SYW - BACSU - GREMLIN Contacts

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SYW - Tryptophan--tRNA ligase

UniProt:	P21656	Sequences: MKQTIFSGIQPSGSVTLGNYIGAMKQFVELQHDYNSYFCIVDQHAITVPQDRLELRKNIRNLAALYLAVGLDPEKATLFIQSEVPAHAQAGWMMQCVAYIGELERMTQFKDKSKGNEAVVSGLLTYPPLMAADILLYGTDLVPVGEDQKQHLELTRNLAERFNKKYNDIFTIPEVKIPKVGARIMSLNDPLKKMSKSDPNQKAYITLLDEPKQLEKKIKSAVTDSEGIVKFDKENKPGVSNLLTIYSILGNTTIEELEAKYEGKGYGEFKGDLAEVVVNALKPIQDRYYELIESEELDRILDEGAERANRTANKMLKKMENAMGLGRKRR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	330 (299)
Sequences:	5845 (2881)
Seq/√Len:	166.6

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
210_E	213_Q	4.811	1.00
60_R	298_D	3.911	1.00
86_A	309_N	3.669	1.00
287_R	290_E	3.416	1.00
4_T	35_N	3.245	1.00
282_K	286_D	2.781	1.00
296_E	299_R	2.694	1.00
74_E	303_E	2.691	1.00
261_Y	272_D	2.621	1.00
100_I	124_L	2.617	1.00
37_Y	77_T	2.525	1.00
256_E	260_K	2.466	1.00
32_H	75_K	2.403	1.00
6_F	39_C	2.400	1.00
140_D	171_T	2.387	1.00
279_N	282_K	2.354	1.00
51_D	54_E	2.325	1.00
258_E	262_E	2.313	1.00
296_E	300_I	2.308	1.00
138_G	171_T	2.298	1.00
146_E	183_R	2.295	1.00
209_D	217_K	2.283	1.00
215_E	219_K	2.243	1.00
255_E	258_E	2.201	1.00
255_E	259_A	2.192	1.00
35_N	77_T	2.170	1.00
64_A	292_I	2.120	1.00
211_P	278_V	2.090	1.00
219_K	271_G	2.088	1.00
104_E	124_L	2.081	1.00
149_K	175_V	2.074	1.00
64_A	297_L	2.039	1.00
267_G	271_G	1.997	1.00
57_K	61_N	1.994	1.00
253_T	256_E	1.993	1.00
252_T	256_E	1.962	1.00
286_D	290_E	1.944	1.00
252_T	260_K	1.937	1.00
226_E	236_K	1.888	1.00
149_K	177_I	1.846	1.00
259_A	262_E	1.839	1.00
218_I	277_V	1.838	1.00
209_D	213_Q	1.815	1.00
121_S	125_T	1.812	1.00
6_F	41_V	1.797	1.00
160_E	172_I	1.784	1.00
69_V	284_I	1.761	1.00
215_E	274_A	1.758	1.00
303_E	306_E	1.753	1.00
63_A	301_L	1.751	1.00
211_P	282_K	1.702	1.00
290_E	294_S	1.695	1.00
264_K	268_E	1.683	1.00
135_L	159_A	1.676	1.00
54_E	57_K	1.668	1.00
71_L	76_A	1.663	1.00
79_F	137_Y	1.660	1.00
28_V	32_H	1.639	1.00
214_L	278_V	1.625	1.00
67_L	291_L	1.619	1.00
103_L	121_S	1.600	1.00
29_E	33_D	1.595	1.00
206_T	209_D	1.594	1.00
299_R	303_E	1.570	1.00
87_H	90_A	1.548	1.00
9_I	66_Y	1.547	1.00
54_E	58_N	1.542	1.00
285_Q	289_Y	1.542	1.00
95_Q	125_T	1.518	1.00
243_L	257_L	1.518	1.00
259_A	263_G	1.511	1.00
