YFMD - BACSU - GREMLIN Contacts

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YFMD - Fe(3+)-citrate import system permease protein YfmD

UniProt:	O34933	Sequences: MYHSAKRRSSSRLMMFIIALIIFIFGLGLNLSVGASDISIIDSLKYLFVWDGSKEQLIISTLRLPRTLIGVFVGASLAVAGALMQAMTRNPLASPQIFGVNAGASLFVVASLVILPASPYSSVIFAFAGAAAGGAIVYMIASSGGMTPVKLALSGMAVHLFLSSMTQAIIILNESGEDVLYWMTGAIDGSNWQDVITIAPFSVIGIGLALVFSGSVSVLGLGDETAKGLGQNMNGIRILISLIILILSGASVAVAGPIGFVGLLVPHIVRKLIGEHYQYVLPFSALFGAILLVYADVLARWIAFPYESPVGIVTAIIGTPFFLYLARKGRNLK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	333 (317)
Sequences:	13873 (9884)
Seq/√Len:	555.2

ECOLI - FEPG FEPD FECC BTUC FECD FHUB
BACSU - YFMD FHUB FHUG YFHA YFME YVRB FEUB YFIZ YCLN FEUC YCLO
HALSA - Q9HMG0 Q9HMG7 BTUCA
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
217_S	276_H	4.016	1.00
75_A	285_A	3.718	1.00
26_G	294_Y	3.509	1.00
111_S	125_F	3.506	1.00
83_L	209_A	3.379	1.00
27_L	67_T	3.288	1.00
232_N	235_G	3.199	1.00
76_S	202_S	3.025	1.00
83_L	240_I	3.014	1.00
71_V	289_A	2.883	1.00
269_V	287_F	2.787	1.00
70_G	187_I	2.765	1.00
42_D	55_E	2.764	1.00
69_I	190_S	2.535	1.00
79_V	285_A	2.522	1.00
76_S	247_L	2.433	1.00
76_S	251_S	2.426	1.00
27_L	71_V	2.419	1.00
106_L	165_M	2.409	1.00
42_D	45_K	2.407	1.00
223_D	237_R	2.352	1.00
23_F	290_I	2.301	1.00
73_V	251_S	2.227	1.00
22_I	290_I	2.215	1.00
82_A	284_S	2.192	1.00
79_V	206_I	2.168	1.00
273_I	283_F	2.117	1.00
71_V	293_V	2.098	1.00
215_S	236_I	2.075	1.00
32_S	40_I	2.060	1.00
73_V	255_A	2.048	1.00
23_F	71_V	2.038	1.00
52_G	55_E	2.036	1.00
39_S	42_D	2.011	1.00
72_F	199_A	2.002	1.00
201_F	250_A	1.999	1.00
110_A	114_I	1.942	1.00
106_L	162_L	1.919	1.00
41_I	45_K	1.911	1.00
212_F	215_S	1.884	1.00
30_N	67_T	1.879	1.00
218_V	231_Q	1.870	1.00
86_A	277_Y	1.868	1.00
84_M	244_I	1.835	1.00
26_G	290_I	1.806	1.00
66_R	296_D	1.804	1.00
208_L	243_I	1.803	1.00
217_S	277_Y	1.800	1.00
109_V	166_T	1.790	1.00
16_F	283_F	1.782	1.00
56_Q	60_S	1.750	1.00
205_G	247_L	1.717	1.00
212_F	239_L	1.717	1.00
53_S	56_Q	1.684	1.00
190_S	194_D	1.618	1.00
68_L	195_V	1.600	1.00
235_G	239_L	1.592	1.00
196_I	200_P	1.581	1.00
191_N	194_D	1.579	1.00
82_A	280_V	1.562	1.00
261_V	292_L	1.551	1.00
29_L	32_S	1.541	1.00
212_F	236_I	1.536	1.00
298_L	302_I	1.529	1.00
46_Y	60_S	1.521	1.00
19_A	286_L	1.521	1.00
205_G	246_I	1.496	1.00
108_V	126_A	1.486	1.00
26_G	293_V	1.471	1.00
29_L	33_V	1.460	1.00
130_A	249_G	1.456	1.00
23_F	286_L	1.432	1.00
