YNJB - ECOLI - GREMLIN Contacts

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YNJB - Protein YnjB

UniProt:	P76223	Sequences: MRHCGWLLGLLSLFSLATHASDWQEIKNEAKGQTVWFNAWGGDTAINRYLDWVSGEMKTHYAINLKIVRLADAADAVKRIQTEAAAGRKTGGSVDLLWVNGENFRTLKEANLLQTGWAETLPNWRYVDTQLPVREDFSVPTQGAESPWGGAQLTFIARRDVTPQPPQTPQALLEFAKANPGTVTYPRPPDFTGTAFLEQLLIMLTPDPAALKEAPDDATFARVTAPLWQYLDVLHPYLWREGKDFPPSPARMDALLKAGTLRLSLTFNPAHAQQKIASGDLPASSYSFGFREGMIGNVHFVTIPANANASAAAKVVANFLLSPDAQLRKADPAVWGDPSVLDPQKLPDGQRESLQSRMPQDLPPVLAEPHAGWVNALEQEWLHRYGTH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG14004
Length:	388 (329)
Sequences:	34992 (27551)
Seq/√Len:	1518.9

ECOLI - YNJB MALE YDCS UGPB YCJN POTD POTF THIB
BACSU - CYCB YESO MDXE ARAN YTCQ MSME YURO LIPO
HALSA - Q9HHQ8 Q9HP00 Q9HNZ3 Q9HMT5 Q9HR87 Q9HR04
SULSO - Q97YY1 Q97ZC3 Q97UZ1 Q97VC2 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
159_R	286_Y	3.399	1.00
36_W	66_K	3.126	1.00
114_Q	310_S	3.033	1.00
34_T	66_K	2.901	1.00
160_D	284_S	2.810	1.00
173_L	233_V	2.781	1.00
115_T	142_Q	2.586	1.00
15_S	18_T	2.542	1.00
14_F	17_A	2.403	1.00
63_I	312_A	2.376	1.00
177_K	237_Y	2.362	1.00
56_E	319_F	2.339	1.00
58_K	64_N	2.336	1.00
61_Y	315_V	2.325	1.00
34_T	64_N	2.282	1.00
168_T	171_A	2.272	1.00
232_D	236_P	2.263	1.00
322_S	325_A	2.256	1.00
13_L	16_L	2.235	1.00
233_V	237_Y	2.234	1.00
229_Q	233_V	2.157	1.00
56_E	59_T	2.126	1.00
16_L	19_H	2.086	1.00
222_R	226_P	2.078	1.00
315_V	318_N	2.062	1.00
75_D	78_K	2.046	1.00
18_T	21_S	2.010	1.00
56_E	328_R	2.007	1.00
17_A	20_A	2.006	1.00
327_L	331_D	1.982	1.00
51_D	55_G	1.962	1.00
19_H	22_D	1.940	1.00
174_E	178_A	1.937	1.00
36_W	68_V	1.934	1.00
56_E	60_H	1.929	1.00
157_A	286_Y	1.927	1.00
309_A	312_A	1.925	1.00
159_R	163_P	1.920	1.00
95_D	309_A	1.905	1.00
161_V	262_R	1.896	1.00
52_W	55_G	1.896	1.00
57_M	315_V	1.810	1.00
117_W	142_Q	1.807	1.00
20_A	23_W	1.804	1.00
55_G	59_T	1.795	1.00
113_L	302_T	1.780	1.00
162_T	263_L	1.739	1.00
225_A	229_Q	1.733	1.00
58_K	61_Y	1.727	1.00
230_Y	233_V	1.726	1.00
226_P	229_Q	1.719	1.00
348_D	352_E	1.696	1.00
47_N	51_D	1.694	1.00
248_S	251_R	1.691	1.00
135_E	138_S	1.666	1.00
138_S	143_G	1.663	1.00
311_A	315_V	1.660	1.00
171_A	174_E	1.658	1.00
54_S	316_V	1.658	1.00
57_M	61_Y	1.654	1.00
54_S	58_K	1.645	1.00
114_Q	305_A	1.620	1.00
72_D	75_D	1.610	1.00
255_L	260_T	1.603	1.00
38_N	83_E	1.600	1.00
173_L	177_K	1.600	1.00
97_L	304_P	1.589	1.00
145_E	300_F	1.587	1.00
174_E	177_K	1.579	1.00
323_P	327_L	1.573	1.00
310_S	314_K	1.569	1.00
33_Q	312_A	1.563	1.00
164_Q	167_Q	1.549	1.00