40_I	63_A	1.509	1.00
63_A	297_L	1.498	1.00
7_S	22_G	1.490	1.00
25_K	280_A	1.483	1.00
100_I	104_E	1.467	1.00
83_E	305_A	1.465	1.00
4_T	37_Y	1.456	1.00
232_D	240_S	1.451	1.00
65_L	288_Y	1.439	1.00
131_A	155_T	1.429	1.00
260_K	272_D	1.427	1.00
302_D	306_E	1.426	1.00
11_P	40_I	1.408	1.00
253_T	272_D	1.405	1.00
268_E	271_G	1.405	1.00
303_E	307_R	1.387	1.00
30_L	176_K	1.361	1.00
274_A	278_V	1.359	1.00
26_Q	29_E	1.357	1.00
87_H	137_Y	1.357	1.00
42_D	82_S	1.355	1.00
295_E	299_R	1.349	1.00
254_I	258_E	1.329	1.00
215_E	275_E	1.307	1.00
59_I	80_I	1.305	1.00
256_E	259_A	1.304	1.00
257_L	261_Y	1.303	1.00
186_S	198_D	1.301	1.00
249_L	276_V	1.289	1.00
25_K	29_E	1.286	1.00
43_Q	88_A	1.285	1.00
99_Y	102_E	1.284	1.00
243_L	254_I	1.284	1.00
141_L	176_K	1.265	1.00
211_P	285_Q	1.259	1.00
53_L	57_K	1.242	1.00
72_D	75_K	1.233	1.00
42_D	83_E	1.229	1.00
214_L	281_L	1.224	1.00
246_Y	273_L	1.222	1.00
79_F	83_E	1.221	1.00
288_Y	292_I	1.218	1.00
192_K	198_D	1.210	1.00
61_N	292_I	1.207	1.00
275_E	279_N	1.203	1.00
289_Y	292_I	1.191	1.00
100_I	109_F	1.176	1.00
294_S	299_R	1.168	1.00
156_R	173_P	1.166	1.00
6_F	37_Y	1.165	1.00
236_K	239_V	1.149	1.00
273_L	276_V	1.140	1.00
35_N	307_R	1.134	1.00
9_I	24_M	1.130	1.00
91_G	95_Q	1.128	1.00
205_I	218_I	1.121	1.00
62_L	66_Y	1.116	1.00
306_E	310_R	1.111	1.00
20_Y	25_K	1.106	1.00
213_Q	216_K	1.103	1.00
216_K	220_S	1.101	1.00
15_V	66_Y	1.097	1.00
8_G	39_C	1.083	1.00
212_K	215_E	1.080	1.00
6_F	139_T	1.076	1.00
107_T	111_D	1.074	1.00
230_K	258_E	1.070	1.00
215_E	278_V	1.063	0.99
85_P	89_Q	1.061	0.99
31_Q	76_A	1.053	0.99
24_M	69_V	1.045	0.99
15_V	62_L	1.019	0.99
251_N	260_K	1.018	0.99
272_D	276_V	1.014	0.99
261_Y	269_F	1.012	0.99
101_G	105_R	1.006	0.99
21_I	249_L	1.004	0.99
98_A	158_L	1.003	0.99
188_N	200_N	1.002	0.99
21_I	248_I	0.997	0.99
160_E	164_K	0.992	0.99
58_N	61_N	0.987	0.99
9_I	22_G	0.986	0.99
219_K	267_G	0.980	0.99
249_L	280_A	0.975	0.99
113_S	116_N	0.974	0.99
67_L	300_I	0.970	0.99
64_A	67_L	0.964	0.99
77_T	307_R	0.952	0.99
134_I	155_T	0.950	0.99
271_G	275_E	0.949	0.99
210_E	289_Y	0.945	0.99
250_G	276_V	0.938	0.99
55_L	59_I	0.936	0.99
215_E	271_G	0.934	0.99
219_K	274_A	0.928	0.99
9_I	27_F	0.927	0.99
5_I	141_L	0.924	0.99
11_P	45_A	0.923	0.99
55_L	58_N	0.920	0.98
7_S	27_F	0.920	0.98
