YFIN - BACSU - GREMLIN Contacts

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YFIN - Putative transport permease YfiN

UniProt:	P94442	Sequences: MKKILAICGIELSLIFKKPQNYLIMFAAPLLLTFVFGSMLSGNDDKVRLAIVDQDDTILSQHYIRQLKAHDDMYVFENMSESKASEKLKQKKIAGIIVISRSFQTQLEKGKHPELIFRHGPELSEAPMVKQYAESALATLNIQVTAAKTASQTAGENWKAAYKTVFAKKHEDIVPAVTRQTLSDKKEGAEASDTASRAAGFSILFVMLTMMGAAGTILEARKNGVWSRLLTASVSRAEIGAGYVLSFFVIGWIQFGILLLSTHWLFGINWGNPAAVIVLVSLFLLTVVGIGLMIAANVRTPEQQLAFGNLFVIATCMVSGMYWPIDIEPKFMQSIAEFLPQKWAMSGLTEIIANGARVTDILGICGILLAFAAITFAAGLKALRA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	385 (351)
Sequences:	11536 (9437)
Seq/√Len:	503.7

ECOLI - YBHR YBHS YHHJ
BACSU - YFIN YFIM 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
279_L	347_G	4.919	1.00
50_A	93_I	4.536	1.00
84_A	96_I	4.302	1.00
80_S	83_K	3.710	1.00
102_S	106_Q	3.513	1.00
87_K	93_I	3.393	1.00
7_I	242_G	3.236	1.00
106_Q	111_K	3.014	1.00
9_G	13_S	3.013	1.00
86_E	90_Q	2.887	1.00
330_K	334_S	2.688	1.00
78_N	87_K	2.558	1.00
81_E	85_S	2.534	1.00
87_K	92_K	2.442	1.00
85_S	89_K	2.439	1.00
180_Q	183_S	2.431	1.00
256_G	277_I	2.416	1.00
280_V	344_A	2.397	1.00
8_C	245_L	2.377	1.00
8_C	249_V	2.372	1.00
235_S	238_E	2.371	1.00
88_L	96_I	2.347	1.00
362_L	366_G	2.261	1.00
141_N	145_T	2.256	1.00
54_Q	81_E	2.203	1.00
293_M	378_A	2.166	1.00
285_L	372_A	2.150	1.00
11_E	243_Y	2.125	1.00
282_L	369_L	2.069	1.00
99_I	103_F	2.056	1.00
366_G	370_A	2.055	1.00
51_I	64_I	2.000	1.00
13_S	16_F	1.996	1.00
5_L	9_G	1.984	1.00
50_A	78_N	1.942	1.00
83_K	87_K	1.919	1.00
260_L	264_W	1.916	1.00
370_A	374_I	1.884	1.00
180_Q	184_D	1.864	1.00
98_V	118_R	1.863	1.00
54_Q	98_V	1.860	1.00
185_K	189_A	1.857	1.00
81_E	98_V	1.839	1.00
53_D	60_S	1.808	1.00
283_F	344_A	1.797	1.00
79_M	83_K	1.795	1.00
286_T	372_A	1.766	1.00
289_G	372_A	1.761	1.00
192_S	195_A	1.722	1.00
357_R	360_D	1.714	1.00
55_D	104_Q	1.698	1.00
46_K	74_Y	1.675	1.00
86_E	89_K	1.639	1.00
176_A	179_R	1.621	1.00
132_Y	136_A	1.617	1.00
53_D	57_T	1.615	1.00
337_E	343_W	1.606	1.00
136_A	140_L	1.601	1.00
10_I	220_A	1.600	1.00
29_P	39_M	1.600	1.00
346_S	364_I	1.568	1.00
29_P	32_L	1.561	1.00
283_F	287_V	1.560	1.00
209_T	213_A	1.560	1.00
181_T	184_D	1.556	1.00
336_A	342_K	1.552	1.00
337_E	342_K	1.533	1.00
255_F	280_V	1.525	1.00
210_M	213_A	1.523	1.00
274_A	278_V	1.521	1.00
251_G	284_L	1.516	1.00
355_G	358_V	1.515	1.00
132_Y	137_L	1.509	1.00
325_I	336_A	1.506	1.00
140_L	144_V	1.476	1.00
218_L	221_R	1.474	1.00
171_E	174_V	1.471	1.00
53_D	56_D	1.470	1.00
371_F	375_T	1.458	1.00
57_T	60_S	1.458	1.00
126_A	130_K	1.452	1.00
83_K	86_E	1.451	1.00
16_F	19_P	1.447	1.00
275_A	351_I	1.446	1.00
