SYW - ECOLI - GREMLIN Contacts

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SYW - Tryptophan--tRNA ligase

UniProt:	P00954	Sequences: MTKPIVFSGAQPSGELTIGNYMGALRQWVNMQDDYHCIYCIVDQHAITVRQDAQKLRKATLDTLALYLACGIDPEKSTIFVQSHVPEHAQLGWALNCYTYFGELSRMTQFKDKSARYAENINAGLFDYPVLMAADILLYQTNLVPVGEDQKQHLELSRDIAQRFNALYGEIFKVPEPFIPKSGARVMSLLEPTKKMSKSDDNRNNVIGLLEDPKSVVKKIKRAVTDSDEPPVVRYDVQNKAGVSNLLDILSAVTGQSIPELEKQFEGKMYGHLKGEVADAVSGMLTELQERYHRFRNDEAFLQQVMKDGAEKASAHASRTLKAVYEAIGFVAKP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11030
Length:	334 (316)
Sequences:	5633 (2802)
Seq/√Len:	157.6

ECOLI - SYW
BACSU - SYW
HALSA - SYY SYW2
SULSO - SYY SYW

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
212_D	215_S	4.548	1.00
140_Q	323_A	3.740	1.00
61_L	303_Q	3.703	1.00
171_I	327_A	3.341	1.00
291_R	294_R	3.293	1.00
87_E	314_S	3.263	1.00
87_E	318_S	3.217	1.00
5_I	36_H	2.999	1.00
38_I	316_H	2.925	1.00
75_E	308_D	2.723	1.00
301_F	304_Q	2.624	1.00
286_T	290_E	2.623	1.00
140_Q	320_T	2.617	1.00
101_F	126_F	2.570	1.00
265_F	276_E	2.487	1.00
33_D	76_K	2.391	1.00
7_F	40_C	2.290	1.00
142_N	173_K	2.270	1.00
283_G	286_T	2.242	1.00
148_E	185_R	2.165	1.00
217_V	221_K	2.158	1.00
38_I	78_T	2.155	1.00
259_P	262_E	2.146	1.00
301_F	305_V	2.120	1.00
211_E	219_K	2.119	1.00
259_P	263_K	2.057	1.00
260_E	264_Q	2.056	1.00
262_E	266_E	2.047	1.00
65_A	296_R	2.036	1.00
105_S	126_F	2.016	1.00
213_P	282_S	1.996	1.00
140_Q	173_K	1.993	1.00
290_E	294_R	1.959	1.00
65_A	302_L	1.957	1.00
94_A	328_I	1.941	1.00
221_K	275_G	1.936	1.00
256_Q	264_Q	1.927	1.00
151_K	177_P	1.894	1.00
256_Q	260_E	1.871	1.00
52_D	55_K	1.852	1.00
36_H	78_T	1.789	1.00
70_C	288_L	1.778	1.00
228_D	240_K	1.773	1.00
257_S	260_E	1.760	1.00
7_F	42_V	1.756	1.00
123_A	127_D	1.742	1.00
308_D	311_E	1.739	1.00
151_K	179_I	1.732	1.00
64_L	306_M	1.728	1.00
91_L	324_V	1.721	1.00
90_Q	325_Y	1.721	1.00
211_E	215_S	1.719	1.00
162_Q	174_V	1.705	1.00
58_K	62_D	1.693	1.00
263_K	266_E	1.675	1.00
217_V	278_A	1.655	1.00
188_S	205_N	1.646	1.00
72_I	77_S	1.640	1.00
213_P	286_T	1.634	1.00
294_R	298_D	1.632	1.00
68_L	295_F	1.629	1.00
220_I	281_V	1.620	1.00
268_K	272_H	1.617	1.00
137_L	161_A	1.613	1.00
216_V	282_S	1.613	1.00
104_L	123_A	1.586	1.00
80_F	139_Y	1.584	1.00
315_A	319_R	1.566	1.00
94_A	324_V	1.559	1.00
298_D	301_F	1.534	1.00
304_Q	308_D	1.512	1.00
289_Q	293_H	1.511	1.00
30_N	34_D	1.507	1.00
318_S	322_K	1.505	1.00
