TRPB - HALSA - GREMLIN Contacts

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TRPB - Tryptophan synthase beta chain

UniProt:	Q9HSC0	Sequences: MSTNTDDTTRTDGTFGDYGGQYVPEVLMPAVEELTDAYERYVLDNEDGFVDDFRQRIRSFGGRPTPLTHAPTLSQRHGVDVYLKREDLLHGGAHKLNNALGQVLLAKYMGKDRIVAETGAGQHGTATAMACAALEMPCEIYMGRTDVNRQRPNVFRMRLHDADVNPVTVGSGTLKEAINETMRDWATNVADTHYVIGSVVGPHPFPSMVRDFQAIISEELRAQSREQLGELPAAVIACAGGGSNTMGAFGAFVGSASLPGAPAGTHEPAPDVDLLAVEAGGSRLGVDDDAGYAPNSASLSTGTEGVLHGARTKLLQTETGQIVESHSVSAGLDYAGVGPELAHLVDTGRITPTNVDDDAALAAFHRLSRDEGVIPALETSHAVAALDQYDGDGPVVVNVSGRGDKDLDTVIEASAANDIDAAPDMEVFEQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	430 (359)
Sequences:	5074 (2407)
Seq/√Len:	127.1

ECOLI - ILVA TRPB SDHD DPAL TDCB CYSK CYSM DCYD
BACSU - ILVA TRPB SDHD THRC CYSK MCCA CYSM
HALSA - TRPB Q9HNH6 Q9HRU4 Q9HMQ7 Q9HNH0 Q9HQ70
SULSO - TRPB2 Q980P1 TRPB1 Q97ZL6 Q97ZT5 Q980F2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
220_L	396_V	4.845	1.00
273_D	351_T	4.598	1.00
131_C	138_C	3.630	1.00
38_Y	211_D	3.432	1.00
141_Y	184_D	3.363	1.00
235_V	248_A	3.299	1.00
144_R	168_T	3.283	1.00
69_H	80_D	3.228	1.00
214_A	218_E	3.090	1.00
359_A	388_Q	2.939	1.00
199_V	246_M	2.901	1.00
234_A	275_L	2.855	1.00
144_R	172_G	2.692	1.00
390_D	393_G	2.686	1.00
139_E	163_D	2.651	1.00
248_A	398_N	2.564	1.00
76_R	366_R	2.544	1.00
67_L	396_V	2.537	1.00
59_S	227_Q	2.505	1.00
113_R	184_D	2.472	1.00
230_E	394_P	2.466	1.00
139_E	165_N	2.446	1.00
80_D	228_L	2.410	1.00
220_L	248_A	2.367	1.00
299_L	345_V	2.333	1.00
65_T	89_L	2.169	1.00
137_P	163_D	2.168	1.00
234_A	273_D	2.162	1.00
180_E	183_R	2.147	1.00
277_V	385_A	2.142	1.00
69_H	74_S	2.130	1.00
221_R	255_S	2.127	1.00
55_Q	59_S	2.088	1.00
71_P	75_Q	2.072	1.00
91_G	129_M	2.051	1.00
106_A	110_G	2.021	1.00
69_H	82_Y	1.989	1.00
80_D	394_P	1.989	1.00
235_V	274_L	1.976	1.00
184_D	188_N	1.938	1.00
379_T	400_S	1.922	1.00
222_A	226_E	1.891	1.00
145_T	148_N	1.890	1.00
365_H	414_S	1.856	1.00
217_S	251_A	1.815	1.00
41_Y	108_Y	1.814	1.00
353_T	385_A	1.776	1.00
386_L	397_V	1.761	1.00
152_P	407_L	1.761	1.00
224_S	228_L	1.748	1.00
341_L	352_P	1.746	1.00
37_A	40_R	1.745	1.00
158_R	163_D	1.737	1.00
224_S	396_V	1.729	1.00
148_N	155_F	1.706	1.00
275_L	351_T	1.706	1.00
233_A	393_G	1.697	1.00
217_S	248_A	1.688	1.00
248_A	274_L	1.677	1.00
83_L	367_L	1.663	1.00
364_F	380_S	1.628	1.00
313_K	346_D	1.628	1.00
224_S	394_P	1.599	1.00
61_G	89_L	1.595	1.00
304_E	311_R	1.594	1.00
113_R	137_P	1.591	1.00
72_T	75_Q	1.569	1.00
64_P	222_A	1.537	1.00
358_D	362_A	1.526	1.00
73_L	383_V	1.522	1.00
114_I	118_T	1.510	1.00
313_K	345_V	1.506	1.00
103_V	195_V	1.504	1.00
188_N	191_D	1.493	1.00
277_V	353_T	1.488	1.00
39_E	207_S	1.487	1.00
361_L	377_L	1.487	1.00
