SYW2 - HALSA - GREMLIN Contacts

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SYW2 - Tryptophan--tRNA ligase 2

UniProt:	Q9HN66	Sequences: MTADGNDVTPYAVESDDLDYEKLLARFGADELTDDQRARFPDHPLVNRGLFYAGRDVDDFLTAGEQSIVTGVGPSGPMHLGHAMVFYFARRLQDEFGARVYVPLSDDEKYWFKDQTPAETGDYLRANLRDLLAVGFDPELTRIVVDTRDADVLYPLATAFAGDVRHATLQNVYGEPDNVGQAFYPAVQTAHLLLPQLVHGEHETLVPIAVDQDPHVRVSRDVAAKARYPVGKPGALLMQFLPSLAGPGKMSSSAGVSIRLTDSPDTVREKVRTHAYTGGRASVEEHRAKGGVPAEDVPFQYLSAFFEPDDAELARIEREYRAGDLLSGELKDLAADRITEFLAAHQRRRAALGDVTEALDAFRLTDDERQRARDAVGFGY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	380 (282)
Sequences:	7049 (3362)
Seq/√Len:	200.2

ECOLI - SYW SYY
BACSU - SYW SYY2 SYY1
HALSA - SYW2 SYY SYW1
SULSO - SYW SYY

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
263_S	266_T	4.283	1.00
125_R	360_D	3.725	1.00
348_R	351_A	3.096	1.00
343_A	347_R	2.591	1.00
358_A	361_A	2.589	1.00
166_H	182_A	2.587	1.00
101_Y	142_R	2.583	1.00
314_A	317_E	2.498	1.00
139_E	365_T	2.487	1.00
320_Y	333_L	2.374	1.00
69_V	103_P	2.295	1.00
315_R	319_E	2.290	1.00
122_D	126_A	2.247	1.00
268_R	272_R	2.225	1.00
116_T	119_E	2.219	1.00
280_R	292_V	2.154	1.00
312_E	315_R	2.141	1.00
170_Q	182_A	2.129	1.00
358_A	362_F	2.121	1.00
340_E	343_A	2.075	1.00
317_E	321_R	2.060	1.00
67_S	99_R	2.049	1.00
318_R	321_R	2.036	1.00
233_P	237_L	2.020	1.00
311_A	315_R	1.936	1.00
314_A	318_R	1.932	1.00
347_R	351_A	1.922	1.00
99_R	142_R	1.907	1.00
230_V	233_P	1.899	1.00
272_R	332_D	1.856	1.00
311_A	319_E	1.854	1.00
129_R	359_L	1.852	1.00
129_R	353_G	1.850	1.00
96_F	140_L	1.841	1.00
262_D	270_K	1.838	1.00
230_V	236_L	1.831	1.00
230_V	234_G	1.795	1.00
264_P	339_T	1.786	1.00
230_V	235_A	1.761	1.00
345_H	349_R	1.759	1.00
210_V	240_F	1.757	1.00
234_G	237_L	1.721	1.00
128_L	363_R	1.719	1.00
69_V	105_S	1.717	1.00
74_P	109_K	1.663	1.00
119_E	122_D	1.657	1.00
179_V	183_F	1.637	1.00
302_L	334_A	1.633	1.00
231_G	237_L	1.606	1.00
318_R	322_A	1.606	1.00
299_F	317_E	1.603	1.00
346_Q	350_A	1.586	1.00
268_R	335_A	1.569	1.00
136_F	141_T	1.566	1.00
116_T	120_T	1.560	1.00
315_R	318_R	1.540	1.00
271_V	338_I	1.538	1.00
166_H	170_Q	1.530	1.00
193_L	223_A	1.523	1.00
223_A	233_P	1.510	1.00
361_A	365_T	1.510	1.00
134_V	345_H	1.508	1.00
312_E	333_L	1.498	1.00
292_V	295_E	1.479	1.00
264_P	343_A	1.461	1.00
351_A	355_V	1.456	1.00
132_L	352_L	1.454	1.00
262_D	266_T	1.451	1.00
243_S	256_V	1.445	1.00
74_P	104_L	1.438	1.00
267_V	339_T	1.436	1.00
161_A	183_F	1.433	1.00
231_G	236_L	1.429	1.00
169_L	179_V	1.426	1.00
303_S	317_E	1.418	1.00
333_L	337_R	1.416	1.00
336_D	340_E	1.398	1.00
355_V	358_A	1.391	1.00
72_V	131_L	1.390	1.00
144_V	195_P	1.378	1.00
148_R	367_D	1.377	1.00
329_E	332_D	1.376	1.00
193_L	226_A	1.373	1.00
357_E	361_A	1.370	1.00
276_Y	292_V	1.356	1.00
313_L	317_E	1.350	1.00
