0sA	2	0.3207	98.2	0.837	Contact Map
4n6hA	1	0.7222	21.4	0.948	Contact Map
4yayA	1	0.7071	15.6	0.951	Contact Map
3i42A	2	0.2879	12.4	0.953	Contact Map
3cfyA	1	0.3232	11.7	0.954	Contact Map
2z73A	2	0.5177	11.6	0.954	Contact Map
3crnA	2	0.3207	11.5	0.954	Contact Map
3vw7A	1	0.4672	11.4	0.954	Contact Map
3ktoA	3	0.3005	11.4	0.954	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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