SYW - SULSO - GREMLIN Contacts

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SYW - Tryptophan--tRNA ligase

UniProt:	Q97ZX0	Sequences: MPDEFTVTPWEVKGKVDYDKLIVQFGTQKITEELKQRIKNLAGDLHVMLRRNVFFSHRDLDLVLNDYEKSKGFFLYTGRAPSLGMHIGHLIPFIFTKWLQEKFNANLYIEITDDEKYMRNPEFTLDQTRSWAYDNILDIIAVGFNPDKTFIFQDTEYIRNMYPITVKIAKKLTFSEVRATFGLDASSNIGLIFYPALQIAPTMFEKKRCLIPAGIDQDPYWRLQRDIAESLGYYKAAQIHSKFLPPLTGPEGKMSSSNPETAIYLVDDPKTVERKIMKYAFSGGQPTIELHRKYGGNPEIDVPFQWLYYFFEEDDNRIKEIEEEYRSGKMLTGELKQILIDKLNNFLEEHRRRREEAKELVHVFKYDGKLAKQMWEKIHE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	380 (279)
Sequences:	7641 (3633)
Seq/√Len:	217.5

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
268_D	271_T	4.261	1.00
74_F	106_N	3.502	1.00
133_Y	365_K	3.393	1.00
353_R	356_E	3.218	1.00
108_Y	150_F	2.724	1.00
363_V	366_Y	2.690	1.00
320_E	324_E	2.518	1.00
348_E	352_R	2.505	1.00
174_F	192_I	2.479	1.00
317_R	320_E	2.456	1.00
319_K	322_E	2.433	1.00
106_N	150_F	2.405	1.00
130_S	134_D	2.276	1.00
76_Y	110_E	2.238	1.00
322_E	326_R	2.210	1.00
273_E	277_M	2.173	1.00
97_K	101_E	2.153	1.00
323_E	326_R	2.149	1.00
325_Y	338_I	2.123	1.00
319_K	323_E	2.089	1.00
124_T	127_Q	2.081	1.00
350_H	354_R	2.068	1.00
127_Q	130_S	2.048	1.00
215_I	243_F	2.042	1.00
363_V	367_D	2.012	1.00
178_R	192_I	1.999	1.00
345_N	348_E	1.980	1.00
323_E	327_S	1.971	1.00
267_D	275_K	1.967	1.00
316_N	320_E	1.912	1.00
352_R	356_E	1.876	1.00
81_P	116_K	1.858	1.00
269_P	344_N	1.816	1.00
277_M	337_Q	1.814	1.00
320_E	323_E	1.789	1.00
137_L	364_F	1.767	1.00
203_M	231_L	1.751	1.00
108_Y	208_R	1.737	1.00
285_Q	297_N	1.735	1.00
218_D	236_A	1.706	1.00
76_Y	112_T	1.694	1.00
252_G	258_N	1.687	1.00
351_R	355_E	1.683	1.00
101_E	148_K	1.672	1.00
228_A	236_A	1.650	1.00
273_E	340_I	1.644	1.00
203_M	228_A	1.637	1.00
136_I	140_I	1.618	1.00
316_N	324_E	1.593	1.00
345_N	350_H	1.590	1.00
338_I	342_K	1.568	1.00
333_G	337_Q	1.554	1.00
189_I	193_F	1.554	1.00
137_L	358_K	1.538	1.00
73_F	209_C	1.527	1.00
317_R	338_I	1.524	1.00
356_E	360_L	1.486	1.00
276_I	343_L	1.485	1.00
74_F	108_Y	1.481	1.00
246_P	261_T	1.468	1.00
360_L	363_V	1.467	1.00
362_H	366_Y	1.464	1.00
120_N	123_F	1.463	1.00
169_A	193_F	1.457	1.00
132_A	153_Q	1.454	1.00
174_F	178_R	1.432	1.00
318_I	322_E	1.427	1.00
310_F	342_K	1.420	1.00
307_L	339_L	1.414	1.00
301_D	322_E	1.408	1.00
269_P	348_E	1.405	1.00
144_F	149_T	1.395	1.00
221_W	238_Q	1.395	1.00
341_D	345_N	1.391	1.00
95_F	98_W	1.390	1.00
328_G	331_L	1.390	1.00
218_D	238_Q	1.381	1.00
283_G	286_P	1.380	1.00
328_G	334_E	1.369	1.00
81_P	111_I	1.366	1.00
293_K	296_G	1.363	1.00
77_T	92_P	1.362	1.00
267_D	271_T	1.353	1.00
334_E	337_Q	1.353	1.00
177_V	189_I	1.351	1.00
352_R	355_E	1.345	1.00
79_R	139_I	1.340	1.00