231_G	234_G	1.347	1.00
107_D	154_Y	1.319	1.00
347_R	350_A	1.314	1.00
130_D	349_R	1.313	1.00
288_A	291_G	1.313	1.00
117_P	120_T	1.297	1.00
196_Q	229_P	1.294	1.00
328_G	332_D	1.280	1.00
335_A	339_T	1.279	1.00
88_F	91_R	1.273	1.00
189_T	219_S	1.273	1.00
248_G	254_A	1.270	1.00
90_R	95_E	1.255	1.00
299_F	313_L	1.254	1.00
231_G	235_A	1.249	1.00
128_L	359_L	1.242	1.00
153_L	195_P	1.228	1.00
305_F	337_R	1.219	1.00
319_E	333_L	1.204	1.00
309_D	312_E	1.201	1.00
104_L	128_L	1.200	1.00
118_A	122_D	1.191	1.00
168_T	221_D	1.189	1.00
306_F	337_R	1.189	1.00
165_R	168_T	1.181	1.00
230_V	237_L	1.179	1.00
349_R	353_G	1.178	1.00
66_Q	204_T	1.177	1.00
310_D	314_A	1.177	1.00
135_G	138_P	1.177	1.00
255_G	273_T	1.170	1.00
268_R	336_D	1.163	1.00
119_E	123_Y	1.156	1.00
197_L	227_R	1.149	1.00
316_I	320_Y	1.147	1.00
128_L	132_L	1.144	1.00
259_R	262_D	1.141	1.00
91_R	95_E	1.138	1.00
350_A	353_G	1.129	1.00
157_A	161_A	1.128	1.00
216_V	235_A	1.128	1.00
69_V	101_Y	1.124	1.00
126_A	353_G	1.094	1.00
224_A	230_V	1.083	1.00
152_V	155_P	1.082	1.00
344_A	347_R	1.081	1.00
85_V	238_M	1.080	1.00
355_V	361_A	1.080	1.00
299_F	303_S	1.080	1.00
340_E	345_H	1.078	1.00
123_Y	126_A	1.078	1.00
78_M	127_N	1.075	1.00
299_F	316_I	1.073	1.00
145_V	148_R	1.072	1.00
116_T	121_G	1.060	1.00
265_D	268_R	1.044	1.00
84_M	304_A	1.044	1.00
264_P	346_Q	1.039	1.00
337_R	340_E	1.025	1.00
118_A	121_G	1.023	1.00
71_G	103_P	1.022	1.00
325_L	329_E	1.020	1.00
233_P	236_L	1.017	1.00
128_L	131_L	1.007	1.00
69_V	197_L	1.005	1.00
124_L	145_V	1.001	1.00
72_V	85_V	0.998	1.00
125_R	356_T	0.997	1.00
120_T	123_Y	0.991	1.00
268_R	339_T	0.991	1.00
196_Q	231_G	0.981	1.00
125_R	129_R	0.977	1.00
70_T	207_P	0.974	0.99
70_T	85_V	0.973	0.99
334_A	337_R	0.972	0.99
213_D	233_P	0.970	0.99
125_R	128_L	0.967	0.99
310_D	319_E	0.962	0.99
123_Y	131_L	0.956	0.99
106_D	148_R	0.954	0.99
262_D	267_V	0.951	0.99
88_F	341_F	0.948	0.99
151_D	155_P	0.940	0.99
269_E	273_T	0.937	0.99
360_D	364_L	0.936	0.99
162_G	180_G	0.928	0.99
267_V	342_L	0.924	0.99
319_E	325_L	0.923	0.99
144_V	148_R	0.923	0.99
160_F	186_A	0.920	0.99
72_V	86_F	0.919	0.99
179_V	186_A	0.919	0.99
320_Y	327_S	0.914	0.99
93_Q	141_T	0.911	0.99
106_D	147_T	0.911	0.99
156_L	190_A	0.906	0.99
224_A	228_Y	0.900	0.99
164_V	222_V	0.899	0.99
161_A	179_V	0.894	0.99
84_M	305_F	0.888	0.99
137_D	140_L	0.887	0.99
221_D	224_A	0.887	0.99
266_T	269_E	0.885	0.99
127_N	131_L	0.884	0.99
294_A	297_V	0.884	0.99
117_P	121_G	0.882	0.99
194_L	197_L	0.880	0.99
260_L	342_L	0.878	0.99
288_A	296_D	0.876	0.99
82_H	86_F	0.868	0.99
243_S	248_G	0.867	0.99
245_A	248_G	0.866	0.99
165_R	178_N	0.863	0.99
232_K	235_A	0.860	0.99
242_P	300_Q	0.855	0.99
272_R	328_G	0.853	0.99
136_F	139_E	0.852	0.99
112_F	115_Q	0.852	0.99
303_S	313_L	0.851	0.99
305_F	341_F	0.848	0.99