177_K	181_G	1.547	1.00
328_R	332_P	1.544	1.00
325_A	328_R	1.543	1.00
173_L	237_Y	1.541	1.00
183_V	186_P	1.536	1.00
205_T	208_P	1.532	1.00
60_H	322_S	1.520	1.00
52_W	56_E	1.476	1.00
79_R	83_E	1.472	1.00
328_R	331_D	1.467	1.00
312_A	315_V	1.463	1.00
158_R	161_V	1.450	1.00
55_G	58_K	1.449	1.00
170_Q	173_L	1.429	1.00
129_T	132_P	1.426	1.00
303_I	317_A	1.425	1.00
307_A	310_S	1.422	1.00
39_A	67_I	1.411	1.00
57_M	316_V	1.389	1.00
254_A	258_A	1.370	1.00
126_Y	343_P	1.368	1.00
159_R	284_S	1.365	1.00
157_A	288_F	1.362	1.00
155_F	288_F	1.361	1.00
170_Q	174_E	1.360	1.00
173_L	230_Y	1.353	1.00
167_Q	171_A	1.345	1.00
179_N	262_R	1.345	1.00
229_Q	232_D	1.330	1.00
32_G	64_N	1.317	1.00
57_M	319_F	1.314	1.00
255_L	261_L	1.313	1.00
223_V	226_P	1.311	1.00
96_L	313_A	1.308	1.00
108_K	144_A	1.299	1.00
57_M	63_I	1.286	1.00
173_L	234_L	1.285	1.00
21_S	24_Q	1.282	1.00
348_D	351_R	1.258	1.00
48_R	51_D	1.257	1.00
167_Q	291_R	1.254	1.00
230_Y	234_L	1.237	1.00
54_S	67_I	1.233	1.00
161_V	179_N	1.233	1.00
121_L	124_W	1.230	1.00
120_T	123_N	1.226	1.00
311_A	314_K	1.225	1.00
184_T	187_R	1.203	1.00
96_L	316_V	1.196	1.00
303_I	313_A	1.193	1.00
233_V	236_P	1.168	1.00
222_R	225_A	1.161	1.00
120_T	124_W	1.160	1.00
52_W	328_R	1.157	1.00
183_V	187_R	1.157	1.00
314_K	318_N	1.156	1.00
115_T	143_G	1.149	1.00
118_A	122_P	1.130	1.00
128_D	131_L	1.124	1.00
63_I	315_V	1.124	1.00
119_E	122_P	1.122	1.00
99_V	302_T	1.118	1.00
54_S	65_L	1.115	1.00
137_F	300_F	1.114	1.00
352_E	355_Q	1.113	1.00
154_T	287_S	1.109	1.00
307_A	313_A	1.106	1.00
33_Q	309_A	1.095	1.00
256_L	285_S	1.094	1.00
274_Q	277_A	1.094	1.00
324_D	327_L	1.093	1.00
13_L	18_T	1.090	1.00
123_N	318_N	1.087	1.00
14_F	18_T	1.085	1.00
323_P	343_P	1.076	1.00
162_T	175_F	1.070	1.00
13_L	17_A	1.069	1.00
175_F	178_A	1.063	1.00
176_A	263_L	1.057	1.00
111_N	305_A	1.054	1.00
155_F	263_L	1.048	1.00
251_R	254_A	1.047	1.00
95_D	307_A	1.046	1.00
15_S	19_H	1.043	1.00
37_F	301_V	1.043	1.00
184_T	261_L	1.042	1.00
158_R	283_A	1.042	1.00
84_A	93_S	1.037	1.00
204_L	208_P	1.037	1.00
319_F	325_A	1.035	1.00
158_R	284_S	1.021	1.00
56_E	324_D	1.018	1.00
79_R	82_T	1.015	1.00
57_M	312_A	1.013	1.00
201_L	204_L	1.007	1.00
324_D	328_R	1.007	1.00
156_I	266_T	1.006	1.00
316_V	320_L	1.005	1.00
166_P	171_A	1.005	1.00
119_E	314_K	1.003	1.00
96_L	317_A	1.003	1.00
81_Q	110_A	0.999	1.00
15_S	20_A	0.993	1.00
303_I	314_K	0.992	1.00
172_L	176_A	0.992	1.00
226_P	230_Y	0.991	1.00
349_G	352_E	0.991	1.00
14_F	19_H	0.989	1.00
77_V	103_N	0.989	1.00
52_W	332_P	0.981	1.00
97_L	302_T	0.979	1.00