272_V	344_N	1.340	1.00
152_F	156_E	1.338	1.00
142_V	350_H	1.336	1.00
234_Y	238_Q	1.316	1.00
119_R	123_F	1.307	1.00
114_D	162_Y	1.307	1.00
349_E	352_R	1.294	1.00
127_Q	131_W	1.289	1.00
181_F	185_A	1.286	1.00
140_I	357_A	1.279	1.00
152_F	205_E	1.262	1.00
199_I	224_Q	1.260	1.00
111_I	136_I	1.258	1.00
301_D	305_Q	1.227	1.00
324_E	338_I	1.222	1.00
150_F	205_E	1.222	1.00
354_R	358_K	1.218	1.00
340_I	344_N	1.218	1.00
292_R	301_D	1.211	1.00
246_P	258_N	1.209	1.00
136_I	364_F	1.186	1.00
264_Y	267_D	1.186	1.00
77_T	212_P	1.179	1.00
173_T	176_E	1.179	1.00
74_F	208_R	1.175	1.00
100_Q	149_T	1.165	1.00
98_W	102_K	1.162	1.00
161_M	164_I	1.156	1.00
92_P	241_S	1.154	1.00
246_P	252_G	1.148	1.00
153_Q	156_E	1.142	1.00
315_D	319_K	1.139	1.00
76_Y	108_Y	1.139	1.00
165_T	169_A	1.134	1.00
297_N	300_I	1.130	1.00
136_I	139_I	1.123	1.00
176_E	226_D	1.119	1.00
123_F	131_W	1.106	1.00
273_E	341_D	1.102	1.00
138_D	354_R	1.102	1.00
341_D	357_A	1.094	1.00
145_N	148_K	1.084	1.00
161_M	205_E	1.076	1.00
76_Y	208_R	1.074	1.00
360_L	366_Y	1.073	1.00
113_D	155_T	1.067	1.00
304_F	321_I	1.064	1.00
210_L	237_A	1.063	1.00
174_F	183_L	1.062	1.00
126_D	130_S	1.061	1.00
143_G	146_P	1.054	1.00
98_W	101_E	1.053	1.00
248_T	252_G	1.052	1.00
355_E	358_K	1.042	1.00
203_M	232_G	1.040	1.00
91_I	309_Y	1.033	1.00
321_I	325_Y	1.032	1.00
304_F	318_I	1.022	1.00
133_Y	136_I	1.016	1.00
273_E	344_N	1.016	1.00
304_F	322_E	1.012	1.00
311_F	342_K	1.011	1.00
79_R	92_P	1.004	1.00
85_M	135_N	1.001	1.00
328_G	332_T	0.991	1.00
339_L	342_K	0.989	1.00
78_G	110_E	0.986	1.00
129_R	133_Y	0.976	1.00
113_D	156_E	0.976	1.00
342_K	345_N	0.976	1.00
293_K	301_D	0.972	1.00
75_L	99_L	0.972	1.00
338_I	341_D	0.968	1.00
73_F	105_A	0.964	1.00
99_L	237_A	0.959	1.00
155_T	159_R	0.954	1.00
235_K	238_Q	0.951	1.00
311_F	315_D	0.949	1.00
334_E	338_I	0.946	1.00
271_T	274_R	0.946	1.00
172_L	227_I	0.944	1.00
267_D	272_V	0.941	1.00
270_K	273_E	0.935	1.00
275_K	344_N	0.928	0.99
75_L	96_T	0.925	0.99
189_I	196_A	0.919	0.99
95_F	346_F	0.914	0.99
269_P	351_R	0.908	0.99
134_D	358_K	0.907	0.99
172_L	223_L	0.906	0.99
79_R	93_F	0.905	0.99
303_P	308_Y	0.901	0.99
177_V	196_A	0.895	0.99
173_T	188_N	0.887	0.99
305_Q	308_Y	0.883	0.99
108_Y	152_F	0.880	0.99
168_I	196_A	0.879	0.99
159_R	163_P	0.877	0.99
123_F	127_Q	0.874	0.99
324_E	327_S	0.873	0.99
73_F	210_L	0.871	0.99
310_F	346_F	0.870	0.99
133_Y	361_V	0.868	0.99
126_D	129_R	0.862	0.99
228_A	232_G	0.854	0.99
110_E	152_F	0.852	0.99
169_A	189_I	0.851	0.99
130_S	133_Y	0.847	0.99
341_D	353_R	0.845	0.99
274_R	278_K	0.843	0.99
79_R	85_M	0.841	0.99
277_M	340_I	0.840	0.99
170_K	190_G	0.838	0.99
303_P	307_L	0.835	0.99
164_I	200_A	0.834	0.99
301_D	325_Y	0.831	0.99
93_F	139_I	0.831	0.99
272_V	347_L	0.828	0.99