350_A	354_D	0.841	0.99
132_L	138_P	0.836	0.98
169_L	186_A	0.836	0.98
135_G	139_E	0.834	0.98
83_A	88_F	0.832	0.98
132_L	362_F	0.828	0.98
80_L	305_F	0.826	0.98
352_L	355_V	0.826	0.98
193_L	227_R	0.826	0.98
72_V	87_Y	0.823	0.98
68_I	89_A	0.822	0.98
339_T	343_A	0.819	0.98
272_R	335_A	0.819	0.98
333_L	336_D	0.816	0.98
299_F	320_Y	0.813	0.98
320_Y	330_L	0.813	0.98
302_L	330_L	0.813	0.98
71_G	105_S	0.812	0.98
78_M	131_L	0.811	0.98
311_A	314_A	0.810	0.98
131_L	134_V	0.808	0.98
361_A	364_L	0.806	0.98
160_F	193_L	0.806	0.98
124_L	128_L	0.805	0.98
326_L	329_E	0.801	0.98
122_D	125_R	0.801	0.98
270_K	338_I	0.794	0.98
276_Y	294_A	0.785	0.98
223_A	227_R	0.781	0.98
72_V	78_M	0.778	0.98
319_E	322_A	0.777	0.98
145_V	363_R	0.772	0.97
329_E	333_L	0.771	0.97
103_P	144_V	0.767	0.97
297_V	300_Q	0.765	0.97
332_D	336_D	0.765	0.97
229_P	236_L	0.760	0.97
290_G	296_D	0.758	0.97
204_T	229_P	0.754	0.97
77_P	259_R	0.753	0.97
229_P	233_P	0.752	0.97
167_A	171_N	0.751	0.97
92_L	205_L	0.749	0.97
70_T	90_R	0.748	0.97
72_V	90_R	0.748	0.97
336_D	352_L	0.748	0.97
87_Y	134_V	0.741	0.97
356_T	359_L	0.739	0.97
192_L	219_S	0.736	0.97
161_A	178_N	0.733	0.96
126_A	130_D	0.732	0.96
165_R	176_P	0.730	0.96
99_R	140_L	0.729	0.96
193_L	197_L	0.727	0.96
336_D	348_R	0.725	0.96
268_R	332_D	0.725	0.96
126_A	349_R	0.720	0.96
340_E	348_R	0.716	0.96
229_P	234_G	0.716	0.96
186_A	222_V	0.714	0.96
293_P	296_D	0.714	0.96
120_T	124_L	0.714	0.96
337_R	341_F	0.713	0.96
196_Q	204_T	0.711	0.96
189_T	218_V	0.709	0.96
303_S	310_D	0.707	0.96
301_Y	305_F	0.697	0.95
229_P	235_A	0.693	0.95
296_D	320_Y	0.689	0.95
91_R	96_F	0.684	0.95
157_A	183_F	0.682	0.95
183_F	186_A	0.679	0.95
77_P	261_T	0.679	0.95
160_F	190_A	0.676	0.95
244_L	270_K	0.674	0.94
106_D	124_L	0.672	0.94
351_A	358_A	0.666	0.94
161_A	186_A	0.663	0.94
298_P	330_L	0.663	0.94
70_T	82_H	0.663	0.94
265_D	328_G	0.661	0.94
213_D	235_A	0.660	0.94
289_K	296_D	0.659	0.94
125_R	359_L	0.658	0.94
344_A	348_R	0.657	0.94
320_Y	325_L	0.656	0.94
300_Q	303_S	0.652	0.93
339_T	342_L	0.646	0.93
73_G	112_F	0.646	0.93
348_R	352_L	0.646	0.93
86_F	131_L	0.646	0.93
121_G	125_R	0.645	0.93
294_A	317_E	0.645	0.93
265_D	269_E	0.645	0.93
297_V	301_Y	0.644	0.93
302_L	306_F	0.644	0.93
101_Y	144_V	0.641	0.93
90_R	102_V	0.637	0.93
339_T	346_Q	0.635	0.92
306_F	316_I	0.635	0.92
116_T	123_Y	0.634	0.92
123_Y	127_N	0.631	0.92
270_K	339_T	0.631	0.92
80_L	338_I	0.630	0.92
68_I	92_L	0.630	0.92
86_F	90_R	0.628	0.92
150_A	153_L	0.626	0.92
88_F	238_M	0.626	0.92
142_R	145_V	0.623	0.92
258_I	271_V	0.623	0.92
277_T	298_P	0.622	0.92
229_P	237_L	0.621	0.92
130_D	134_V	0.619	0.92
82_H	85_V	0.617	0.91
352_L	356_T	0.616	0.91
351_A	354_D	0.615	0.91
353_G	356_T	0.615	0.91
255_G	269_E	0.614	0.91
353_G	359_L	0.613	0.91
133_A	139_E	0.610	0.91
