YFIZ - BACSU - GREMLIN Contacts

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YFIZ - Probable siderophore transport system permease protein YfiZ

UniProt:	O31568	Sequences: MICKKASSKWIVLVCLIFILLTAVCASVVYGYTGTSWRQVYQAFTSFNGTNEHVIIKDVRLPRALVATVVGASLAAAGALMQALTKNPLASPGIFGINAGAGFFIVAGSFFLHIQSPQALVWSSFLGAAFTAAIVYAAGSLGREGLTPIKLTLAGAAMAAMFSSLTQGLLSVNELELAQVLFWLTGSVQGRSLDLLMTMFPYAAAALVICFFLGQKINLLVMGEDVAKGLGQKTGLLKFVMALCVVMLAGSAVAIAGPISFIGIIIPHFARFVVGNDYRWVLPFSAVLGAILLVCADIGARYIIMPQEVPVGVMTAIIGMPVFVYIARRGAKL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	333 (319)
Sequences:	13884 (9958)
Seq/√Len:	557.6

ECOLI - FEPG FEPD FECC BTUC FECD FHUB
BACSU - YFIZ FHUG FHUB YVRB YFME YFHA FEUB YFMD FEUC YCLN YCLO
HALSA - Q9HMG0 BTUCA Q9HMG7
SULSO - Q97ZU1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
218_N	277_D	4.375	1.00
72_A	286_A	3.734	1.00
108_G	123_S	3.605	1.00
23_A	295_C	3.532	1.00
80_L	210_C	3.455	1.00
24_V	64_A	3.296	1.00
233_K	236_L	3.215	1.00
73_S	203_A	3.085	1.00
80_L	241_M	3.039	1.00
68_T	290_A	2.960	1.00
67_A	188_V	2.872	1.00
270_A	288_L	2.800	1.00
39_Q	52_E	2.707	1.00
66_V	191_R	2.609	1.00
76_A	286_A	2.530	1.00
73_S	248_L	2.500	1.00
73_S	252_A	2.483	1.00
39_Q	42_Q	2.443	1.00
24_V	68_T	2.433	1.00
103_F	165_L	2.369	1.00
224_E	238_K	2.367	1.00
20_L	291_I	2.266	1.00
70_V	252_A	2.243	1.00
19_I	291_I	2.236	1.00
79_A	285_S	2.214	1.00
76_A	207_L	2.174	1.00
274_V	284_F	2.174	1.00
29_V	37_W	2.095	1.00
70_V	256_A	2.054	1.00
68_T	294_V	2.048	1.00
20_L	68_T	2.043	1.00
216_K	237_L	2.007	1.00
49_G	52_E	2.004	1.00
69_V	200_F	1.985	1.00
103_F	162_F	1.980	1.00
36_S	39_Q	1.969	1.00
202_Y	251_S	1.950	1.00
107_A	111_F	1.916	1.00
63_R	297_D	1.895	1.00
27_S	64_A	1.877	1.00
83_A	278_Y	1.875	1.00
81_M	245_V	1.871	1.00
218_N	278_Y	1.859	1.00
23_A	291_I	1.852	1.00
213_L	216_K	1.827	1.00
219_L	232_Q	1.816	1.00
38_R	42_Q	1.815	1.00
106_V	166_T	1.794	1.00
13_L	284_F	1.791	1.00
209_I	244_C	1.771	1.00
206_A	248_L	1.708	1.00
53_H	57_K	1.682	1.00
191_R	195_L	1.675	1.00
213_L	240_V	1.634	1.00
50_T	53_H	1.600	1.00
236_L	240_V	1.589	1.00
79_A	281_V	1.570	1.00
65_L	196_L	1.553	1.00
128_A	250_G	1.543	1.00
299_G	303_I	1.539	1.00
26_A	29_V	1.539	1.00
197_M	201_P	1.529	1.00
262_I	293_L	1.529	1.00
192_S	195_L	1.526	1.00
105_I	124_S	1.515	1.00
213_L	237_L	1.501	1.00
43_A	57_K	1.498	1.00
206_A	247_M	1.488	1.00
23_A	294_V	1.467	1.00
132_A	246_V	1.457	1.00
16_L	287_V	1.454	1.00
20_L	287_V	1.449	1.00