129_V	132_Y	1.441	1.00
126_A	132_Y	1.441	1.00
48_R	74_Y	1.440	1.00
142_I	146_A	1.439	1.00
279_L	365_C	1.437	1.00
248_F	285_L	1.429	1.00
177_V	180_Q	1.418	1.00
143_Q	146_A	1.400	1.00
350_E	356_A	1.400	1.00
130_K	134_E	1.398	1.00
248_F	281_S	1.395	1.00
141_N	144_V	1.371	1.00
174_V	179_R	1.364	1.00
252_W	281_S	1.353	1.00
180_Q	185_K	1.345	1.00
52_V	84_A	1.329	1.00
296_A	382_A	1.323	1.00
279_L	351_I	1.321	1.00
57_T	104_Q	1.317	1.00
282_L	365_C	1.313	1.00
179_R	183_S	1.308	1.00
363_G	367_I	1.296	1.00
62_H	65_R	1.292	1.00
29_P	35_V	1.290	1.00
127_P	130_K	1.278	1.00
282_L	372_A	1.277	1.00
210_M	214_A	1.273	1.00
65_R	68_K	1.268	1.00
272_N	275_A	1.263	1.00
300_T	303_Q	1.256	1.00
333_Q	337_E	1.252	1.00
134_E	138_A	1.243	1.00
175_P	179_R	1.240	1.00
104_Q	108_E	1.237	1.00
131_Q	135_S	1.231	1.00
59_L	104_Q	1.229	1.00
82_S	85_S	1.223	1.00
367_I	371_F	1.222	1.00
54_Q	101_R	1.218	1.00
93_I	96_I	1.212	1.00
60_S	104_Q	1.205	1.00
218_L	304_Q	1.205	1.00
339_L	342_K	1.203	1.00
350_E	354_N	1.183	1.00
220_A	243_Y	1.165	1.00
290_I	311_F	1.156	1.00
331_F	334_S	1.150	1.00
179_R	184_D	1.150	1.00
12_L	253_I	1.150	1.00
367_I	370_A	1.146	1.00
237_A	241_A	1.138	1.00
179_R	182_L	1.133	1.00
130_K	136_A	1.130	1.00
293_M	379_G	1.129	1.00
377_A	381_K	1.111	1.00
334_S	337_E	1.102	1.00
102_S	105_T	1.099	1.00
140_L	143_Q	1.091	1.00
138_A	141_N	1.088	1.00
259_L	280_V	1.087	1.00
13_S	17_K	1.087	1.00
59_L	107_L	1.083	1.00
313_I	316_C	1.083	1.00
182_L	185_K	1.080	1.00
35_V	39_M	1.080	1.00
137_L	141_N	1.079	1.00
32_L	36_F	1.076	1.00
286_T	371_F	1.072	1.00
66_Q	69_A	1.072	1.00
126_A	136_A	1.063	1.00
79_M	87_K	1.061	1.00
23_L	27_A	1.053	1.00
50_A	87_K	1.049	1.00
330_K	333_Q	1.048	1.00
88_L	93_I	1.047	1.00
211_M	214_A	1.045	1.00
209_T	212_G	1.042	1.00
127_P	131_Q	1.039	1.00
342_K	346_S	1.033	1.00
237_A	380_L	1.024	1.00
55_D	102_S	1.017	1.00
139_T	142_I	1.017	1.00
58_I	61_Q	1.013	1.00
82_S	86_E	1.013	1.00
356_A	360_D	1.006	1.00
131_Q	134_E	1.006	1.00
238_E	242_G	1.004	1.00
129_V	136_A	1.002	1.00
34_F	38_S	1.000	1.00
178_T	181_T	1.000	1.00
218_L	222_K	0.998	1.00
136_A	141_N	0.996	1.00
286_T	375_T	0.995	1.00
81_E	84_A	0.993	1.00
181_T	185_K	0.989	1.00
209_T	214_A	0.989	1.00
249_V	253_I	0.986	1.00
334_S	338_F	0.984	1.00
81_E	96_I	0.980	1.00
365_C	369_L	0.974	1.00
346_S	350_E	0.973	1.00
113_P	117_F	0.966	1.00
116_I	119_H	0.962	1.00
36_F	39_M	0.958	1.00
173_I	177_V	0.954	1.00
127_P	132_Y	0.954	1.00
343_W	367_I	0.953	1.00
191_A	194_T	0.952	1.00
142_I	145_T	0.951	1.00
329_P	333_Q	0.951	1.00
133_A	136_A	0.951	1.00
8_C	242_G	0.950	1.00
343_W	364_I	0.944	1.00
135_S	139_T	0.943	1.00
115_L	118_R	0.936	1.00
296_A	379_G	0.931	1.00