279_Y	282_P	1.422	1.00
15_M	283_F	1.406	1.00
187_I	292_L	1.403	1.00
107_F	125_F	1.389	1.00
30_N	297_V	1.388	1.00
299_A	310_V	1.383	1.00
134_G	245_L	1.379	1.00
205_G	243_I	1.363	1.00
298_L	313_V	1.352	1.00
269_V	283_F	1.348	1.00
19_A	283_F	1.332	1.00
23_F	289_A	1.328	1.00
44_L	48_F	1.324	1.00
19_A	287_F	1.319	1.00
133_G	162_L	1.305	1.00
200_P	204_I	1.300	1.00
208_L	212_F	1.297	1.00
80_A	247_L	1.285	1.00
196_I	199_A	1.284	1.00
212_F	240_I	1.264	1.00
69_I	254_V	1.255	1.00
105_S	166_T	1.244	1.00
72_F	195_V	1.235	1.00
265_V	287_F	1.229	1.00
265_V	291_L	1.223	1.00
57_L	61_T	1.220	1.00
161_F	319_T	1.219	1.00
227_K	234_N	1.217	1.00
269_V	280_V	1.214	1.00
37_D	40_I	1.212	1.00
46_Y	56_Q	1.209	1.00
225_T	228_G	1.203	1.00
101_N	248_S	1.202	1.00
255_A	258_I	1.201	1.00
16_F	279_Y	1.194	1.00
78_A	265_V	1.194	1.00
19_A	290_I	1.192	1.00
235_G	238_I	1.191	1.00
107_F	129_G	1.184	1.00
218_V	229_L	1.179	1.00
198_I	254_V	1.171	1.00
54_K	57_L	1.170	1.00
125_F	129_G	1.169	1.00
236_I	239_L	1.163	1.00
70_G	293_V	1.154	1.00
277_Y	280_V	1.151	1.00
87_M	240_I	1.150	1.00
207_G	211_V	1.144	1.00
75_A	289_A	1.142	1.00
14_M	17_I	1.139	1.00
234_N	237_R	1.131	1.00
103_G	133_G	1.123	1.00
208_L	239_L	1.113	1.00
105_S	183_M	1.106	1.00
234_N	238_I	1.105	1.00
118_S	121_S	1.104	1.00
135_A	139_M	1.089	1.00
109_V	179_V	1.086	1.00
36_S	58_I	1.078	1.00
70_G	292_L	1.076	1.00
209_A	243_I	1.074	1.00
159_H	163_S	1.073	1.00
106_L	110_A	1.065	1.00
113_V	169_I	1.064	1.00
124_I	128_A	1.061	1.00
68_L	192_W	1.061	1.00
69_I	195_V	1.060	1.00
72_F	198_I	1.059	1.00
75_A	78_A	1.055	1.00
282_P	285_A	1.047	1.00
82_A	281_L	1.044	1.00
102_A	162_L	1.035	1.00
142_S	234_N	1.033	1.00
222_G	226_A	1.030	1.00
273_I	279_Y	1.029	1.00
82_A	277_Y	1.023	1.00
300_R	307_E	1.021	1.00
198_I	202_S	1.021	1.00
32_S	43_S	1.016	1.00
168_A	172_L	1.015	1.00
299_A	313_V	1.006	1.00
110_A	169_I	1.004	1.00
137_V	158_V	1.004	1.00
216_V	240_I	0.996	1.00
127_F	246_I	0.996	1.00
236_I	240_I	0.994	1.00
204_I	207_G	0.993	1.00
33_V	301_W	0.990	1.00
60_S	64_L	0.989	1.00
290_I	294_Y	0.988	1.00
279_Y	283_F	0.978	1.00
51_D	56_Q	0.973	1.00
103_G	129_G	0.970	1.00
20_L	24_I	0.967	1.00
21_I	25_F	0.965	1.00
27_L	293_V	0.965	1.00
298_L	301_W	0.965	1.00
205_G	250_A	0.961	1.00
46_Y	55_E	0.961	1.00
46_Y	59_I	0.961	1.00
101_N	257_P	0.959	1.00
303_A	306_Y	0.949	1.00
320_P	324_Y	0.945	1.00
132_A	136_I	0.939	1.00
20_L	286_L	0.937	1.00
258_I	292_L	0.937	1.00