26_A	30_Y	1.438	1.00
300_A	311_V	1.436	1.00
104_F	123_S	1.409	1.00
188_V	293_L	1.388	1.00
12_V	284_F	1.383	1.00
299_G	314_M	1.375	1.00
27_S	298_I	1.371	1.00
280_W	283_P	1.364	1.00
16_L	284_F	1.353	1.00
206_A	244_C	1.334	1.00
201_P	205_A	1.332	1.00
77_A	248_L	1.328	1.00
41_Y	45_T	1.321	1.00
270_A	284_F	1.321	1.00
270_A	281_V	1.299	1.00
102_G	166_T	1.281	1.00
66_V	255_I	1.275	1.00
16_L	288_L	1.268	1.00
209_I	213_L	1.263	1.00
161_M	320_M	1.249	1.00
213_L	241_M	1.249	1.00
197_M	200_F	1.244	1.00
228_K	235_G	1.238	1.00
69_V	196_L	1.236	1.00
54_V	58_D	1.235	1.00
131_T	162_F	1.233	1.00
98_N	249_A	1.232	1.00
20_L	290_A	1.230	1.00
266_I	292_L	1.227	1.00
75_A	266_I	1.202	1.00
266_I	288_L	1.200	1.00
236_L	239_F	1.193	1.00
278_Y	281_V	1.188	1.00
104_F	127_G	1.188	1.00
219_L	230_L	1.177	1.00
84_L	241_M	1.177	1.00
13_L	280_W	1.168	1.00
16_L	291_I	1.166	1.00
226_V	229_G	1.163	1.00
256_A	259_I	1.162	1.00
199_M	255_I	1.156	1.00
51_N	54_V	1.151	1.00
43_A	53_H	1.151	1.00
34_G	37_W	1.140	1.00
102_G	184_L	1.138	1.00
237_L	240_V	1.134	1.00
116_S	119_A	1.120	1.00
106_V	180_V	1.117	1.00
72_A	290_A	1.110	1.00
67_A	294_V	1.107	1.00
133_A	137_A	1.105	1.00
125_F	247_M	1.104	1.00
100_G	127_G	1.095	1.00
235_G	238_K	1.093	1.00
208_V	212_F	1.091	1.00
100_G	131_T	1.091	1.00
103_F	107_A	1.090	1.00
122_W	126_L	1.088	1.00
110_F	169_L	1.088	1.00
174_E	178_A	1.086	1.00
33_T	55_I	1.085	1.00
69_V	199_M	1.083	1.00
67_A	293_L	1.080	1.00
11_I	14_V	1.079	1.00
223_G	227_A	1.079	1.00
123_S	127_G	1.078	1.00
209_I	240_V	1.077	1.00
79_A	282_L	1.068	1.00
301_R	308_E	1.064	1.00
66_V	196_L	1.061	1.00
72_A	75_A	1.061	1.00
210_C	244_C	1.061	1.00
235_G	239_F	1.056	1.00
65_L	193_L	1.054	1.00
159_A	163_S	1.043	1.00
79_A	278_Y	1.040	1.00
199_M	203_A	1.036	1.00
283_P	286_A	1.026	1.00
99_A	162_F	1.016	1.00
173_N	176_E	1.014	1.00
30_Y	302_Y	1.007	1.00
48_N	53_H	1.006	1.00
140_S	235_G	1.001	1.00
43_A	56_I	1.001	1.00
274_V	280_W	0.998	1.00
135_V	158_M	0.990	1.00
29_V	40_V	0.988	1.00
47_F	53_H	0.983	1.00
57_K	61_L	0.982	1.00
291_I	295_C	0.982	1.00
297_D	301_R	0.980	1.00
280_W	284_F	0.980	1.00
299_G	302_Y	0.976	1.00
168_G	172_V	0.976	1.00
300_A	314_M	0.975	1.00
205_A	208_V	0.975	1.00
206_A	251_S	0.973	1.00
107_A	169_L	0.968	1.00
24_V	294_V	0.965	1.00
25_C	29_V	0.960	1.00
98_N	258_P	0.960	1.00
17_I	21_L	0.959	1.00
43_A	48_N	0.958	1.00
43_A	52_E	0.957	1.00
237_L	241_M	0.956	1.00
217_I	241_M	0.952	1.00
18_F	22_T	0.950	1.00