107_K	110_G	1.480	1.00
287_D	301_T	1.475	1.00
298_S	315_L	1.466	1.00
379_T	399_V	1.440	1.00
61_G	65_T	1.421	1.00
103_V	114_I	1.418	1.00
129_M	160_H	1.406	1.00
355_V	384_A	1.400	1.00
35_T	39_E	1.389	1.00
105_L	110_G	1.378	1.00
148_N	151_R	1.370	1.00
228_L	394_P	1.369	1.00
183_R	188_N	1.364	1.00
277_V	355_V	1.360	1.00
168_T	172_G	1.356	1.00
236_I	386_L	1.348	1.00
343_H	347_T	1.340	1.00
298_S	301_T	1.339	1.00
171_S	324_E	1.339	1.00
114_I	131_C	1.338	1.00
366_R	387_D	1.336	1.00
76_R	370_D	1.336	1.00
307_L	312_T	1.334	1.00
363_A	384_A	1.329	1.00
385_A	389_Y	1.328	1.00
127_T	140_I	1.327	1.00
253_V	350_I	1.324	1.00
234_A	395_V	1.317	1.00
114_I	117_E	1.315	1.00
276_A	352_P	1.309	1.00
77_H	387_D	1.308	1.00
383_V	397_V	1.305	1.00
57_I	61_G	1.299	1.00
47_D	51_D	1.288	1.00
280_G	356_D	1.287	1.00
147_V	166_P	1.277	1.00
113_R	118_T	1.275	1.00
236_I	389_Y	1.274	1.00
54_R	218_E	1.271	1.00
113_R	117_E	1.266	1.00
115_V	118_T	1.265	1.00
178_I	200_V	1.259	1.00
73_L	81_V	1.250	1.00
312_T	342_A	1.218	0.99
295_N	301_T	1.204	0.99
114_I	119_G	1.202	0.99
144_R	147_V	1.194	0.99
86_E	400_S	1.184	0.99
36_D	40_R	1.162	0.99
236_I	275_L	1.153	0.99
151_R	155_F	1.150	0.99
99_A	130_A	1.149	0.99
38_Y	42_V	1.149	0.99
105_L	111_K	1.148	0.99
82_Y	394_P	1.145	0.99
225_R	228_L	1.145	0.99
275_L	385_A	1.132	0.99
280_G	354_N	1.125	0.99
299_L	352_P	1.125	0.99
82_Y	228_L	1.122	0.99
37_A	41_Y	1.122	0.99
106_A	109_M	1.117	0.99
39_E	43_L	1.109	0.99
91_G	96_L	1.103	0.99
220_L	252_F	1.095	0.99
32_E	35_T	1.094	0.99
196_I	200_V	1.090	0.99
249_F	274_L	1.087	0.99
77_H	386_L	1.083	0.99
73_L	366_R	1.076	0.99
65_T	93_A	1.070	0.99
72_T	370_D	1.067	0.99
220_L	398_N	1.060	0.99
234_A	393_G	1.056	0.98
366_R	370_D	1.054	0.98
409_T	412_E	1.050	0.98
53_F	57_I	1.044	0.98
196_I	199_V	1.044	0.98
68_T	85_R	1.043	0.98
103_V	134_L	1.041	0.98
365_H	369_R	1.039	0.98
144_R	148_N	1.037	0.98
386_L	395_V	1.034	0.98
275_L	389_Y	1.030	0.98
56_R	133_A	1.029	0.98
197_G	201_G	1.029	0.98
295_N	299_L	1.029	0.98
207_S	211_D	1.026	0.98
80_D	392_D	1.024	0.98
113_R	139_E	1.024	0.98
152_P	408_D	1.024	0.98
203_H	207_S	1.021	0.98
364_F	410_V	1.014	0.98
113_R	119_G	1.013	0.98
42_V	211_D	1.009	0.98
50_V	53_F	1.008	0.98
210_R	340_E	1.007	0.98
408_D	412_E	1.006	0.98
32_E	36_D	1.006	0.98
277_V	354_N	1.001	0.98
82_Y	224_S	0.999	0.98
183_R	321_Q	0.994	0.98
200_V	310_A	0.984	0.98
218_E	251_A	0.981	0.98
361_L	413_A	0.980	0.98
77_H	366_R	0.980	0.98
363_A	383_V	0.979	0.97
125_T	156_R	0.975	0.97
409_T	413_A	0.974	0.97
147_V	158_R	0.973	0.97
178_I	196_I	0.971	0.97
411_I	415_A	0.971	0.97
362_A	366_R	0.968	0.97
214_A	251_A	0.968	0.97
356_D	359_A	0.966	0.97
178_I	182_M	0.966	0.97
155_F	411_I	0.966	0.97
304_E	313_K	0.966	0.97