306_E	309_N	0.917	0.98
61_N	288_Y	0.908	0.98
188_N	198_D	0.906	0.98
265_G	268_E	0.905	0.98
260_K	263_G	0.903	0.98
234_E	240_S	0.893	0.98
131_A	158_L	0.892	0.98
103_L	128_P	0.890	0.98
159_A	172_I	0.887	0.98
289_Y	293_E	0.885	0.98
187_L	217_K	0.884	0.98
121_S	128_P	0.883	0.98
157_N	160_E	0.882	0.98
286_D	289_Y	0.874	0.98
206_T	217_K	0.871	0.98
231_F	240_S	0.867	0.98
94_M	135_L	0.859	0.98
90_A	132_A	0.858	0.98
207_L	281_L	0.858	0.98
261_Y	266_Y	0.854	0.98
80_I	83_E	0.854	0.98
218_I	273_L	0.843	0.97
278_V	282_K	0.842	0.97
161_R	165_K	0.842	0.97
52_R	55_L	0.841	0.97
37_Y	79_F	0.835	0.97
185_M	228_I	0.835	0.97
27_F	38_F	0.834	0.97
243_L	258_E	0.834	0.97
8_G	41_V	0.829	0.97
53_L	56_R	0.829	0.97
211_P	215_E	0.827	0.97
291_L	294_S	0.825	0.97
295_E	310_R	0.822	0.97
276_V	279_N	0.820	0.97
227_G	265_G	0.813	0.97
17_L	249_L	0.811	0.97
42_D	59_I	0.805	0.96
278_V	285_Q	0.804	0.96
236_K	240_S	0.802	0.96
237_P	240_S	0.797	0.96
5_I	34_Y	0.794	0.96
77_T	80_I	0.791	0.96
292_I	297_L	0.790	0.96
96_C	122_G	0.790	0.96
230_K	233_K	0.787	0.96
66_Y	69_V	0.787	0.96
283_P	286_D	0.786	0.96
238_G	273_L	0.777	0.96
178_P	182_A	0.773	0.96
95_Q	121_S	0.771	0.96
162_F	166_Y	0.770	0.95
276_V	280_A	0.769	0.95
56_R	59_I	0.768	0.95
140_D	174_E	0.767	0.95
291_L	296_E	0.765	0.95
237_P	262_E	0.765	0.95
128_P	158_L	0.763	0.95
187_L	221_A	0.761	0.95
240_S	261_Y	0.758	0.95
298_D	302_D	0.756	0.95
246_Y	276_V	0.756	0.95
252_T	257_L	0.756	0.95
98_A	154_L	0.755	0.95
238_G	258_E	0.754	0.95
65_L	208_L	0.754	0.95
80_I	301_L	0.752	0.95
30_L	141_L	0.751	0.95
268_E	272_D	0.751	0.95
74_E	307_R	0.751	0.95
62_L	65_L	0.751	0.95
212_K	216_K	0.751	0.95
94_M	128_P	0.744	0.95
250_G	253_T	0.743	0.95
290_E	293_E	0.742	0.94
14_S	206_T	0.736	0.94
152_L	175_V	0.735	0.94
299_R	302_D	0.735	0.94
247_S	254_I	0.734	0.94
131_A	135_L	0.731	0.94
307_R	310_R	0.728	0.94
247_S	257_L	0.726	0.94
61_N	64_A	0.726	0.94
290_E	296_E	0.724	0.94
27_F	66_Y	0.722	0.94
159_A	163_N	0.721	0.94
34_Y	141_L	0.711	0.93
99_Y	120_V	0.710	0.93
17_L	277_V	0.708	0.93
39_C	79_F	0.707	0.93
208_L	288_Y	0.707	0.93
19_N	23_A	0.706	0.93
97_V	165_K	0.706	0.93
299_R	306_E	0.704	0.93
244_T	247_S	0.703	0.93
283_P	287_R	0.702	0.93
14_S	208_L	0.702	0.93
278_V	281_L	0.699	0.93
211_P	281_L	0.695	0.92