31_M	178_F	1.476	1.00
29_V	33_D	1.473	1.00
4_P	142_N	1.471	1.00
41_I	64_L	1.469	1.00
208_G	211_E	1.455	1.00
247_L	261_L	1.455	1.00
84_H	310_A	1.447	1.00
10_A	67_Y	1.416	1.00
55_K	58_K	1.411	1.00
66_L	292_Y	1.405	1.00
101_F	105_S	1.405	1.00
88_H	139_Y	1.403	1.00
133_A	157_S	1.398	1.00
143_L	178_F	1.391	1.00
64_L	302_L	1.390	1.00
204_N	222_R	1.388	1.00
308_D	312_K	1.368	1.00
307_K	311_E	1.366	1.00
300_A	304_Q	1.360	1.00
96_N	127_D	1.352	1.00
272_H	275_G	1.341	1.00
258_I	262_E	1.316	1.00
188_S	200_D	1.309	1.00
12_P	41_I	1.308	1.00
60_T	81_V	1.302	1.00
217_V	279_D	1.301	1.00
27_Q	30_N	1.297	1.00
278_A	282_S	1.290	1.00
264_Q	276_E	1.285	1.00
26_R	30_N	1.284	1.00
320_T	324_V	1.271	1.00
236_D	239_N	1.271	1.00
264_Q	269_M	1.270	1.00
247_L	258_I	1.266	1.00
55_K	59_A	1.261	1.00
322_K	326_E	1.260	1.00
44_Q	89_A	1.257	1.00
253_V	280_A	1.249	1.00
263_K	267_G	1.247	1.00
26_R	284_M	1.232	1.00
257_S	276_E	1.231	1.00
260_E	263_K	1.228	1.00
100_Y	103_E	1.228	1.00
279_D	283_G	1.210	1.00
250_L	277_V	1.205	1.00
213_P	289_Q	1.185	1.00
61_L	299_E	1.184	1.00
277_V	280_A	1.179	1.00
5_I	38_I	1.178	1.00
73_D	76_K	1.174	1.00
292_Y	296_R	1.160	1.00
158_R	175_P	1.155	1.00
5_I	316_H	1.151	1.00
16_L	67_Y	1.147	1.00
92_G	96_N	1.143	1.00
101_F	110_F	1.142	1.00
235_Y	244_S	1.141	1.00
293_H	296_R	1.136	1.00
25_L	70_C	1.136	1.00
43_D	83_S	1.133	1.00
261_L	265_F	1.132	1.00
62_D	296_R	1.128	1.00
21_Y	26_R	1.126	1.00
43_D	84_H	1.124	1.00
108_T	112_D	1.124	1.00
216_V	285_L	1.123	1.00
314_S	318_S	1.123	1.00
319_R	322_K	1.118	1.00
298_D	304_Q	1.112	1.00
10_A	25_L	1.111	1.00
233_V	236_D	1.105	1.00
311_E	315_A	1.093	0.99
54_Q	58_K	1.087	0.99
7_F	38_I	1.087	0.99
94_A	325_Y	1.085	0.99
217_V	282_S	1.084	0.99
8_S	23_G	1.079	0.99
321_L	325_Y	1.070	0.99
240_K	243_V	1.060	0.99
36_H	312_K	1.052	0.99
214_K	217_V	1.039	0.99
7_F	141_T	1.038	0.99
9_G	40_C	1.038	0.99
68_L	305_V	1.034	0.99
88_H	91_L	1.031	0.99
102_G	106_R	1.028	0.99
207_I	220_I	1.014	0.99
32_Q	77_S	1.014	0.99
236_D	244_S	1.014	0.99
99_T	160_I	1.009	0.99
22_M	252_A	1.007	0.99
86_P	90_Q	1.006	0.99
255_G	264_Q	1.004	0.99
194_K	200_D	0.998	0.99
22_M	253_V	0.997	0.99
63_T	67_Y	0.984	0.99
4_P	143_L	0.980	0.99
218_K	222_R	0.978	0.99
192_P	242_G	0.975	0.99
4_P	35_Y	0.975	0.99
265_F	273_L	0.968	0.99
162_Q	166_A	0.956	0.99
78_T	312_K	0.954	0.99
16_L	63_T	0.953	0.99
215_S	218_K	0.945	0.98
136_I	157_S	0.939	0.98