345_N	353_R	0.827	0.99
277_M	333_G	0.822	0.99
324_E	328_G	0.822	0.99
128_T	131_W	0.819	0.99
168_I	203_M	0.818	0.99
236_A	239_I	0.817	0.99
72_G	106_N	0.817	0.99
324_E	330_M	0.816	0.99
119_R	122_E	0.815	0.99
124_T	128_T	0.815	0.99
133_Y	137_L	0.815	0.99
122_E	128_T	0.814	0.99
199_I	223_L	0.814	0.99
85_M	139_I	0.810	0.99
78_G	112_T	0.810	0.99
258_N	261_T	0.809	0.99
171_K	230_S	0.805	0.99
87_I	343_L	0.804	0.98
357_A	360_L	0.804	0.98
358_K	361_V	0.804	0.98
229_E	233_Y	0.803	0.98
89_H	93_F	0.802	0.98
123_F	128_T	0.801	0.98
337_Q	341_D	0.797	0.98
275_K	343_L	0.796	0.98
226_D	229_E	0.788	0.98
168_I	200_A	0.786	0.98
325_Y	335_L	0.785	0.98
325_Y	332_T	0.785	0.98
357_A	361_V	0.783	0.98
125_L	128_T	0.779	0.98
245_P	305_Q	0.778	0.98
234_Y	237_A	0.778	0.98
99_L	210_L	0.775	0.98
316_N	319_K	0.769	0.98
84_G	264_Y	0.767	0.98
344_N	348_E	0.761	0.98
273_E	337_Q	0.755	0.98
248_T	258_N	0.755	0.98
140_I	367_D	0.754	0.98
341_D	354_R	0.753	0.98
265_L	347_L	0.750	0.98
281_F	284_G	0.749	0.98
321_I	338_I	0.749	0.98
143_G	147_D	0.747	0.98
272_V	348_E	0.745	0.98
324_E	334_E	0.744	0.98
239_I	242_K	0.738	0.97
304_F	335_L	0.737	0.97
143_G	148_K	0.733	0.97
141_A	144_F	0.732	0.97
355_E	359_E	0.728	0.97
139_I	151_I	0.727	0.97
299_E	339_L	0.723	0.97
120_N	124_T	0.721	0.97
193_F	196_A	0.721	0.97
202_T	224_Q	0.717	0.97
263_I	276_I	0.717	0.97
307_L	310_F	0.716	0.97
91_I	310_F	0.714	0.97
358_K	364_F	0.714	0.97
342_K	346_F	0.704	0.97
84_G	266_V	0.704	0.97
304_F	308_Y	0.701	0.96
302_V	306_W	0.698	0.96
308_Y	318_I	0.698	0.96
120_N	128_T	0.697	0.96
85_M	89_H	0.692	0.96
331_L	334_E	0.691	0.96
113_D	153_Q	0.689	0.96
315_D	318_I	0.688	0.96
308_Y	321_I	0.685	0.96
349_E	353_R	0.684	0.96
311_F	321_I	0.683	0.96
169_A	196_A	0.680	0.96
90_L	95_F	0.680	0.96
79_R	94_I	0.678	0.96
125_L	129_R	0.675	0.96
113_D	132_A	0.673	0.96
295_G	301_D	0.670	0.95
292_R	296_G	0.670	0.95
165_T	193_F	0.668	0.95
286_P	331_L	0.667	0.95
117_Y	125_L	0.665	0.95
175_S	179_A	0.663	0.95
361_V	365_K	0.663	0.95
361_V	364_F	0.662	0.95
169_A	188_N	0.659	0.95
73_F	104_N	0.654	0.95
140_I	146_P	0.653	0.95
97_K	109_I	0.652	0.95
308_Y	322_E	0.649	0.95
353_R	357_A	0.648	0.95
144_F	147_D	0.645	0.94
171_K	231_L	0.636	0.94
137_L	140_I	0.635	0.94
258_N	262_A	0.633	0.94
311_F	317_R	0.632	0.94
321_I	330_M	0.630	0.94
354_R	357_A	0.629	0.94
87_I	310_F	0.629	0.94
89_H	92_P	0.624	0.93
180_T	222_R	0.624	0.93
196_A	227_I	0.623	0.93
79_R	97_K	0.622	0.93
134_D	354_R	0.615	0.93
234_Y	239_I	0.611	0.93
276_I	339_L	0.610	0.93
356_E	359_E	0.608	0.92
247_L	275_K	0.607	0.92
77_T	97_K	0.605	0.92
344_N	351_R	0.601	0.92
351_R	354_R	0.601	0.92
94_I	142_V	0.601	0.92
300_I	322_E	0.600	0.92
77_T	89_H	0.599	0.92
270_K	274_R	0.599	0.92
165_T	189_I	0.596	0.92