95_Q	128_P	0.694	0.92
295_E	298_D	0.693	0.92
56_R	60_R	0.693	0.92
243_L	269_F	0.690	0.92
207_L	284_I	0.682	0.92
223_T	242_L	0.681	0.92
299_R	310_R	0.677	0.91
230_K	240_S	0.672	0.91
222_V	238_G	0.670	0.91
187_L	220_S	0.670	0.91
10_Q	48_V	0.668	0.91
226_E	230_K	0.668	0.91
7_S	38_F	0.667	0.91
275_E	278_V	0.667	0.91
30_L	36_S	0.662	0.90
91_G	125_T	0.662	0.90
102_E	105_R	0.661	0.90
87_H	136_L	0.657	0.90
266_Y	269_F	0.655	0.90
242_L	269_F	0.654	0.90
46_I	50_Q	0.649	0.89
159_A	170_F	0.645	0.89
88_A	91_G	0.645	0.89
162_F	169_I	0.643	0.89
305_A	309_N	0.642	0.89
271_G	274_A	0.642	0.89
231_F	244_T	0.641	0.89
114_K	118_A	0.640	0.89
60_R	297_L	0.636	0.89
97_V	161_R	0.635	0.88
178_P	181_G	0.634	0.88
57_K	60_R	0.633	0.88
23_A	27_F	0.633	0.88
28_V	31_Q	0.629	0.88
156_R	174_E	0.627	0.88
94_M	158_L	0.626	0.88
237_P	258_E	0.626	0.88
233_K	240_S	0.623	0.88
302_D	310_R	0.623	0.88
51_D	59_I	0.622	0.87
231_F	234_E	0.622	0.87
91_G	128_P	0.620	0.87
251_N	255_E	0.619	0.87
10_Q	62_L	0.618	0.87
63_A	66_Y	0.617	0.87
14_S	61_N	0.616	0.87
115_G	118_A	0.615	0.87
94_M	132_A	0.613	0.87
79_F	87_H	0.612	0.87
85_P	129_L	0.610	0.86
272_D	275_E	0.610	0.86
253_T	276_V	0.610	0.86
66_Y	78_L	0.610	0.86
44_H	129_L	0.607	0.86
281_L	285_Q	0.606	0.86
304_G	308_A	0.606	0.86
4_T	138_G	0.605	0.86
240_S	266_Y	0.604	0.86
107_T	150_Q	0.604	0.86
185_M	244_T	0.604	0.86
97_V	162_F	0.604	0.86
116_N	119_V	0.603	0.86
261_Y	264_K	0.601	0.86
109_F	113_S	0.599	0.85
142_V	152_L	0.598	0.85
260_K	269_F	0.598	0.85
77_T	308_A	0.597	0.85
226_E	265_G	0.595	0.85
227_G	261_Y	0.593	0.85
29_E	32_H	0.592	0.85
167_N	174_E	0.592	0.85
43_Q	93_M	0.591	0.85
185_M	241_N	0.591	0.85
97_V	158_L	0.590	0.85
15_V	65_L	0.589	0.84
282_K	285_Q	0.589	0.84
121_S	124_L	0.589	0.84
138_G	169_I	0.587	0.84
194_M	197_S	0.587	0.84
92_W	96_C	0.586	0.84
102_E	161_R	0.583	0.84
246_Y	269_F	0.582	0.84
255_E	262_E	0.580	0.84
168_D	171_T	0.579	0.83
73_P	300_I	0.578	0.83
95_Q	120_V	0.578	0.83
147_D	193_K	0.577	0.83
94_M	171_T	0.577	0.83
290_E	295_E	0.577	0.83
92_W	122_G	0.576	0.83
162_F	170_F	0.575	0.83
67_L	78_L	0.575	0.83
101_G	107_T	0.573	0.83
125_T	128_P	0.572	0.83
141_L	174_E	0.571	0.83
20_Y	280_A	0.571	0.83
84_V	305_A	0.570	0.83
301_L	305_A	0.570	0.83
51_D	58_N	0.566	0.82
9_I	15_V	0.566	0.82
