YDCS - ECOLI - GREMLIN Contacts

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YDCS - Putative ABC transporter periplasmic-binding protein YdcS

UniProt:	P76108	Sequences: MSKTFARSSLCALSMTIMTAHAAEPPTNLDKPEGRLDIIAWPGYIERGQTDKQYDWVTQFEKETGCAVNVKTAATSDEMVSLMTKGGYDLVTASGDASLRLIMGKRVQPINTALIPNWKTLDPRVVKGDWFNVGGKVYGTPYQWGPNLLMYNTKTFPTPPDSWQVVFVEQNLPDGKSNKGRVQAYDGPIYIADAALFVKATQPQLGISDPYQLTEEQYQAVLKVLRAQHSLIHRYWHDTTVQMSDFKNEGVVASSAWPYQANALKAEGQPVATVFPKEGVTGWADTTMLHSEAKHPVCAYKWMNWSLTPKVQGDVAAWFGSLPVVPEGCKASPLLGEKGCETNGFNYFDKIAFWKTPIAEGGKFVPYSRWTQDYIAIMGGR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13762
Length:	381 (335)
Sequences:	37012 (30076)
Seq/√Len:	1643.2

ECOLI - YDCS POTD YCJN POTF MALE YNJB UGPB THIB
BACSU - MDXE CYCB YURO YESO ARAN YTCQ LIPO MSME
HALSA - Q9HP00 Q9HHQ8 Q9HR87 Q9HMT5 Q9HNZ3 Q9HR04
SULSO - Q97YY1 Q97ZC3 Q97VC2 Q97UZ1 Q97UF5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
35_R	69_N	3.971	1.00
153_T	272_A	3.508	1.00
108_Q	296_P	3.453	1.00
37_D	69_N	3.374	1.00
35_R	67_A	3.047	1.00
154_K	270_P	2.991	1.00
226_R	230_S	2.837	1.00
167_F	227_A	2.814	1.00
109_P	136_K	2.801	1.00
66_C	298_C	2.672	1.00
64_T	301_K	2.614	1.00
223_K	227_A	2.513	1.00
162_S	165_V	2.513	1.00
61_E	67_A	2.466	1.00
54_Y	58_T	2.411	1.00
59_Q	305_W	2.399	1.00
308_T	311_V	2.356	1.00
59_Q	62_K	2.333	1.00
301_K	304_N	2.327	1.00
216_E	220_A	2.216	1.00
153_T	157_P	2.160	1.00
78_E	82_L	2.155	1.00
151_Y	272_A	2.152	1.00
59_Q	63_E	2.135	1.00
168_V	172_L	2.107	1.00
89_D	295_H	2.099	1.00
55_D	58_T	2.093	1.00
37_D	71_K	2.067	1.00
220_A	223_K	2.051	1.00
111_N	136_K	2.023	1.00
61_E	64_T	2.021	1.00
313_G	317_A	2.013	1.00
107_V	288_M	2.001	1.00
34_G	298_C	1.984	1.00
60_F	301_K	1.979	1.00
295_H	298_C	1.962	1.00
59_Q	314_D	1.945	1.00
58_T	62_K	1.933	1.00
165_V	168_V	1.918	1.00
156_F	253_A	1.917	1.00
224_V	227_A	1.909	1.00
139_G	286_T	1.897	1.00
168_V	171_N	1.890	1.00
155_T	252_V	1.888	1.00
33_E	67_A	1.871	1.00
60_F	64_T	1.867	1.00
297_V	301_K	1.856	1.00
238_D	241_V	1.837	1.00
219_Q	223_K	1.826	1.00
120_T	327_E	1.800	1.00
57_V	61_E	1.787	1.00
132_N	137_V	1.786	1.00
91_V	290_H	1.759	1.00
123_P	127_K	1.735	1.00
57_V	302_W	1.732	1.00
39_I	82_L	1.700	1.00
19_T	22_A	1.697	1.00
167_F	228_Q	1.694	1.00
108_Q	291_S	1.663	1.00
158_T	161_D	1.660	1.00
309_P	313_G	1.660	1.00
311_V	314_D	1.643	1.00
58_T	61_E	1.631	1.00
164_Q	167_F	1.622	1.00
245_D	250_G	1.611	1.00
161_D	165_V	1.599	1.00
160_P	165_V	1.568	1.00
55_D	59_Q	1.558	1.00
298_C	301_K	1.558	1.00
14_S	17_I	1.553	1.00
34_G	295_H	1.552	1.00
296_P	300_Y	1.552	1.00