307_L	311_F	0.596	0.92
298_P	301_D	0.596	0.92
141_A	145_N	0.595	0.92
128_T	132_A	0.595	0.92
119_R	128_T	0.593	0.92
120_N	127_Q	0.593	0.92
136_I	151_I	0.590	0.91
144_F	151_I	0.589	0.91
176_E	179_A	0.588	0.91
180_T	223_L	0.587	0.91
269_P	347_L	0.587	0.91
90_L	346_F	0.583	0.91
316_N	321_I	0.579	0.91
176_E	230_S	0.579	0.91
267_D	352_R	0.578	0.90
362_H	365_K	0.578	0.90
131_W	134_D	0.577	0.90
139_I	142_V	0.577	0.90
135_N	139_I	0.574	0.90
318_I	321_I	0.572	0.90
140_I	143_G	0.572	0.90
203_M	227_I	0.572	0.90
359_E	362_H	0.570	0.90
264_Y	275_K	0.570	0.90
222_R	225_R	0.569	0.90
330_M	338_I	0.569	0.90
298_P	326_R	0.568	0.90
136_I	141_A	0.567	0.90
325_Y	336_K	0.566	0.90
95_F	241_S	0.566	0.90
129_R	132_A	0.564	0.89
269_P	273_E	0.564	0.89
150_F	153_Q	0.563	0.89
166_V	170_K	0.563	0.89
182_G	185_A	0.562	0.89
303_P	310_F	0.562	0.89
356_E	363_V	0.561	0.89
74_F	207_K	0.560	0.89
93_F	97_K	0.560	0.89
330_M	335_L	0.560	0.89
160_N	164_I	0.560	0.89
301_D	318_I	0.559	0.89
299_E	322_E	0.558	0.89
270_K	333_G	0.557	0.89
80_A	135_N	0.556	0.89
245_P	302_V	0.555	0.89
138_D	142_V	0.555	0.89
281_F	299_E	0.555	0.89
97_K	139_I	0.554	0.89
322_E	325_Y	0.552	0.88
84_G	134_D	0.552	0.88
138_D	266_V	0.551	0.88
221_W	236_A	0.550	0.88
311_F	318_I	0.550	0.88
164_I	196_A	0.549	0.88
109_I	139_I	0.548	0.88
136_I	143_G	0.546	0.88
307_L	335_L	0.545	0.88
92_P	212_P	0.545	0.88
140_I	151_I	0.542	0.87
344_N	347_L	0.541	0.87
249_G	261_T	0.540	0.87
301_D	304_F	0.539	0.87
105_A	210_L	0.538	0.87
181_F	184_D	0.537	0.87
183_L	186_S	0.536	0.87
265_L	346_F	0.533	0.87
98_W	104_N	0.531	0.86
297_N	301_D	0.529	0.86
114_D	167_K	0.528	0.86
176_E	180_T	0.526	0.86
84_G	131_W	0.523	0.86
101_E	104_N	0.522	0.85
195_P	199_I	0.520	0.85
177_V	195_P	0.518	0.85
168_I	199_I	0.516	0.85
197_L	234_Y	0.513	0.84
91_I	95_F	0.513	0.84
276_I	341_D	0.513	0.84
259_P	262_A	0.513	0.84
79_R	109_I	0.512	0.84
199_I	203_M	0.510	0.84
300_I	303_P	0.508	0.84
79_R	89_H	0.507	0.84
162_Y	197_L	0.506	0.84
83_L	89_H	0.505	0.84
209_C	235_K	0.504	0.83
337_Q	361_V	0.504	0.83
209_C	234_Y	0.504	0.83
211_I	221_W	0.503	0.83
152_F	157_Y	0.503	0.83
294_Y	301_D	0.502	0.83
131_W	139_I	0.502	0.83
317_R	342_K	0.500	0.83
296_G	301_D	0.500	0.83

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	0.9395	100	0.124	Contact Map
2ip1A	1	0.9263	100	0.171	Contact Map
3i05A	2	0.8395	100	0.174	Contact Map
3tzeA	2	0.9105	100	0.18	Contact Map
1r6uA	2	0.9684	100	0.182	Contact Map
3hv0A	2	0.8895	100	0.184	Contact Map
1r6tA	2	0.9658	100	0.19	Contact Map
3focA	4	0.9605	100	0.198	Contact Map
3a04A	2	0.9289	100	0.198	Contact Map
4j76A	2	0.9368	100	0.207	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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