259_I	293_L	0.947	1.00
277_D	280_W	0.945	1.00
28_V	64_A	0.931	1.00
266_I	270_A	0.929	1.00
198_T	201_P	0.928	1.00
23_A	298_I	0.928	1.00
281_V	285_S	0.919	1.00
115_Q	119_A	0.919	1.00
42_Q	46_S	0.917	1.00
64_A	298_I	0.912	1.00
130_F	134_I	0.911	1.00
201_P	204_A	0.908	1.00
40_V	56_I	0.907	1.00
316_A	321_P	0.904	1.00
321_P	325_Y	0.902	1.00
103_F	166_T	0.899	1.00
12_V	15_C	0.892	1.00
322_V	325_Y	0.892	1.00
11_I	15_C	0.891	1.00
252_A	256_A	0.891	1.00
304_I	307_Q	0.890	1.00
140_S	143_R	0.889	1.00
193_L	196_L	0.888	1.00
25_C	37_W	0.884	1.00
69_V	203_A	0.873	1.00
232_Q	237_L	0.871	1.00
97_I	128_A	0.870	1.00
53_H	58_D	0.866	1.00
225_D	228_K	0.865	1.00
12_V	16_L	0.865	1.00
42_Q	47_F	0.857	1.00
72_A	207_L	0.856	1.00
35_T	56_I	0.856	1.00
273_V	288_L	0.855	1.00
17_I	287_V	0.851	1.00
31_G	60_R	0.849	1.00
218_N	279_R	0.847	1.00
239_F	243_L	0.843	1.00
180_V	184_L	0.842	1.00
135_V	139_G	0.841	1.00
77_A	245_V	0.839	1.00
73_S	77_A	0.839	1.00
105_I	120_L	0.836	1.00
224_E	228_K	0.834	1.00
300_A	310_P	0.833	1.00
136_Y	239_F	0.831	1.00
78_G	267_P	0.826	1.00
209_I	212_F	0.825	1.00
295_C	299_G	0.823	1.00
42_Q	45_T	0.822	1.00
103_F	169_L	0.819	1.00
93_G	98_N	0.809	1.00
109_S	120_L	0.807	1.00
21_L	25_C	0.806	1.00
213_L	244_C	0.804	1.00
64_A	294_V	0.801	1.00
101_A	128_A	0.798	1.00
278_Y	283_P	0.794	1.00
61_L	193_L	0.793	1.00
108_G	120_L	0.792	1.00
174_E	177_L	0.792	1.00
178_A	181_L	0.792	1.00
214_G	279_R	0.792	1.00
20_L	24_V	0.792	1.00
271_R	281_V	0.790	1.00
204_A	208_V	0.789	1.00
302_Y	305_M	0.788	1.00
175_L	179_Q	0.782	1.00
75_A	79_A	0.781	1.00
202_Y	206_A	0.781	1.00
29_V	34_G	0.778	1.00
234_T	238_K	0.778	1.00
303_I	306_P	0.777	1.00
137_A	140_S	0.776	1.00
242_A	246_V	0.776	1.00
224_E	234_T	0.774	1.00
194_D	197_M	0.773	1.00
30_Y	34_G	0.769	1.00
126_L	130_F	0.768	1.00
262_I	315_T	0.767	1.00
99_A	102_G	0.767	1.00
27_S	301_R	0.767	1.00
210_C	241_M	0.765	1.00
50_T	54_V	0.764	1.00
270_A	274_V	0.762	1.00
136_Y	235_G	0.761	1.00
81_M	95_F	0.758	1.00
195_L	255_I	0.757	1.00
304_I	309_V	0.756	1.00
72_A	203_A	0.755	1.00
100_G	162_F	0.750	1.00
63_R	301_R	0.750	1.00
317_I	321_P	0.750	1.00
293_L	315_T	0.743	1.00
21_L	24_V	0.742	1.00
140_S	145_G	0.738	1.00
287_V	291_I	0.737	1.00
119_A	122_W	0.736	1.00
125_F	128_A	0.736	1.00
203_A	252_A	0.735	1.00
270_A	273_V	0.734	1.00
227_A	234_T	0.733	1.00
125_F	129_A	0.730	1.00
35_T	52_E	0.728	1.00
91_S	94_I	0.727	1.00
63_R	308_E	0.727	1.00
211_F	214_G	0.722	1.00