67_T	297_V	0.933	1.00
113_V	173_N	0.933	1.00
28_G	32_S	0.932	1.00
106_L	166_T	0.929	1.00
200_P	203_V	0.923	1.00
31_L	67_T	0.922	1.00
296_D	300_R	0.919	1.00
280_V	284_S	0.917	1.00
43_S	59_I	0.913	1.00
197_T	200_P	0.911	1.00
265_V	269_V	0.910	1.00
45_K	49_V	0.906	1.00
28_G	40_I	0.903	1.00
50_W	56_Q	0.902	1.00
56_Q	61_T	0.901	1.00
122_S	125_F	0.900	1.00
272_L	287_F	0.893	1.00
26_G	297_V	0.890	1.00
231_Q	236_I	0.887	1.00
192_W	195_V	0.883	1.00
15_M	19_A	0.883	1.00
238_I	242_L	0.882	1.00
100_V	130_A	0.879	1.00
34_G	63_R	0.874	1.00
276_H	279_Y	0.873	1.00
223_D	227_K	0.873	1.00
15_M	18_I	0.870	1.00
75_A	206_I	0.870	1.00
315_A	320_P	0.870	1.00
14_M	18_I	0.870	1.00
321_F	324_Y	0.868	1.00
294_Y	298_L	0.868	1.00
72_F	202_S	0.867	1.00
251_S	255_A	0.866	1.00
45_K	48_F	0.863	1.00
217_S	278_Q	0.858	1.00
46_Y	51_D	0.855	1.00
38_I	59_I	0.853	1.00
80_A	244_I	0.847	1.00
45_K	50_W	0.844	1.00
24_I	28_G	0.843	1.00
224_E	227_K	0.838	1.00
81_G	266_P	0.835	1.00
106_L	169_I	0.832	1.00
122_S	126_A	0.830	1.00
179_V	183_M	0.827	1.00
108_V	122_S	0.826	1.00
33_V	37_D	0.826	1.00
208_L	211_V	0.824	1.00
53_S	57_L	0.820	1.00
193_Q	196_I	0.819	1.00
127_F	131_A	0.818	1.00
233_M	237_R	0.814	1.00
104_A	130_A	0.813	1.00
32_S	37_D	0.810	1.00
111_S	122_S	0.806	1.00
67_T	293_V	0.805	1.00
209_A	240_I	0.804	1.00
23_F	27_L	0.803	1.00
194_D	254_V	0.802	1.00
76_S	80_A	0.797	1.00
241_S	245_L	0.796	1.00
112_L	122_S	0.794	1.00
203_V	207_G	0.791	1.00
223_D	233_M	0.791	1.00
299_A	309_P	0.790	1.00
64_L	192_W	0.789	1.00
270_R	280_V	0.788	1.00
212_F	243_I	0.787	1.00
96_Q	101_N	0.779	1.00
213_S	278_Q	0.778	1.00
133_G	137_V	0.776	1.00
103_G	162_L	0.776	1.00
121_S	124_I	0.774	1.00
269_V	273_I	0.773	1.00
286_L	290_I	0.772	1.00
177_E	180_L	0.770	1.00
45_K	51_D	0.769	1.00
139_M	142_S	0.765	1.00
138_Y	238_I	0.762	1.00
78_A	82_A	0.761	1.00
38_I	55_E	0.758	1.00
75_A	202_S	0.756	1.00
142_S	146_M	0.755	1.00
303_A	308_S	0.753	1.00
102_A	105_S	0.749	1.00
30_N	300_R	0.749	1.00
210_L	213_S	0.746	1.00
142_S	145_G	0.746	1.00
110_A	165_M	0.743	1.00
84_M	98_F	0.741	1.00
202_S	251_S	0.740	1.00
24_I	27_L	0.737	1.00
198_I	250_A	0.737	1.00
201_F	205_G	0.736	1.00
100_V	134_G	0.732	1.00
211_V	215_S	0.730	1.00
57_L	60_S	0.730	1.00
215_S	231_Q	0.729	1.00
261_V	314_T	0.729	1.00
226_A	233_M	0.727	1.00
43_S	46_Y	0.726	1.00
120_Y	124_I	0.723	1.00
301_W	304_F	0.723	1.00
25_F	28_G	0.722	1.00
292_L	314_T	0.721	1.00
278_Q	282_P	0.718	1.00