259_R	270_K	0.609	0.91
352_L	358_A	0.609	0.91
172_V	218_V	0.607	0.91
310_D	313_L	0.605	0.91
163_D	222_V	0.604	0.91
78_M	82_H	0.604	0.91
72_V	82_H	0.603	0.90
164_V	218_V	0.603	0.90
73_G	127_N	0.600	0.90
189_T	193_L	0.599	0.90
319_E	329_E	0.598	0.90
317_E	320_Y	0.597	0.90
153_L	156_L	0.597	0.90
196_Q	227_R	0.595	0.90
357_E	360_D	0.593	0.90
133_A	137_D	0.591	0.90
98_A	205_L	0.590	0.89
161_A	176_P	0.589	0.89
313_L	316_I	0.588	0.89
291_G	296_D	0.587	0.89
136_F	143_I	0.586	0.89
295_E	299_F	0.575	0.88
77_P	126_A	0.573	0.88
158_T	162_G	0.572	0.88
157_A	179_V	0.572	0.88
235_A	238_M	0.572	0.88
133_A	138_P	0.571	0.88
311_A	316_I	0.570	0.88
302_L	337_R	0.570	0.88
260_L	345_H	0.569	0.88
264_P	268_R	0.569	0.88
217_R	220_R	0.568	0.88
133_A	136_F	0.567	0.88
131_L	143_I	0.567	0.88
168_T	171_N	0.567	0.88
121_G	124_L	0.565	0.87
163_D	226_A	0.565	0.87
292_V	296_D	0.564	0.87
261_T	349_R	0.564	0.87
90_R	131_L	0.564	0.87
130_D	261_T	0.564	0.87
316_I	330_L	0.562	0.87
144_V	153_L	0.561	0.87
168_T	225_K	0.559	0.87
271_V	334_A	0.557	0.87
160_F	189_T	0.557	0.87
295_E	298_P	0.556	0.87
268_R	271_V	0.555	0.86
163_D	225_K	0.554	0.86
325_L	333_L	0.552	0.86
363_R	367_D	0.551	0.86
346_Q	349_R	0.550	0.86
260_L	341_F	0.549	0.86
92_L	234_G	0.547	0.86
267_V	343_A	0.546	0.86
303_S	316_I	0.546	0.86
264_P	342_L	0.545	0.85
236_L	239_Q	0.544	0.85
127_N	130_D	0.542	0.85
183_F	187_V	0.540	0.85
295_E	303_S	0.540	0.85
250_M	331_K	0.538	0.85
227_R	231_G	0.537	0.85
296_D	313_L	0.537	0.85
65_E	99_R	0.535	0.84
77_P	123_Y	0.533	0.84
206_V	216_V	0.533	0.84
356_T	360_D	0.531	0.84
169_L	185_P	0.531	0.84
83_A	341_F	0.529	0.84
134_V	137_D	0.529	0.84
292_V	303_S	0.529	0.84
325_L	330_L	0.527	0.84
107_D	159_A	0.527	0.84
293_P	321_R	0.527	0.84
316_I	325_L	0.526	0.83
298_P	302_L	0.524	0.83
170_Q	175_E	0.524	0.83
241_L	304_A	0.522	0.83
312_E	337_R	0.521	0.83
179_V	182_A	0.520	0.83
84_M	88_F	0.520	0.83
296_D	327_S	0.518	0.82
126_A	132_L	0.518	0.82
316_I	333_L	0.517	0.82
280_R	291_G	0.515	0.82
362_F	366_D	0.515	0.82
298_P	303_S	0.513	0.82
263_S	350_A	0.511	0.82
153_L	194_L	0.510	0.82
168_T	172_V	0.506	0.81
332_D	335_A	0.506	0.81
91_R	97_G	0.504	0.81
110_Y	159_A	0.504	0.81
85_V	207_P	0.504	0.81
280_R	289_K	0.502	0.81
67_S	101_Y	0.500	0.80

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
3jxeA	2	0.9079	100	0.164	Contact Map
3i05A	2	0.8237	100	0.185	Contact Map
3tzeA	2	0.8921	100	0.207	Contact Map
2ip1A	1	0.9026	100	0.209	Contact Map
1r6uA	2	0.95	100	0.213	Contact Map
1r6tA	2	0.9447	100	0.218	Contact Map
3a04A	2	0.9237	100	0.218	Contact Map
3hv0A	2	0.8737	100	0.221	Contact Map
3focA	4	0.9395	100	0.231	Contact Map
3hzrA	2	0.9342	100	0.245	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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