60_F	302_W	1.545	1.00
167_F	171_N	1.534	1.00
224_V	228_Q	1.516	1.00
152_N	155_T	1.516	1.00
63_E	308_T	1.509	1.00
314_D	318_W	1.507	1.00
217_Q	220_A	1.466	1.00
289_L	303_M	1.459	1.00
149_L	274_V	1.441	1.00
314_D	317_A	1.438	1.00
244_S	248_N	1.433	1.00
102_I	138_Y	1.431	1.00
151_Y	274_V	1.425	1.00
167_F	224_V	1.418	1.00
60_F	305_W	1.408	1.00
153_T	270_P	1.391	1.00
60_F	66_C	1.381	1.00
90_L	299_A	1.368	1.00
223_K	226_R	1.365	1.00
293_A	296_P	1.365	1.00
164_Q	168_V	1.364	1.00
177_S	180_G	1.354	1.00
127_K	132_N	1.350	1.00
40_A	70_V	1.346	1.00
155_T	173_P	1.339	1.00
148_L	273_T	1.338	1.00
177_S	181_R	1.333	1.00
113_A	116_P	1.321	1.00
105_K	291_S	1.315	1.00
173_P	252_V	1.313	1.00
109_P	112_T	1.309	1.00
116_P	119_K	1.304	1.00
161_D	277_K	1.303	1.00
216_E	219_Q	1.303	1.00
170_Q	253_A	1.283	1.00
78_E	81_S	1.282	1.00
346_N	349_D	1.271	1.00
21_H	24_E	1.264	1.00
131_F	286_T	1.257	1.00
93_A	288_M	1.256	1.00
66_C	301_K	1.254	1.00
332_S	336_G	1.254	1.00
241_V	244_S	1.251	1.00
123_P	126_V	1.249	1.00
57_V	70_V	1.246	1.00
345_F	349_D	1.233	1.00
297_V	300_Y	1.215	1.00
245_D	251_V	1.214	1.00
300_Y	304_N	1.208	1.00
90_L	302_W	1.200	1.00
206_G	210_P	1.194	1.00
11_C	15_M	1.193	1.00
293_A	299_A	1.190	1.00
332_S	335_L	1.185	1.00
227_A	230_S	1.183	1.00
60_F	298_C	1.181	1.00
149_L	253_A	1.174	1.00
289_L	299_A	1.166	1.00
327_E	330_K	1.154	1.00
156_F	169_E	1.142	1.00
309_P	327_E	1.140	1.00
33_E	65_G	1.126	1.00
57_V	68_V	1.122	1.00
81_S	85_K	1.115	1.00
36_L	298_C	1.111	1.00
117_N	304_N	1.106	1.00
150_M	256_A	1.102	1.00
122_D	326_P	1.101	1.00
109_P	137_V	1.100	1.00
290_H	293_A	1.094	1.00
310_K	313_G	1.092	1.00
169_E	172_L	1.091	1.00
302_W	306_S	1.090	1.00
325_V	328_G	1.089	1.00
289_L	300_Y	1.083	1.00
166_V	170_Q	1.077	1.00
36_L	302_W	1.076	1.00
196_L	201_T	1.071	1.00
38_I	287_T	1.070	1.00
305_W	311_V	1.069	1.00
190_Y	193_D	1.068	1.00
246_F	271_V	1.065	1.00
101_L	107_V	1.059	1.00
63_E	305_W	1.056	1.00
310_K	314_D	1.048	1.00
102_I	133_V	1.045	1.00
91_V	288_M	1.043	1.00
220_A	224_V	1.042	1.00
13_L	16_T	1.041	1.00
346_N	350_K	1.038	1.00
89_D	293_A	1.038	1.00
120_T	325_V	1.038	1.00
198_V	201_T	1.035	1.00
168_V	177_S	1.034	1.00
169_E	253_A	1.033	1.00
152_N	270_P	1.031	1.00
115_I	118_W	1.028	1.00
263_A	266_A	1.022	1.00
291_S	296_P	1.020	1.00
83_M	106_R	1.017	1.00
20_A	23_A	1.015	1.00
55_D	314_D	1.012	1.00
100_R	104_G	1.012	1.00
90_L	303_M	1.009	1.00
302_W	305_W	0.998	1.00
17_I	21_H	0.996	1.00
181_R	252_V	0.991	1.00
232_I	235_Y	0.987	1.00
331_A	334_L	0.986	1.00
287_T	303_M	0.982	1.00
142_Y	287_T	0.980	1.00
313_G	331_A	0.978	1.00
155_T	181_R	0.970	1.00