269_V	272_L	0.718	1.00
110_A	115_L	0.718	1.00
277_Y	282_P	0.716	1.00
302_I	305_P	0.715	1.00
324_Y	328_K	0.714	1.00
66_R	300_R	0.714	1.00
31_L	64_L	0.711	1.00
68_L	72_F	0.711	1.00
316_I	320_P	0.711	1.00
219_L	233_M	0.709	1.00
23_F	293_V	0.708	1.00
88_T	152_A	0.708	1.00
66_R	307_E	0.708	1.00
206_I	210_L	0.706	1.00
138_Y	234_N	0.705	1.00
109_V	170_I	0.705	1.00
69_I	198_I	0.704	1.00
128_A	132_A	0.702	1.00
52_G	56_Q	0.700	1.00
227_K	233_M	0.700	1.00
79_V	209_A	0.697	1.00
137_V	141_A	0.696	1.00
80_A	248_S	0.695	1.00
250_A	253_A	0.693	1.00
271_K	325_L	0.692	1.00
199_A	203_V	0.687	1.00
289_A	293_V	0.687	1.00
36_S	40_I	0.687	1.00
94_S	97_I	0.686	1.00
292_L	310_V	0.684	1.00
112_L	178_D	0.684	1.00
19_A	23_F	0.680	1.00
129_G	133_G	0.678	1.00
173_N	176_G	0.678	1.00
130_A	245_L	0.674	1.00
250_A	254_V	0.673	1.00
170_I	180_L	0.672	1.00
187_I	310_V	0.670	1.00
198_I	201_F	0.669	1.00
31_L	59_I	0.667	1.00
258_I	310_V	0.666	1.00
57_L	62_L	0.665	1.00
205_G	209_A	0.663	1.00
261_V	291_L	0.662	1.00
78_A	285_A	0.658	1.00
192_W	196_I	0.656	1.00
268_I	271_K	0.655	1.00
27_L	31_L	0.655	1.00
77_L	261_V	0.654	1.00
105_S	257_P	0.650	1.00
111_S	121_S	0.648	1.00
266_P	284_S	0.647	1.00
86_A	220_G	0.647	1.00
15_M	272_L	0.646	1.00
102_A	159_H	0.646	1.00
33_V	297_V	0.645	1.00
36_S	39_S	0.644	1.00
295_A	313_V	0.643	1.00
268_I	291_L	0.642	1.00
180_L	183_M	0.641	1.00
167_Q	171_I	0.641	1.00
79_V	281_L	0.636	1.00
291_L	295_A	0.633	1.00
268_I	287_F	0.632	1.00
131_A	249_G	0.632	1.00
128_A	131_A	0.632	1.00
163_S	183_M	0.631	1.00
291_L	317_I	0.630	1.00
107_F	111_S	0.629	1.00
134_G	241_S	0.629	1.00
264_L	322_F	0.628	1.00
64_L	68_L	0.627	1.00
30_N	293_V	0.626	1.00
175_S	178_D	0.623	1.00
28_G	44_L	0.621	1.00
59_I	64_L	0.618	1.00
167_Q	182_W	0.617	1.00
83_L	243_I	0.616	1.00
201_F	246_I	0.615	1.00
49_V	52_G	0.614	1.00
18_I	22_I	0.614	1.00
40_I	44_L	0.612	1.00
39_S	55_E	0.610	1.00
38_I	46_Y	0.609	1.00
75_A	79_V	0.609	1.00
73_V	187_I	0.608	1.00
240_I	244_I	0.608	1.00
136_I	139_M	0.606	1.00
285_A	289_A	0.606	1.00
112_L	179_V	0.605	1.00
264_L	268_I	0.603	1.00
219_L	236_I	0.603	1.00
111_S	115_L	0.603	1.00
294_Y	297_V	0.602	1.00
147_T	150_K	0.600	1.00
134_G	138_Y	0.600	1.00
154_S	157_A	0.598	1.00
46_Y	50_W	0.598	1.00
25_F	29_L	0.597	1.00
327_R	330_R	0.597	1.00
41_I	44_L	0.594	1.00
263_L	325_L	0.594	1.00
163_S	167_Q	0.594	1.00
101_N	104_A	0.593	1.00
215_S	218_V	0.593	1.00
133_G	158_V	0.593	1.00
239_L	243_I	0.590	1.00