97_I	132_A	0.721	1.00
212_F	216_K	0.720	1.00
107_A	165_L	0.719	1.00
279_R	283_P	0.717	1.00
131_T	135_V	0.716	1.00
46_S	53_H	0.714	1.00
28_V	61_L	0.712	1.00
199_M	251_S	0.705	1.00
216_K	232_Q	0.702	1.00
40_V	43_A	0.700	1.00
140_S	146_L	0.700	1.00
251_S	254_A	0.700	1.00
33_T	37_W	0.699	1.00
77_A	249_A	0.697	1.00
106_V	170_L	0.696	1.00
128_A	246_V	0.695	1.00
54_V	57_K	0.693	1.00
49_G	53_H	0.693	1.00
325_Y	329_R	0.691	1.00
85_T	152_T	0.690	1.00
129_A	250_G	0.689	1.00
76_A	210_C	0.689	1.00
75_A	286_A	0.688	1.00
22_T	25_C	0.685	1.00
200_F	204_A	0.684	1.00
251_S	255_I	0.684	1.00
109_S	179_Q	0.684	1.00
132_A	242_A	0.684	1.00
42_Q	48_N	0.684	1.00
54_V	59_V	0.683	1.00
65_L	69_V	0.681	1.00
293_L	311_V	0.681	1.00
220_L	234_T	0.680	1.00
74_L	262_I	0.678	1.00
102_G	258_P	0.674	1.00
20_L	294_V	0.673	1.00
228_K	234_T	0.671	1.00
199_M	202_Y	0.670	1.00
259_I	311_V	0.670	1.00
290_A	294_V	0.669	1.00
207_L	211_F	0.668	1.00
140_S	144_E	0.666	1.00
66_V	199_M	0.666	1.00
128_A	132_A	0.665	1.00
33_T	36_S	0.663	1.00
116_S	121_V	0.662	1.00
117_P	121_V	0.662	1.00
138_A	154_A	0.661	1.00
272_F	326_I	0.660	1.00
206_A	210_C	0.657	1.00
76_A	282_L	0.657	1.00
269_F	272_F	0.655	1.00
181_L	184_L	0.653	1.00
292_L	296_A	0.653	1.00
83_A	221_V	0.652	1.00
16_L	20_L	0.649	1.00
265_I	323_F	0.648	1.00
269_F	288_L	0.646	1.00
188_V	311_V	0.646	1.00
37_W	40_V	0.644	1.00
163_S	184_L	0.640	1.00
12_V	273_V	0.639	1.00
167_Q	183_W	0.637	1.00
30_Y	298_I	0.637	1.00
24_V	28_V	0.632	1.00
262_I	292_L	0.631	1.00
202_Y	247_M	0.631	1.00
267_P	285_S	0.631	1.00
193_L	197_M	0.630	1.00
118_Q	122_W	0.630	1.00
28_V	56_I	0.629	1.00
170_L	181_L	0.629	1.00
147_T	150_K	0.628	1.00
176_E	179_Q	0.627	1.00
286_A	290_A	0.627	1.00
167_Q	171_S	0.625	1.00
134_I	137_A	0.625	1.00
91_S	263_G	0.622	1.00
107_A	112_L	0.620	1.00
108_G	119_A	0.619	1.00
61_L	65_L	0.619	1.00
35_T	43_A	0.618	1.00
269_F	292_L	0.618	1.00
70_V	188_V	0.617	1.00
15_C	19_I	0.616	1.00
104_F	108_G	0.616	1.00
292_L	318_I	0.615	1.00
56_I	61_L	0.614	1.00
296_A	314_M	0.613	1.00
295_C	298_I	0.613	1.00
72_A	76_A	0.610	1.00
109_S	180_V	0.609	1.00
154_A	157_A	0.609	1.00
300_A	308_E	0.609	1.00
98_N	101_A	0.608	1.00
80_L	244_C	0.608	1.00
120_L	123_S	0.606	1.00
129_A	246_V	0.606	1.00
22_T	26_A	0.606	1.00
139_G	154_A	0.604	1.00
99_A	159_A	0.604	1.00
265_I	269_F	0.602	1.00
127_G	131_T	0.598	1.00
163_S	167_Q	0.598	1.00
216_K	219_L	0.597	1.00
132_A	136_Y	0.595	1.00
149_I	152_T	0.595	1.00
85_T	88_P	0.595	1.00