187_M	245_N	0.937	0.98
123_A	130_V	0.935	0.98
163_R	167_L	0.931	0.98
244_S	265_F	0.923	0.98
10_A	28_W	0.921	0.98
43_D	60_T	0.921	0.98
180_P	184_A	0.920	0.98
276_E	280_A	0.919	0.98
172_F	324_V	0.916	0.98
254_T	280_A	0.910	0.98
253_V	284_M	0.910	0.98
209_L	285_L	0.907	0.98
319_R	323_A	0.901	0.98
10_A	23_G	0.899	0.98
87_E	317_A	0.899	0.98
212_D	293_H	0.898	0.98
12_P	46_A	0.892	0.98
62_D	292_Y	0.889	0.98
104_L	130_V	0.889	0.98
247_L	262_E	0.885	0.98
8_S	28_W	0.880	0.98
221_K	278_A	0.874	0.97
323_A	327_A	0.870	0.97
234_R	239_N	0.868	0.97
4_P	34_D	0.866	0.97
15_E	59_A	0.865	0.97
293_H	297_N	0.860	0.97
200_D	205_N	0.857	0.97
323_A	326_E	0.853	0.97
161_A	174_V	0.850	0.97
320_T	323_A	0.843	0.97
18_I	253_V	0.840	0.97
96_N	123_A	0.839	0.97
95_L	137_L	0.837	0.97
311_E	314_S	0.836	0.97
28_W	39_Y	0.821	0.96
154_L	177_P	0.819	0.96
290_E	293_H	0.819	0.96
91_L	134_A	0.811	0.96
6_V	143_L	0.808	0.96
80_F	84_H	0.805	0.96
256_Q	261_L	0.801	0.96
208_G	219_K	0.800	0.96
217_V	275_G	0.799	0.96
81_V	84_H	0.798	0.96
264_Q	267_G	0.791	0.95
171_I	324_V	0.787	0.95
275_G	279_D	0.786	0.95
75_E	312_K	0.784	0.95
271_G	275_G	0.777	0.95
238_Q	244_S	0.776	0.95
161_A	165_N	0.774	0.95
254_T	257_S	0.774	0.95
169_G	327_A	0.771	0.95
66_L	210_L	0.766	0.95
251_S	261_L	0.764	0.94
189_L	219_K	0.761	0.94
6_V	35_Y	0.761	0.94
20_N	24_A	0.757	0.94
164_F	168_Y	0.757	0.94
300_A	315_A	0.753	0.94
287_E	290_E	0.753	0.94
9_G	42_V	0.752	0.94
282_S	289_Q	0.751	0.94
159_D	162_Q	0.750	0.94
300_A	303_Q	0.750	0.94
78_T	81_V	0.749	0.94
282_S	286_T	0.749	0.94
97_C	124_G	0.747	0.94
250_L	280_A	0.746	0.94
81_V	306_M	0.744	0.94
54_Q	57_R	0.744	0.94
234_R	262_E	0.743	0.94
130_V	160_I	0.741	0.94
204_N	218_K	0.740	0.94
315_A	318_S	0.740	0.94
280_A	283_G	0.736	0.93
213_P	217_V	0.735	0.93
296_R	302_L	0.733	0.93
241_A	244_S	0.732	0.93
270_Y	273_L	0.731	0.93
133_A	160_I	0.729	0.93
294_R	297_N	0.729	0.93
317_A	320_T	0.727	0.93
220_I	277_V	0.727	0.93
295_F	301_F	0.724	0.93
95_L	130_V	0.721	0.93
78_T	316_H	0.720	0.93
213_P	285_L	0.719	0.93
272_H	276_E	0.717	0.92
242_G	262_E	0.716	0.92
85_V	317_A	0.715	0.92
280_A	284_M	0.714	0.92
133_A	137_L	0.704	0.92
241_A	266_E	0.704	0.92
28_W	67_Y	0.701	0.92
234_R	237_V	0.701	0.92
233_V	237_V	0.701	0.92
264_Q	270_Y	0.697	0.91
117_Y	120_N	0.696	0.91
100_Y	122_N	0.696	0.91
303_Q	307_K	0.695	0.91
138_L	321_L	0.692	0.91
225_T	246_L	0.690	0.91
180_P	183_G	0.689	0.91