94_S	262_G	0.590	1.00
299_A	307_E	0.589	1.00
140_I	154_S	0.589	1.00
141_A	154_S	0.589	1.00
40_I	43_S	0.588	1.00
84_M	93_A	0.586	1.00
193_Q	197_T	0.584	1.00
268_I	321_F	0.584	1.00
187_I	255_A	0.581	1.00
89_R	223_D	0.580	1.00
202_S	206_I	0.578	0.99
146_M	150_K	0.578	0.99
264_L	321_F	0.578	0.99
15_M	273_I	0.578	0.99
211_V	214_G	0.576	0.99
88_T	91_P	0.575	0.99
16_F	20_L	0.574	0.99
102_A	163_S	0.573	0.99
195_V	198_I	0.571	0.99
131_A	245_L	0.571	0.99
43_S	48_F	0.570	0.99
245_L	249_G	0.568	0.99
248_S	252_V	0.567	0.99
249_G	253_A	0.564	0.99
69_I	73_V	0.562	0.99
29_L	297_V	0.561	0.99
232_N	238_I	0.561	0.99
214_G	217_S	0.560	0.99
239_L	242_L	0.559	0.99
84_M	100_V	0.557	0.99
197_T	201_F	0.557	0.99
287_F	290_I	0.557	0.99
49_V	53_S	0.556	0.99
149_V	152_A	0.554	0.99
16_F	286_L	0.554	0.99
141_A	151_L	0.553	0.99
83_L	244_I	0.553	0.99
232_N	239_L	0.552	0.99
26_G	29_L	0.551	0.99
282_P	286_L	0.550	0.99
51_D	55_E	0.548	0.99
37_D	41_I	0.547	0.99
132_A	135_A	0.547	0.99
178_D	181_Y	0.544	0.99
204_I	208_L	0.544	0.99
217_S	220_G	0.544	0.99
70_G	310_V	0.543	0.99
195_V	199_A	0.541	0.99
299_A	302_I	0.540	0.99
43_S	47_L	0.539	0.99
119_P	123_V	0.535	0.99
42_D	51_D	0.534	0.99
108_V	125_F	0.534	0.99
50_W	53_S	0.533	0.99
293_V	297_V	0.533	0.99
114_I	117_A	0.531	0.99
170_I	176_G	0.530	0.99
82_A	269_V	0.530	0.99
69_I	255_A	0.530	0.99
296_D	307_E	0.528	0.99
103_G	158_V	0.527	0.99
154_S	158_V	0.526	0.99
297_V	301_W	0.525	0.99
197_T	250_A	0.523	0.99
123_V	126_A	0.522	0.99
36_S	55_E	0.520	0.99
138_Y	142_S	0.518	0.99
274_G	278_Q	0.518	0.99
170_I	179_V	0.515	0.99
79_V	202_S	0.513	0.99
164_S	315_A	0.513	0.99
324_Y	327_R	0.511	0.99
176_G	179_V	0.509	0.99
22_I	26_G	0.509	0.99
54_K	58_I	0.508	0.99
170_I	183_M	0.508	0.99
18_I	21_I	0.507	0.99
32_S	44_L	0.506	0.99
100_V	137_V	0.505	0.99
35_A	305_P	0.504	0.99
17_I	21_I	0.502	0.99
209_A	213_S	0.502	0.99
118_S	123_V	0.500	0.99
269_V	284_S	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
4g1uA	2	0.8829	100	0.206	Contact Map
2nq2A	2	0.9189	100	0.209	Contact Map
2qi9A	2	0.958	100	0.211	Contact Map
3rlbA	1	0.5045	17.2	0.965	Contact Map
4xtrG	1	0.0661	15.5	0.965	Contact Map
2m20A	2	0.0841	13.4	0.966	Contact Map
2l9uA	2	0.0871	11.2	0.968	Contact Map
4huqS	1	0.4715	10.5	0.968	Contact Map
3hd7A	1	0.1021	9.7	0.968	Contact Map
3w4tA	1	0.8979	9.3	0.969	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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