249_A	253_V	0.593	1.00
38_R	41_Y	0.591	1.00
67_A	311_V	0.589	1.00
25_C	41_Y	0.587	1.00
37_W	41_Y	0.586	1.00
198_T	202_Y	0.584	1.00
188_V	256_A	0.583	1.00
12_V	274_V	0.583	1.00
27_S	294_V	0.578	1.00
36_S	52_E	0.575	0.99
203_A	207_L	0.574	0.99
212_F	215_Q	0.572	0.99
40_V	45_T	0.572	0.99
269_F	322_V	0.570	0.99
13_L	17_I	0.570	0.99
297_D	308_E	0.570	0.99
81_M	97_I	0.567	0.99
240_V	244_C	0.564	0.99
241_M	245_V	0.564	0.99
97_I	135_V	0.564	0.99
264_I	326_I	0.564	0.99
130_F	133_A	0.564	0.99
218_N	283_P	0.561	0.99
136_Y	140_S	0.561	0.99
81_M	90_A	0.561	0.99
265_I	322_V	0.560	0.99
250_G	254_A	0.559	0.99
300_A	303_I	0.559	0.99
66_V	70_V	0.558	0.99
44_F	56_I	0.557	0.99
48_N	52_E	0.556	0.99
99_A	163_S	0.555	0.99
240_V	243_L	0.555	0.99
47_F	50_T	0.554	0.99
39_Q	48_N	0.553	0.99
108_G	112_L	0.553	0.99
220_L	237_L	0.553	0.99
218_N	221_V	0.551	0.99
194_D	198_T	0.549	0.99
246_V	250_G	0.544	0.99
298_I	302_Y	0.543	0.99
170_L	184_L	0.542	0.99
154_A	158_M	0.540	0.99
26_A	298_I	0.539	0.99
126_L	129_A	0.536	0.99
80_L	245_V	0.534	0.99
215_Q	218_N	0.534	0.99
29_V	41_Y	0.532	0.99
143_R	146_L	0.531	0.99
205_A	209_I	0.531	0.99
39_Q	46_S	0.531	0.99
325_Y	328_R	0.530	0.99
233_K	240_V	0.526	0.99
23_A	26_A	0.523	0.99
15_C	18_F	0.523	0.99
288_L	291_I	0.522	0.99
134_I	158_M	0.522	0.99
100_G	158_M	0.520	0.99
328_R	331_A	0.520	0.99
146_L	150_K	0.516	0.99
139_G	151_L	0.515	0.99
283_P	287_V	0.514	0.99
19_I	23_A	0.514	0.99
196_L	199_M	0.513	0.99
233_K	239_F	0.513	0.99
207_L	210_C	0.513	0.99
217_I	278_Y	0.513	0.99
268_H	271_R	0.512	0.99
260_S	265_I	0.511	0.99
270_A	285_S	0.508	0.99
294_V	298_I	0.508	0.99
34_G	38_R	0.508	0.99
275_G	279_R	0.508	0.99
20_L	64_A	0.507	0.99
66_V	256_A	0.506	0.99
203_A	208_V	0.506	0.99
75_A	289_G	0.505	0.99
39_Q	43_A	0.504	0.99
164_S	265_I	0.503	0.99
170_L	177_L	0.501	0.99
259_I	315_T	0.501	0.99
86_K	224_E	0.501	0.99
207_L	286_A	0.500	0.99
266_I	296_A	0.500	0.99

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
2nq2A	2	0.9219	100	0.182	Contact Map
2qi9A	2	0.9489	100	0.191	Contact Map
4g1uA	2	0.8889	100	0.193	Contact Map
1pw4A	1	0.8739	16.6	0.964	Contact Map
3dh4A	3	0.6126	14.8	0.965	Contact Map
2xq2A	2	0.5856	12.2	0.966	Contact Map
3rlfF	1	0.4024	9.4	0.968	Contact Map
4tquM	1	0.4204	7	0.97	Contact Map
3rlbA	1	0.5045	5.8	0.971	Contact Map
3wdoA	1	0.8739	5.6	0.971	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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