22_D	25_E	0.975	1.00
17_A	21_S	0.974	1.00
182_T	262_R	0.971	1.00
201_L	205_T	0.969	1.00
60_H	324_D	0.967	1.00
160_D	283_A	0.965	1.00
200_L	204_L	0.962	1.00
125_R	128_D	0.958	1.00
60_H	319_F	0.956	1.00
127_V	132_P	0.956	1.00
106_T	110_A	0.955	1.00
120_T	314_K	0.953	1.00
107_L	113_L	0.947	1.00
23_W	26_I	0.946	1.00
114_Q	314_K	0.945	1.00
126_Y	341_L	0.944	1.00
323_P	341_L	0.943	1.00
127_V	131_L	0.942	1.00
118_A	121_L	0.941	1.00
185_Y	188_P	0.940	1.00
108_K	139_V	0.937	1.00
16_L	20_A	0.935	1.00
175_F	263_L	0.931	1.00
35_V	316_V	0.928	1.00
218_A	221_A	0.928	1.00
303_I	307_A	0.927	1.00
162_T	179_N	0.925	1.00
301_V	317_A	0.923	1.00
80_I	97_L	0.921	1.00
53_V	56_E	0.919	1.00
129_T	135_E	0.918	1.00
191_F	195_A	0.916	1.00
56_E	325_A	0.913	1.00
87_G	306_N	0.913	1.00
35_V	312_A	0.910	1.00
125_R	132_P	0.907	1.00
304_P	307_A	0.906	1.00
178_A	181_G	0.904	1.00
65_L	316_V	0.902	1.00
305_A	310_S	0.899	1.00
93_S	304_P	0.897	1.00
183_V	188_P	0.896	1.00
172_L	263_L	0.894	1.00
273_Q	277_A	0.893	1.00
53_V	325_A	0.893	1.00
32_G	62_A	0.890	1.00
164_Q	171_A	0.886	1.00
145_E	302_T	0.885	1.00
128_D	342_D	0.885	1.00
148_W	301_V	0.882	1.00
266_T	270_A	0.879	1.00
38_N	94_V	0.879	1.00
58_K	65_L	0.878	1.00
221_A	225_A	0.875	1.00
355_Q	358_M	0.874	1.00
176_A	180_P	0.870	1.00
48_R	52_W	0.866	1.00
204_L	226_P	0.864	1.00
105_R	109_E	0.862	1.00
254_A	257_K	0.862	1.00
84_A	112_L	0.856	1.00
113_L	144_A	0.855	1.00
49_Y	52_W	0.855	1.00
201_L	206_P	0.854	1.00
232_D	235_H	0.851	1.00
78_K	82_T	0.850	1.00
327_L	344_Q	0.847	1.00
341_L	344_Q	0.845	1.00
122_P	125_R	0.844	1.00
202_I	205_T	0.841	1.00
18_T	22_D	0.831	1.00
28_N	31_K	0.831	1.00
275_K	279_G	0.824	1.00
157_A	165_P	0.824	1.00
219_T	224_T	0.820	1.00
125_R	129_T	0.810	1.00
126_Y	129_T	0.808	1.00
62_A	315_V	0.807	1.00
351_R	355_Q	0.805	1.00
115_T	144_A	0.803	1.00
160_D	163_P	0.802	1.00
184_T	189_P	0.798	1.00
35_V	309_A	0.796	1.00
119_E	124_W	0.792	1.00
279_G	283_A	0.784	1.00
273_Q	276_I	0.781	1.00
138_S	141_T	0.780	1.00
199_Q	203_M	0.779	1.00
116_G	317_A	0.774	1.00
235_H	238_L	0.774	1.00
221_A	224_T	0.773	1.00
202_I	207_D	0.771	1.00
78_K	81_Q	0.770	1.00
114_Q	304_P	0.770	1.00
301_V	320_L	0.766	1.00
178_A	182_T	0.765	1.00
316_V	319_F	0.761	1.00
279_G	282_P	0.761	1.00
77_V	106_T	0.760	1.00
114_Q	303_I	0.759	1.00
17_A	22_D	0.759	1.00
250_A	253_D	0.755	1.00
169_P	173_L	0.754	1.00
313_A	317_A	0.745	1.00
119_E	123_N	0.745	1.00
186_P	189_P	0.742	1.00
83_E	88_R	0.741	1.00
274_Q	278_S	0.737	1.00
187_R	190_D	0.730	1.00
77_V	81_Q	0.727	1.00
18_T	23_W	0.726	1.00