39_I	88_Y	0.969	1.00
86_G	292_E	0.967	1.00
289_L	293_A	0.965	1.00
18_M	21_H	0.956	1.00
34_G	65_G	0.954	1.00
80_V	84_T	0.950	1.00
11_C	14_S	0.950	1.00
56_W	59_Q	0.948	1.00
59_Q	310_K	0.948	1.00
256_A	260_Q	0.947	1.00
115_I	304_N	0.946	1.00
344_G	347_Y	0.943	1.00
55_D	318_W	0.943	1.00
15_M	18_M	0.942	1.00
231_L	234_R	0.938	1.00
177_S	183_Q	0.937	1.00
309_P	325_V	0.936	1.00
166_V	253_A	0.936	1.00
158_T	165_V	0.935	1.00
15_M	19_T	0.935	1.00
63_E	310_K	0.930	1.00
313_G	328_G	0.927	1.00
14_S	18_M	0.925	1.00
197_F	202_Q	0.911	1.00
177_S	182_V	0.910	1.00
343_N	346_N	0.909	1.00
333_P	336_G	0.907	1.00
12_A	16_T	0.902	1.00
16_T	19_T	0.902	1.00
262_N	266_A	0.896	1.00
82_L	85_K	0.896	1.00
215_E	219_Q	0.895	1.00
139_G	288_M	0.895	1.00
56_W	311_V	0.893	1.00
68_V	302_W	0.887	1.00
99_L	103_M	0.884	1.00
108_Q	293_A	0.884	1.00
59_Q	311_V	0.881	1.00
178_N	181_R	0.880	1.00
131_F	137_V	0.880	1.00
195_A	200_A	0.870	1.00
114_L	117_N	0.870	1.00
154_K	157_P	0.864	1.00
299_A	303_M	0.863	1.00
151_Y	159_P	0.863	1.00
11_C	17_I	0.856	1.00
107_V	138_Y	0.852	1.00
206_G	209_D	0.849	1.00
195_A	199_K	0.847	1.00
178_N	182_V	0.843	1.00
215_E	218_Y	0.843	1.00
21_H	25_P	0.841	1.00
108_Q	300_Y	0.840	1.00
244_S	247_K	0.836	1.00
114_L	300_Y	0.834	1.00
194_A	197_F	0.833	1.00
213_L	218_Y	0.831	1.00
121_L	307_L	0.830	1.00
10_L	14_S	0.827	1.00
108_Q	290_H	0.821	1.00
17_I	20_A	0.820	1.00
61_E	68_V	0.819	1.00
77_D	81_S	0.819	1.00
347_Y	350_K	0.819	1.00
225_L	229_H	0.817	1.00
348_F	351_I	0.815	1.00
132_N	135_G	0.810	1.00
226_R	229_H	0.806	1.00
102_I	107_V	0.805	1.00
126_V	137_V	0.804	1.00
29_L	32_P	0.802	1.00
108_Q	112_T	0.801	1.00
336_G	339_G	0.795	1.00
13_L	17_I	0.792	1.00
195_A	198_V	0.790	1.00
212_Q	215_E	0.790	1.00
52_K	55_D	0.789	1.00
109_P	138_Y	0.789	1.00
120_T	309_P	0.785	1.00
196_L	200_A	0.784	1.00
167_F	170_Q	0.783	1.00
121_L	126_V	0.782	1.00
345_F	348_F	0.779	1.00
197_F	200_A	0.775	1.00
242_Q	254_S	0.775	1.00
345_F	350_K	0.773	1.00
326_P	330_K	0.771	1.00
7_R	10_L	0.769	1.00
185_Y	251_V	0.769	1.00
34_G	66_C	0.767	1.00
122_D	125_V	0.764	1.00
240_T	243_M	0.762	1.00
163_W	167_F	0.761	1.00
12_A	15_M	0.760	1.00
338_K	341_E	0.759	1.00
77_D	80_V	0.759	1.00
287_T	306_S	0.756	1.00
334_L	338_K	0.754	1.00
193_D	201_T	0.752	1.00
108_Q	292_E	0.752	1.00
82_L	87_G	0.751	1.00
61_E	66_C	0.749	1.00
123_P	326_P	0.748	1.00
159_P	169_E	0.744	1.00
91_V	107_V	0.743	1.00
92_T	287_T	0.739	1.00
108_Q	289_L	0.737	1.00
7_R	11_C	0.733	1.00
9_S	13_L	0.733	1.00
65_G	301_K	0.732	1.00
110_I	303_M	0.726	1.00
10_L	13_L	0.724	1.00
145_G	283_W	0.724	1.00