286_T	368_L	0.930	1.00
203_I	344_A	0.928	1.00
369_L	373_A	0.927	1.00
79_M	84_A	0.920	1.00
248_F	288_V	0.920	1.00
374_I	378_A	0.915	1.00
289_G	376_F	0.914	1.00
196_S	200_G	0.911	1.00
206_V	210_M	0.910	1.00
293_M	375_T	0.909	1.00
325_I	328_E	0.908	1.00
240_G	380_L	0.903	1.00
292_L	379_G	0.900	1.00
10_I	13_S	0.898	1.00
132_Y	140_L	0.892	1.00
115_L	119_H	0.890	1.00
242_G	246_S	0.888	1.00
309_N	313_I	0.888	1.00
312_V	315_T	0.887	1.00
261_S	265_L	0.887	1.00
128_M	131_Q	0.886	1.00
133_A	137_L	0.886	1.00
129_V	133_A	0.885	1.00
198_A	201_F	0.872	1.00
129_V	137_L	0.870	1.00
260_L	263_H	0.870	1.00
289_G	375_T	0.865	1.00
344_A	347_G	0.863	1.00
7_I	234_V	0.860	1.00
306_A	309_N	0.859	1.00
120_G	123_L	0.856	1.00
12_L	249_V	0.852	1.00
12_L	16_F	0.850	1.00
11_E	15_I	0.849	1.00
29_P	33_T	0.847	1.00
298_V	303_Q	0.846	1.00
192_S	196_S	0.844	1.00
177_V	181_T	0.843	1.00
174_V	180_Q	0.841	1.00
376_F	380_L	0.838	1.00
12_L	246_S	0.838	1.00
331_F	335_I	0.837	1.00
191_A	195_A	0.837	1.00
289_G	379_G	0.833	1.00
190_E	194_T	0.829	1.00
252_W	256_G	0.827	1.00
358_V	362_L	0.827	1.00
329_P	332_M	0.826	1.00
177_V	183_S	0.824	1.00
316_C	319_S	0.824	1.00
98_V	116_I	0.820	1.00
5_L	8_C	0.819	1.00
132_Y	135_S	0.815	1.00
56_D	101_R	0.813	1.00
199_A	203_I	0.812	1.00
30_L	34_F	0.812	1.00
359_T	363_G	0.810	1.00
193_D	197_R	0.809	1.00
293_M	297_N	0.809	1.00
244_V	288_V	0.807	1.00
190_E	195_A	0.802	1.00
85_S	118_R	0.802	1.00
207_M	211_M	0.801	1.00
178_T	183_S	0.800	1.00
32_L	39_M	0.799	1.00
144_V	147_A	0.798	1.00
275_A	278_V	0.796	1.00
32_L	35_V	0.794	1.00
58_I	62_H	0.792	1.00
10_I	14_L	0.792	1.00
78_N	93_I	0.792	1.00
220_A	225_V	0.789	1.00
72_D	75_V	0.789	1.00
66_Q	143_Q	0.787	1.00
276_V	348_L	0.786	1.00
204_L	208_L	0.786	1.00
284_L	288_V	0.785	1.00
128_M	132_Y	0.784	1.00
202_S	210_M	0.784	1.00
328_E	333_Q	0.783	1.00
131_Q	140_L	0.781	1.00
50_A	96_I	0.778	1.00
49_L	97_I	0.776	1.00
215_G	218_L	0.775	1.00
234_V	239_I	0.774	1.00
96_I	118_R	0.774	1.00
240_G	292_L	0.773	1.00
48_R	94_A	0.773	1.00
203_I	206_V	0.773	1.00
18_K	21_N	0.771	1.00
97_I	117_F	0.770	1.00
143_Q	147_A	0.769	1.00
53_D	64_I	0.764	1.00
273_P	277_I	0.763	1.00
78_N	84_A	0.762	1.00
298_V	307_F	0.762	1.00
135_S	138_A	0.758	1.00
225_V	228_R	0.755	1.00
360_D	363_G	0.755	1.00
291_G	295_A	0.754	1.00
311_F	315_T	0.752	1.00
193_D	196_S	0.748	1.00
131_Q	136_A	0.743	1.00
274_A	277_I	0.742	1.00
270_W	273_P	0.742	1.00
175_P	183_S	0.741	1.00
32_L	40_L	0.741	1.00
174_V	178_T	0.741	1.00
189_A	193_D	0.737	1.00
230_L	239_I	0.728	1.00
219_E	223_N	0.728	1.00
350_E	364_I	0.727	1.00
134_E	137_L	0.725	1.00
336_A	339_L	0.723	1.00
184_D	189_A	0.721	1.00
293_M	296_A	0.719	1.00