16_L	21_S	0.725	1.00
276_I	279_G	0.723	1.00
114_Q	307_A	0.722	1.00
179_N	263_L	0.720	1.00
82_T	86_A	0.719	1.00
201_L	208_P	0.718	1.00
177_K	180_P	0.718	1.00
247_P	255_L	0.716	1.00
199_Q	202_I	0.713	1.00
238_L	242_G	0.712	1.00
198_E	202_I	0.707	1.00
168_T	292_E	0.706	1.00
183_V	189_P	0.706	1.00
68_V	79_R	0.706	1.00
151_A	297_N	0.705	1.00
30_A	33_Q	0.703	1.00
156_I	287_S	0.703	1.00
318_N	322_S	0.700	1.00
13_L	19_H	0.698	1.00
252_M	264_S	0.696	1.00
108_K	113_L	0.695	1.00
165_P	175_F	0.693	1.00
205_T	209_A	0.689	1.00
137_F	143_G	0.687	1.00
88_R	93_S	0.685	1.00
337_D	340_V	0.684	1.00
255_L	258_A	0.683	1.00
253_D	257_K	0.681	1.00
201_L	224_T	0.679	1.00
347_P	350_Q	0.678	1.00
165_P	288_F	0.677	1.00
202_I	206_P	0.675	1.00
163_P	284_S	0.672	1.00
27_K	30_A	0.671	1.00
228_W	232_D	0.670	1.00
184_T	188_P	0.668	1.00
343_P	346_L	0.668	1.00
126_Y	342_D	0.667	1.00
104_F	145_E	0.664	1.00
203_M	208_P	0.662	1.00
97_L	113_L	0.660	1.00
173_L	176_A	0.660	1.00
14_F	20_A	0.656	1.00
175_F	179_N	0.656	1.00
165_P	171_A	0.655	1.00
197_L	201_L	0.653	1.00
15_S	21_S	0.650	1.00
347_P	351_R	0.649	1.00
180_P	238_L	0.648	1.00
36_W	95_D	0.648	1.00
192_T	195_A	0.647	1.00
231_L	235_H	0.646	1.00
352_E	356_S	0.645	1.00
209_A	215_P	0.645	1.00
26_I	29_E	0.642	1.00
38_N	68_V	0.641	1.00
156_I	272_A	0.638	1.00
257_K	278_S	0.638	1.00
199_Q	205_T	0.638	1.00
169_P	230_Y	0.638	1.00
118_A	124_W	0.636	1.00
353_S	356_S	0.635	1.00
81_Q	106_T	0.635	1.00
128_D	132_P	0.635	1.00
75_D	79_R	0.634	1.00
98_W	301_V	0.633	1.00
196_F	200_L	0.630	1.00
68_V	94_V	0.629	1.00
157_A	162_T	0.628	1.00
332_P	335_W	0.628	1.00
160_D	259_G	0.628	1.00
36_W	39_A	0.627	1.00
200_L	203_M	0.627	1.00
250_A	254_A	0.627	1.00
346_L	351_R	0.627	1.00
166_P	263_L	0.623	1.00
53_V	320_L	0.622	1.00
127_V	321_L	0.621	1.00
38_N	70_L	0.621	1.00
58_K	62_A	0.621	1.00
156_I	285_S	0.620	1.00
115_T	118_A	0.620	1.00
209_A	213_E	0.620	1.00
135_E	139_V	0.619	1.00
95_D	308_N	0.616	1.00
64_N	67_I	0.616	1.00
315_V	319_F	0.615	1.00
104_F	108_K	0.615	1.00
123_N	126_Y	0.614	1.00
356_S	359_P	0.613	1.00
220_F	224_T	0.613	1.00
220_F	225_A	0.613	1.00
349_G	353_S	0.613	1.00
117_W	314_K	0.612	1.00
61_Y	312_A	0.612	1.00
204_L	230_Y	0.611	1.00
103_N	106_T	0.610	1.00
158_R	259_G	0.607	1.00
247_P	251_R	0.604	1.00
70_L	79_R	0.604	1.00
53_V	328_R	0.601	1.00
176_A	237_Y	0.600	1.00
310_S	313_A	0.599	1.00
129_T	342_D	0.598	1.00
126_Y	323_P	0.598	1.00
191_F	194_T	0.597	1.00
31_K	34_T	0.596	1.00
100_N	103_N	0.595	1.00
350_Q	354_L	0.594	1.00
203_M	207_D	0.593	1.00