47_R	54_Y	0.718	1.00
339_G	342_T	0.717	1.00
7_R	14_S	0.714	1.00
157_P	270_P	0.712	1.00
156_F	173_P	0.710	1.00
122_D	126_V	0.707	1.00
64_T	298_C	0.706	1.00
36_L	295_H	0.703	1.00
10_L	16_T	0.702	1.00
240_T	244_S	0.699	1.00
194_A	198_V	0.697	1.00
343_N	347_Y	0.696	1.00
243_M	247_K	0.694	1.00
183_Q	251_V	0.689	1.00
296_P	299_A	0.683	1.00
201_T	204_Q	0.683	1.00
198_V	202_Q	0.682	1.00
80_V	100_R	0.682	1.00
111_N	137_V	0.681	1.00
9_S	12_A	0.679	1.00
98_S	139_G	0.678	1.00
344_G	348_F	0.677	1.00
22_A	25_P	0.676	1.00
39_I	73_A	0.675	1.00
304_N	308_T	0.674	1.00
117_N	120_T	0.674	1.00
261_A	265_K	0.674	1.00
6_A	9_S	0.672	1.00
214_T	217_Q	0.668	1.00
163_W	224_V	0.665	1.00
337_E	340_C	0.665	1.00
199_K	220_A	0.662	1.00
150_M	273_T	0.658	1.00
113_A	117_N	0.657	1.00
56_W	305_W	0.655	1.00
37_D	89_D	0.653	1.00
334_L	337_E	0.653	1.00
196_L	199_K	0.651	1.00
150_M	261_A	0.651	1.00
119_K	126_V	0.650	1.00
38_I	70_V	0.648	1.00
81_S	84_T	0.647	1.00
193_D	200_A	0.646	1.00
179_K	182_V	0.645	1.00
262_N	265_K	0.644	1.00
97_A	100_R	0.642	1.00
214_T	219_Q	0.642	1.00
328_G	331_A	0.642	1.00
111_N	300_Y	0.641	1.00
71_K	88_Y	0.640	1.00
121_L	125_V	0.638	1.00
67_A	70_V	0.638	1.00
6_A	17_I	0.637	1.00
79_M	91_V	0.634	1.00
152_N	249_E	0.634	1.00
165_V	169_E	0.633	1.00
83_M	290_H	0.633	1.00
150_M	271_V	0.632	1.00
38_I	90_L	0.631	1.00
195_A	202_Q	0.630	1.00
222_L	226_R	0.630	1.00
159_P	274_V	0.628	1.00
201_T	217_Q	0.628	1.00
33_E	66_C	0.628	1.00
193_D	196_L	0.626	1.00
124_R	127_K	0.626	1.00
73_A	78_E	0.626	1.00
343_N	350_K	0.625	1.00
89_D	294_K	0.623	1.00
112_T	300_Y	0.623	1.00
245_D	248_N	0.622	1.00
9_S	15_M	0.621	1.00
344_G	350_K	0.621	1.00
221_V	225_L	0.620	1.00
90_L	287_T	0.619	1.00
190_Y	194_A	0.618	1.00
56_W	314_D	0.616	1.00
344_G	351_I	0.616	1.00
160_P	169_E	0.615	1.00
89_D	299_A	0.614	1.00
112_T	136_K	0.613	1.00
36_L	299_A	0.613	1.00
93_A	101_L	0.612	1.00
192_A	196_L	0.612	1.00
193_D	197_F	0.612	1.00
233_H	236_W	0.611	1.00
241_V	245_D	0.611	1.00
44_Y	47_R	0.611	1.00
151_Y	156_F	0.611	1.00
343_N	348_F	0.611	1.00
218_Y	221_V	0.610	1.00
335_L	338_K	0.610	1.00
171_N	178_N	0.609	1.00
34_G	301_K	0.608	1.00
169_E	173_P	0.607	1.00
217_Q	221_V	0.604	1.00
61_E	65_G	0.598	1.00
194_A	202_Q	0.593	1.00
162_S	278_E	0.590	1.00
180_G	183_Q	0.587	1.00
260_Q	264_L	0.586	1.00
286_T	290_H	0.586	1.00
39_I	71_K	0.586	1.00
178_N	183_Q	0.585	1.00
8_S	12_A	0.585	1.00
28_N	31_K	0.585	1.00
74_A	78_E	0.585	1.00
125_V	144_W	0.585	1.00
173_P	181_R	0.584	1.00
301_K	305_W	0.583	1.00
154_K	249_E	0.580	1.00
98_S	102_I	0.579	1.00
12_A	17_I	0.579	1.00
149_L	255_S	0.578	1.00