372_A	376_F	0.719	1.00
8_C	246_S	0.718	1.00
131_Q	138_A	0.717	1.00
320_G	324_P	0.716	1.00
139_T	143_Q	0.712	1.00
131_Q	141_N	0.710	1.00
293_M	382_A	0.710	1.00
173_I	181_T	0.710	1.00
36_F	40_L	0.708	1.00
49_L	53_D	0.708	1.00
29_P	34_F	0.707	1.00
317_M	323_W	0.707	1.00
176_A	180_Q	0.706	1.00
60_S	99_I	0.704	1.00
115_L	120_G	0.703	1.00
29_P	36_F	0.700	1.00
128_M	136_A	0.698	1.00
275_A	361_I	0.697	1.00
34_F	37_G	0.696	1.00
312_V	316_C	0.695	1.00
78_N	81_E	0.693	1.00
126_A	131_Q	0.693	1.00
60_S	63_Y	0.692	1.00
294_I	298_V	0.690	1.00
126_A	129_V	0.689	1.00
203_I	207_M	0.689	1.00
222_K	301_P	0.688	1.00
369_L	372_A	0.687	1.00
259_L	276_V	0.687	1.00
173_I	179_R	0.687	1.00
63_Y	99_I	0.686	1.00
177_V	182_L	0.686	1.00
59_L	64_I	0.686	1.00
84_A	87_K	0.686	1.00
113_P	119_H	0.684	1.00
282_L	368_L	0.684	1.00
343_W	346_S	0.683	1.00
244_V	289_G	0.682	1.00
310_L	314_A	0.681	1.00
175_P	180_Q	0.679	1.00
174_V	183_S	0.672	1.00
217_I	220_A	0.671	1.00
244_V	285_L	0.671	1.00
256_G	273_P	0.670	1.00
61_Q	65_R	0.668	1.00
127_P	136_A	0.667	1.00
74_Y	77_E	0.667	1.00
33_T	262_T	0.665	1.00
110_G	113_P	0.664	1.00
68_K	75_V	0.664	1.00
113_P	120_G	0.663	1.00
277_I	280_V	0.662	1.00
341_Q	345_M	0.660	1.00
361_I	365_C	0.660	1.00
19_P	22_Y	0.659	1.00
29_P	41_S	0.658	1.00
113_P	118_R	0.654	1.00
343_W	371_F	0.651	1.00
280_V	348_L	0.651	1.00
279_L	361_I	0.651	1.00
33_T	36_F	0.650	1.00
35_V	38_S	0.650	1.00
134_E	146_A	0.648	1.00
25_M	28_A	0.648	1.00
30_L	33_T	0.647	1.00
87_K	90_Q	0.645	1.00
315_T	339_L	0.643	1.00
375_T	379_G	0.641	1.00
172_D	175_P	0.641	1.00
366_G	369_L	0.640	1.00
229_L	239_I	0.639	1.00
15_I	25_M	0.639	1.00
8_C	12_L	0.639	1.00
245_L	249_V	0.637	1.00
130_K	133_A	0.636	1.00
204_L	207_M	0.634	1.00
324_P	328_E	0.632	1.00
64_I	68_K	0.632	1.00
340_P	343_W	0.631	1.00
37_G	40_L	0.630	1.00
220_A	239_I	0.630	1.00
200_G	205_F	0.630	1.00
363_G	366_G	0.629	1.00
39_M	42_G	0.628	1.00
263_H	267_G	0.628	1.00
130_K	139_T	0.625	1.00
287_V	291_G	0.625	1.00
199_A	202_S	0.625	1.00
52_V	78_N	0.624	1.00
356_A	359_T	0.621	1.00
62_H	66_Q	0.619	1.00
179_R	185_K	0.618	1.00
137_L	140_L	0.618	1.00
132_Y	141_N	0.616	1.00
138_A	142_I	0.614	1.00
241_A	245_L	0.610	1.00
318_V	323_W	0.610	1.00
347_G	364_I	0.609	1.00
115_L	122_E	0.606	0.99
307_F	311_F	0.604	0.99
132_Y	139_T	0.604	0.99
226_W	239_I	0.604	0.99
199_A	208_L	0.601	0.99
52_V	96_I	0.600	0.99
100_S	116_I	0.599	0.99
321_M	345_M	0.598	0.99
126_A	134_E	0.593	0.99
191_A	196_S	0.588	0.99
127_P	141_N	0.586	0.99
349_T	353_A	0.586	0.99
53_D	61_Q	0.585	0.99
174_V	177_V	0.582	0.99
176_A	184_D	0.582	0.99
373_A	377_A	0.579	0.99
199_A	206_V	0.579	0.99
106_Q	113_P	0.578	0.99