88_H	138_L	0.688	0.91
164_F	171_I	0.685	0.91
56_L	60_T	0.682	0.90
304_Q	307_K	0.682	0.90
61_L	302_L	0.682	0.90
209_L	288_L	0.680	0.90
287_E	291_R	0.679	0.90
86_P	321_L	0.679	0.90
251_S	258_I	0.675	0.90
110_F	114_S	0.675	0.90
210_L	292_Y	0.672	0.90
240_K	244_S	0.671	0.90
56_L	59_A	0.670	0.90
80_F	88_H	0.666	0.89
315_A	323_A	0.664	0.89
189_L	222_R	0.663	0.89
40_C	80_F	0.663	0.89
11_Q	49_V	0.663	0.89
214_K	218_K	0.662	0.89
142_N	176_E	0.662	0.89
242_G	277_V	0.659	0.89
31_M	143_L	0.657	0.89
299_E	302_L	0.654	0.89
164_F	328_I	0.648	0.88
98_Y	328_I	0.647	0.88
15_E	210_L	0.646	0.88
47_I	51_Q	0.645	0.88
234_R	244_S	0.645	0.88
67_Y	79_I	0.645	0.88
189_L	223_A	0.645	0.88
279_D	282_S	0.644	0.88
95_L	160_I	0.643	0.88
36_H	316_H	0.643	0.88
15_E	62_D	0.642	0.88
247_L	273_L	0.642	0.88
35_Y	143_L	0.640	0.87
38_I	80_F	0.640	0.87
295_F	299_E	0.639	0.87
229_E	269_M	0.638	0.87
96_N	122_N	0.637	0.87
250_L	273_L	0.636	0.87
65_A	68_L	0.636	0.87
24_A	28_W	0.635	0.87
8_S	39_Y	0.635	0.87
294_R	301_F	0.635	0.87
186_V	252_A	0.633	0.87
304_Q	311_E	0.633	0.87
282_S	285_L	0.628	0.86
108_T	152_Q	0.628	0.86
98_Y	167_L	0.628	0.86
248_D	251_S	0.628	0.86
96_N	130_V	0.628	0.86
18_I	281_V	0.627	0.86
30_N	33_D	0.626	0.86
196_M	199_S	0.626	0.86
318_S	321_L	0.624	0.86
316_H	320_T	0.624	0.86
59_A	62_D	0.624	0.86
92_G	127_D	0.622	0.86
98_Y	160_I	0.622	0.86
265_F	268_K	0.621	0.86
321_L	324_V	0.621	0.86
170_E	173_K	0.620	0.86
102_G	108_T	0.620	0.86
295_F	298_D	0.618	0.86
237_V	244_S	0.616	0.85
31_M	37_C	0.616	0.85
311_E	322_K	0.614	0.85
11_Q	63_T	0.614	0.85
53_A	56_L	0.608	0.85
226_D	229_E	0.606	0.84
85_V	310_A	0.605	0.84
316_H	319_R	0.605	0.84
64_L	79_I	0.605	0.84
239_N	244_S	0.604	0.84
29_V	32_Q	0.604	0.84
103_E	163_R	0.604	0.84
257_S	280_A	0.603	0.84
310_A	314_S	0.603	0.84
275_G	278_A	0.602	0.84
312_K	315_A	0.602	0.84
161_A	172_F	0.600	0.84
57_R	61_L	0.599	0.84
45_H	131_L	0.598	0.84
285_L	289_Q	0.598	0.84
67_Y	70_C	0.598	0.84
103_E	159_D	0.598	0.84
74_P	305_V	0.597	0.84
93_W	97_C	0.596	0.83
320_T	327_A	0.594	0.83
157_S	175_P	0.594	0.83
144_V	154_L	0.593	0.83
57_R	60_T	0.591	0.83
304_Q	315_A	0.591	0.83
324_V	327_A	0.587	0.83
255_G	259_P	0.585	0.82
15_E	208_G	0.583	0.82
156_L	160_I	0.583	0.82
103_E	106_R	0.583	0.82
62_D	65_A	0.583	0.82
27_Q	180_P	0.582	0.82
224_V	242_G	0.581	0.82
78_T	313_A	0.579	0.82
307_K	318_S	0.578	0.82
168_Y	328_I	0.578	0.82
171_I	320_T	0.578	0.82