157_A	263_L	0.591	1.00
286_Y	289_G	0.589	1.00
19_H	23_W	0.587	1.00
159_R	283_A	0.586	1.00
306_N	310_S	0.585	1.00
155_F	265_L	0.584	1.00
77_V	107_L	0.583	1.00
303_I	310_S	0.582	1.00
99_V	107_L	0.582	1.00
213_E	217_D	0.581	1.00
114_Q	306_N	0.581	1.00
51_D	67_I	0.579	1.00
251_R	255_L	0.578	1.00
117_W	143_G	0.578	1.00
171_A	175_F	0.577	1.00
249_P	252_M	0.577	1.00
37_F	96_L	0.576	1.00
326_Q	340_V	0.575	1.00
202_I	208_P	0.574	1.00
146_S	321_L	0.569	1.00
127_V	130_Q	0.567	1.00
138_S	142_Q	0.566	1.00
326_Q	330_A	0.565	1.00
272_A	276_I	0.565	1.00
176_A	179_N	0.563	1.00
29_E	32_G	0.561	1.00
146_S	317_A	0.560	1.00
58_K	63_I	0.558	1.00
81_Q	84_A	0.558	1.00
203_M	206_P	0.557	1.00
227_L	231_L	0.556	1.00
95_D	313_A	0.556	1.00
354_L	357_R	0.555	1.00
131_L	150_G	0.554	1.00
33_Q	62_A	0.553	1.00
37_F	67_I	0.551	1.00
53_V	319_F	0.551	1.00
162_T	165_P	0.550	1.00
314_K	317_A	0.550	1.00
177_K	233_V	0.549	1.00
151_A	299_H	0.549	1.00
243_K	246_P	0.549	1.00
108_K	111_N	0.548	1.00
24_Q	27_K	0.547	1.00
323_P	326_Q	0.543	1.00
213_E	216_D	0.540	1.00
183_V	190_D	0.539	1.00
223_V	227_L	0.537	1.00
117_W	120_T	0.536	1.00
348_D	353_S	0.536	1.00
149_G	299_H	0.536	1.00
16_L	22_D	0.536	1.00
33_Q	63_I	0.535	1.00
162_T	262_R	0.535	1.00
37_F	54_S	0.534	1.00
76_A	97_L	0.533	1.00
180_P	237_Y	0.528	1.00
19_H	24_Q	0.527	1.00
68_V	83_E	0.526	1.00
166_P	175_F	0.522	1.00
152_Q	268_N	0.522	1.00
198_E	201_L	0.522	1.00
122_P	318_N	0.520	1.00
326_Q	341_L	0.520	1.00
214_A	217_D	0.519	1.00
126_Y	131_L	0.519	1.00
17_A	23_W	0.519	1.00
186_P	190_D	0.518	1.00
194_T	198_E	0.517	1.00
37_F	98_W	0.516	1.00
327_L	347_P	0.515	1.00
218_A	224_T	0.515	1.00
35_V	95_D	0.515	1.00
126_Y	130_Q	0.513	1.00
335_W	340_V	0.511	1.00
54_S	64_N	0.510	1.00
342_D	346_L	0.509	1.00
121_L	318_N	0.508	1.00
116_G	303_I	0.506	1.00
33_Q	36_W	0.506	1.00
126_Y	132_P	0.504	1.00
184_T	190_D	0.503	1.00
171_A	176_A	0.502	1.00
252_M	261_L	0.502	1.00
105_R	108_K	0.502	1.00
192_T	196_F	0.502	1.00
117_W	138_S	0.501	1.00
116_G	314_K	0.500	1.00
112_L	115_T	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
3uorA	1	0.8763	100	0.21	Contact Map
4r2fA	1	0.8737	100	0.214	Contact Map
2zyoA	1	0.8711	100	0.233	Contact Map
2xd3A	1	0.8557	100	0.24	Contact Map
4mfiA	1	0.8789	100	0.244	Contact Map
4r9fA	1	0.8763	100	0.249	Contact Map
3k01A	1	0.8995	100	0.249	Contact Map
4hw8A	2	0.8608	100	0.25	Contact Map
4r6kA	1	0.8789	100	0.254	Contact Map
3j9pD	4	0	100	0.254	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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