181_R	250_G	0.578	1.00
120_T	326_P	0.576	1.00
132_N	136_K	0.576	1.00
196_L	202_Q	0.572	1.00
159_P	165_V	0.570	1.00
173_P	253_A	0.570	1.00
184_A	187_G	0.567	1.00
119_K	122_D	0.567	1.00
101_L	106_R	0.566	1.00
260_Q	263_A	0.566	1.00
114_L	297_V	0.565	1.00
110_I	300_Y	0.565	1.00
214_T	218_Y	0.565	1.00
80_V	104_G	0.564	1.00
156_F	252_V	0.564	1.00
300_Y	303_M	0.563	1.00
161_D	166_V	0.561	1.00
34_G	37_D	0.560	1.00
243_M	256_A	0.560	1.00
331_A	335_L	0.559	1.00
143_Q	285_D	0.559	1.00
25_P	28_N	0.559	1.00
237_H	241_V	0.558	1.00
232_I	236_W	0.556	1.00
102_I	105_K	0.554	1.00
118_W	126_V	0.554	1.00
151_Y	253_A	0.553	1.00
309_P	312_Q	0.552	1.00
38_I	92_T	0.552	1.00
43_G	47_R	0.551	1.00
242_Q	251_V	0.551	1.00
185_Y	189_I	0.550	1.00
64_T	302_W	0.550	1.00
18_M	22_A	0.549	1.00
6_A	13_L	0.545	1.00
192_A	198_V	0.542	1.00
345_F	351_I	0.542	1.00
338_K	342_T	0.540	1.00
64_T	305_W	0.539	1.00
56_W	306_S	0.539	1.00
289_L	296_P	0.539	1.00
33_E	64_T	0.539	1.00
130_W	133_V	0.538	1.00
99_L	102_I	0.537	1.00
11_C	16_T	0.537	1.00
295_H	299_A	0.535	1.00
190_Y	195_A	0.533	1.00
233_H	237_H	0.533	1.00
186_D	189_I	0.532	1.00
333_P	337_E	0.532	1.00
312_Q	324_V	0.531	1.00
122_D	329_C	0.530	1.00
329_C	332_S	0.529	1.00
89_D	296_P	0.529	1.00
110_I	289_L	0.527	1.00
71_K	82_L	0.526	1.00
71_K	78_E	0.525	1.00
199_K	202_Q	0.524	1.00
194_A	199_K	0.523	1.00
140_T	303_M	0.522	1.00
34_G	64_T	0.521	1.00
126_V	132_N	0.521	1.00
140_T	307_L	0.520	1.00
194_A	200_A	0.520	1.00
170_Q	228_Q	0.520	1.00
192_A	201_T	0.519	1.00
163_W	170_Q	0.519	1.00
349_D	352_A	0.518	1.00
8_S	11_C	0.518	1.00
305_W	308_T	0.517	1.00
19_T	23_A	0.516	1.00
164_Q	278_E	0.512	1.00
37_D	40_A	0.512	1.00
179_K	183_Q	0.512	1.00
94_S	97_A	0.512	1.00
54_Y	70_V	0.511	1.00
221_V	224_V	0.510	1.00
237_H	245_D	0.510	1.00
312_Q	316_A	0.509	1.00
191_I	194_A	0.508	1.00
145_G	285_D	0.507	1.00
259_Y	321_S	0.507	1.00
10_L	17_I	0.505	1.00
171_N	227_A	0.504	1.00
114_L	304_N	0.503	1.00
37_D	88_Y	0.503	1.00
321_S	324_V	0.502	1.00
231_L	237_H	0.501	1.00
199_K	224_V	0.500	1.00
209_D	212_Q	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
4r2fA	1	0.8845	100	0.231	Contact Map
4r9fA	1	0.8871	100	0.242	Contact Map
3uorA	1	0.8819	100	0.243	Contact Map
4mfiA	1	0.8976	100	0.252	Contact Map
3vxbA	1	0.8845	100	0.269	Contact Map
3woaA	1	0.9528	100	0.272	Contact Map
2xd3A	1	0.8714	100	0.284	Contact Map
2zyoA	1	0.8871	100	0.289	Contact Map
4c1uA	1	0.8845	100	0.302	Contact Map
4g68A	1	0.8819	100	0.303	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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