64_A	288_Y	0.566	0.82
154_L	158_L	0.559	0.81
46_I	93_M	0.558	0.81
230_K	236_K	0.557	0.81
115_G	119_V	0.557	0.81
102_E	157_N	0.556	0.81
110_K	114_K	0.554	0.81
15_V	19_N	0.553	0.81
109_F	112_K	0.551	0.80
302_D	305_A	0.550	0.80
211_P	274_A	0.548	0.80
10_Q	19_N	0.547	0.80
83_E	302_D	0.547	0.80
113_S	119_V	0.546	0.80
34_Y	140_D	0.545	0.80
215_E	218_I	0.545	0.80
211_P	214_L	0.544	0.80
39_C	139_T	0.543	0.79
113_S	123_L	0.543	0.79
26_Q	178_P	0.542	0.79
246_Y	272_D	0.540	0.79
240_S	254_I	0.539	0.79
58_N	65_L	0.538	0.79
58_N	62_L	0.537	0.79
57_K	310_R	0.537	0.79
38_F	76_A	0.532	0.78
106_M	150_Q	0.531	0.78
49_P	165_K	0.531	0.78
97_V	166_Y	0.530	0.78
39_C	133_D	0.530	0.78
52_R	56_R	0.529	0.78
14_S	58_N	0.529	0.78
91_G	121_S	0.529	0.78
38_F	71_L	0.529	0.78
184_I	248_I	0.528	0.77
98_A	102_E	0.524	0.77
87_H	92_W	0.524	0.77
84_V	136_L	0.524	0.77
199_P	204_Y	0.524	0.77
209_D	214_L	0.524	0.77
252_T	255_E	0.523	0.77
265_G	269_F	0.523	0.77
135_L	170_F	0.522	0.77
36_S	76_A	0.521	0.77
106_M	154_L	0.520	0.76
218_I	274_A	0.520	0.76
287_R	291_L	0.518	0.76
15_V	24_M	0.517	0.76
10_Q	112_K	0.517	0.76
154_L	157_N	0.516	0.76
166_Y	173_P	0.515	0.76
295_E	306_E	0.515	0.76
226_E	264_K	0.515	0.76
155_T	173_P	0.514	0.76
39_C	137_Y	0.512	0.75
239_V	258_E	0.512	0.75
108_Q	112_K	0.512	0.75
225_S	266_Y	0.511	0.75
7_S	23_A	0.510	0.75
51_D	55_L	0.509	0.75
183_R	192_K	0.509	0.75
95_Q	118_A	0.508	0.75
186_S	189_D	0.507	0.75
257_L	272_D	0.507	0.75
251_N	254_I	0.506	0.74
84_V	87_H	0.506	0.74
212_K	267_G	0.506	0.74
277_V	280_A	0.506	0.74
210_E	285_Q	0.506	0.74
216_K	267_G	0.505	0.74
228_I	263_G	0.505	0.74
47_T	126_Y	0.504	0.74
227_G	231_F	0.504	0.74
136_L	139_T	0.503	0.74
88_A	92_W	0.502	0.74
214_L	283_P	0.500	0.74
90_A	93_M	0.500	0.74

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
2yy5A	2	0.997	100	0.13	Contact Map
3prhA	2	0.9576	100	0.142	Contact Map
1i6kA	2	0.9879	100	0.146	Contact Map
3n9iA	2	0.9909	100	0.152	Contact Map
3sz3A	2	0.997	100	0.17	Contact Map
2el7A	2	0.9333	100	0.23	Contact Map
3tzlA	2	0.9545	100	0.254	Contact Map
2g36A	2	0.9545	100	0.254	Contact Map
1yi8B	2	0.9758	100	0.269	Contact Map
2dlcX	2	0.8394	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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