11_Q	20_N	0.576	0.81
191_E	194_K	0.576	0.81
299_E	303_Q	0.573	0.81
85_V	88_H	0.572	0.81
47_I	57_R	0.572	0.81
10_A	16_L	0.571	0.81
286_T	289_Q	0.571	0.81
65_A	292_Y	0.570	0.81
16_L	66_L	0.567	0.80
187_M	248_D	0.564	0.80
64_L	67_Y	0.564	0.80
164_F	324_V	0.564	0.80
173_K	323_A	0.563	0.80
245_N	248_D	0.563	0.80
13_S	51_Q	0.562	0.80
269_M	272_H	0.561	0.80
138_L	317_A	0.560	0.80
241_A	262_E	0.559	0.79
217_V	220_I	0.557	0.79
213_P	216_V	0.553	0.79
246_L	273_L	0.553	0.79
44_Q	94_A	0.552	0.79
84_H	307_K	0.551	0.78
309_G	313_A	0.551	0.78
148_E	181_K	0.550	0.78
21_Y	284_M	0.548	0.78
92_G	130_V	0.547	0.78
127_D	130_V	0.546	0.78
192_P	277_V	0.545	0.78
123_A	126_F	0.544	0.78
314_S	317_A	0.544	0.78
245_N	249_I	0.544	0.78
16_L	20_N	0.543	0.77
114_S	117_Y	0.543	0.77
25_L	77_S	0.542	0.77
39_Y	77_S	0.542	0.77
107_M	152_Q	0.542	0.77
109_Q	113_K	0.541	0.77
109_Q	152_Q	0.540	0.77
143_L	176_E	0.540	0.77
281_V	284_M	0.537	0.77
220_I	278_A	0.536	0.77
47_I	94_A	0.535	0.76
250_L	276_E	0.532	0.76
110_F	113_K	0.530	0.76
244_S	273_L	0.530	0.76
158_R	176_E	0.529	0.76
306_M	310_A	0.528	0.75
4_P	176_E	0.528	0.75
16_L	25_L	0.527	0.75
297_N	300_A	0.527	0.75
50_R	167_L	0.526	0.75
96_N	120_N	0.522	0.75
35_Y	142_N	0.522	0.75
307_K	315_A	0.521	0.75
300_A	311_E	0.521	0.75
243_V	262_E	0.520	0.74
164_F	172_F	0.520	0.74
107_M	156_L	0.517	0.74
235_Y	248_D	0.517	0.74
99_T	156_L	0.515	0.74
213_P	278_A	0.515	0.74
92_G	95_L	0.515	0.74
98_Y	164_F	0.514	0.74
127_D	131_L	0.513	0.73
39_Y	72_I	0.512	0.73
212_D	216_V	0.512	0.73
224_V	227_S	0.512	0.73
140_Q	316_H	0.512	0.73
256_Q	259_P	0.511	0.73
11_Q	113_K	0.511	0.73
311_E	318_S	0.510	0.73
92_G	123_A	0.508	0.73
40_C	141_T	0.508	0.73
88_H	93_W	0.508	0.73
291_R	295_F	0.508	0.73
90_Q	321_L	0.507	0.73
244_S	258_I	0.507	0.73
95_L	173_K	0.503	0.72
85_V	138_L	0.503	0.72
250_L	265_F	0.502	0.72
250_L	261_L	0.501	0.72
228_D	234_R	0.500	0.72

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
3n9iA	2	0.994	100	0.115	Contact Map
2yy5A	2	0.985	100	0.126	Contact Map
3sz3A	2	1	100	0.136	Contact Map
3prhA	2	0.9461	100	0.138	Contact Map
1i6kA	2	0.976	100	0.142	Contact Map
2el7A	2	0.9281	100	0.222	Contact Map
2g36A	2	0.9461	100	0.248	Contact Map
3tzlA	2	0.9461	100	0.25	Contact Map
1yi8B	2	0.9701	100	0.251	Contact Map
2dlcX	2	0.8353	100	0.299	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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