37_G	266_F	0.578	0.99
19_P	23_L	0.578	0.99
114_E	117_F	0.576	0.99
255_F	259_L	0.575	0.99
78_N	83_K	0.574	0.99
34_F	261_S	0.573	0.99
198_A	202_S	0.573	0.99
290_I	375_T	0.573	0.99
325_I	342_K	0.573	0.99
337_E	340_P	0.570	0.99
218_L	224_G	0.570	0.99
11_E	246_S	0.569	0.99
275_A	365_C	0.569	0.99
53_D	104_Q	0.568	0.99
200_G	209_T	0.568	0.99
55_D	60_S	0.566	0.99
214_A	304_Q	0.566	0.99
175_P	182_L	0.564	0.99
56_D	60_S	0.564	0.99
200_G	203_I	0.563	0.99
229_L	243_Y	0.561	0.99
254_Q	258_L	0.560	0.99
80_S	84_A	0.559	0.99
25_M	29_P	0.559	0.99
208_L	211_M	0.558	0.99
128_M	137_L	0.557	0.99
27_A	31_L	0.556	0.99
364_I	368_L	0.555	0.99
140_L	145_T	0.551	0.99
220_A	224_G	0.551	0.99
77_E	81_E	0.548	0.99
190_E	193_D	0.547	0.99
221_R	224_G	0.546	0.99
6_A	9_G	0.546	0.99
136_A	139_T	0.546	0.99
198_A	204_L	0.545	0.99
175_P	181_T	0.545	0.99
61_Q	64_I	0.544	0.99
7_I	239_I	0.544	0.99
173_I	176_A	0.544	0.99
63_Y	103_F	0.544	0.99
44_D	47_V	0.544	0.99
221_R	226_W	0.543	0.99
130_K	135_S	0.542	0.99
177_V	184_D	0.541	0.99
196_S	207_M	0.540	0.99
259_L	273_P	0.538	0.99
141_N	146_A	0.538	0.99
131_Q	137_L	0.537	0.99
254_Q	257_I	0.536	0.99
133_A	139_T	0.536	0.99
32_L	41_S	0.535	0.99
174_V	182_L	0.533	0.99
43_N	46_K	0.532	0.99
49_L	95_G	0.531	0.99
340_P	344_A	0.531	0.99
226_W	240_G	0.530	0.99
355_G	359_T	0.530	0.99
28_A	36_F	0.529	0.99
68_K	71_D	0.528	0.99
57_T	102_S	0.528	0.99
280_V	284_L	0.527	0.99
200_G	208_L	0.526	0.99
278_V	282_L	0.526	0.99
350_E	360_D	0.525	0.99
198_A	211_M	0.524	0.99
215_G	295_A	0.524	0.99
203_I	341_Q	0.523	0.98
194_T	197_R	0.521	0.98
27_A	32_L	0.520	0.98
190_E	196_S	0.520	0.98
306_A	315_T	0.520	0.98
368_L	371_F	0.517	0.98
117_F	121_P	0.517	0.98
275_A	279_L	0.517	0.98
233_S	239_I	0.516	0.98
15_I	246_S	0.515	0.98
253_I	256_G	0.515	0.98
106_Q	114_E	0.514	0.98
315_T	341_Q	0.514	0.98
347_G	361_I	0.512	0.98
371_F	374_I	0.508	0.98
113_P	116_I	0.507	0.98
14_L	220_A	0.507	0.98
51_I	75_V	0.506	0.98
219_E	222_K	0.506	0.98
127_P	135_S	0.505	0.98
364_I	367_I	0.505	0.98
53_D	99_I	0.505	0.98
131_Q	139_T	0.504	0.98
38_S	41_S	0.504	0.98
128_M	133_A	0.504	0.98
29_P	42_G	0.501	0.98
262_T	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	0.3636	99.3	0.75	Contact Map
2p0sA	2	0.3299	97.8	0.849	Contact Map
4n6hA	1	0.7351	18.8	0.948	Contact Map
3hdgA	2	0.3065	14.9	0.95	Contact Map
3ktoA	3	0.2935	13.4	0.951	Contact Map
3hdvA	3	0.3039	12.1	0.952	Contact Map
3b2nA	1	0.2909	11.9	0.952	Contact Map
3cg4A	1	0.3039	11.5	0.953	Contact Map
4yayA	1	0.7247	11.2	0.953	Contact Map
3cnbA	1	0.2987	10.4	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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