220_L	235_V	0.965	0.97
221_R	225_R	0.964	0.97
48_G	51_D	0.962	0.97
246_M	341_L	0.960	0.97
225_R	230_E	0.960	0.97
56_R	100_L	0.957	0.97
156_R	374_I	0.952	0.97
359_A	384_A	0.952	0.97
383_V	399_V	0.951	0.97
159_L	365_H	0.951	0.97
367_L	383_V	0.948	0.97
368_S	375_P	0.947	0.97
114_I	136_M	0.946	0.97
236_I	277_V	0.946	0.97
144_R	166_P	0.944	0.97
155_F	158_R	0.933	0.97
38_Y	212_F	0.930	0.97
283_R	287_D	0.929	0.97
310_A	314_L	0.925	0.96
183_R	187_T	0.924	0.96
235_V	252_F	0.924	0.96
312_T	336_G	0.924	0.96
50_V	54_R	0.923	0.96
255_S	270_P	0.921	0.96
113_R	116_A	0.920	0.96
151_R	408_D	0.920	0.96
151_R	158_R	0.918	0.96
384_A	388_Q	0.914	0.96
368_S	374_I	0.914	0.96
58_R	226_E	0.913	0.96
112_D	137_P	0.910	0.96
48_G	52_D	0.909	0.96
253_V	344_L	0.907	0.96
70_A	73_L	0.907	0.96
234_A	389_Y	0.906	0.96
195_V	198_S	0.900	0.96
115_V	184_D	0.900	0.96
231_L	272_V	0.898	0.96
64_P	223_Q	0.896	0.96
403_G	406_D	0.895	0.96
194_Y	197_G	0.894	0.96
52_D	107_K	0.893	0.96
236_I	385_A	0.892	0.96
54_R	58_R	0.890	0.96
115_V	119_G	0.885	0.95
68_T	87_D	0.885	0.95
155_F	407_L	0.883	0.95
235_V	396_V	0.882	0.95
50_V	57_I	0.880	0.95
408_D	411_I	0.878	0.95
353_T	388_Q	0.878	0.95
46_E	108_Y	0.876	0.95
373_V	399_V	0.875	0.95
249_F	348_G	0.874	0.95
179_N	183_R	0.873	0.95
103_V	136_M	0.872	0.95
39_E	42_V	0.871	0.95
375_P	380_S	0.868	0.95
71_P	133_A	0.862	0.95
105_L	109_M	0.862	0.95
113_R	192_T	0.861	0.95
198_S	201_G	0.858	0.95
155_F	414_S	0.856	0.95
107_K	134_L	0.856	0.95
41_Y	48_G	0.854	0.95
139_E	184_D	0.848	0.94
106_A	111_K	0.847	0.94
155_F	159_L	0.844	0.94
193_H	197_G	0.840	0.94
307_L	322_I	0.839	0.94
350_I	353_T	0.836	0.94
141_Y	180_E	0.835	0.94
355_V	385_A	0.832	0.94
375_P	379_T	0.832	0.94
208_M	212_F	0.826	0.93
178_I	325_S	0.825	0.93
171_S	176_E	0.823	0.93
156_R	160_H	0.822	0.93
81_V	395_V	0.819	0.93
74_S	79_V	0.818	0.93
56_R	134_L	0.818	0.93
116_A	119_G	0.816	0.93
169_V	180_E	0.806	0.93
380_S	383_V	0.803	0.92
194_Y	198_S	0.799	0.92
235_V	251_A	0.799	0.92
41_Y	46_E	0.795	0.92
328_V	361_L	0.791	0.92
103_V	130_A	0.789	0.92
231_L	255_S	0.785	0.92
79_V	386_L	0.782	0.91
127_T	131_C	0.781	0.91
283_R	286_V	0.781	0.91
224_S	230_E	0.777	0.91
130_A	195_V	0.776	0.91
148_N	412_E	0.767	0.91
111_K	193_H	0.764	0.91
176_E	179_N	0.763	0.90
193_H	198_S	0.763	0.90
195_V	199_V	0.763	0.90
216_I	244_N	0.760	0.90
273_D	393_G	0.759	0.90
295_N	298_S	0.753	0.90
31_V	35_T	0.751	0.90
402_R	406_D	0.751	0.90
296_S	299_L	0.748	0.90
145_T	172_G	0.743	0.89
295_N	300_S	0.741	0.89
251_A	254_G	0.741	0.89
94_H	244_N	0.737	0.89
367_L	399_V	0.736	0.89
382_A	397_V	0.730	0.88
232_P	396_V	0.730	0.88
298_S	304_E	0.727	0.88
108_Y	111_K	0.727	0.88
217_S	252_F	0.726	0.88
210_R	250_G	0.726	0.88
67_L	227_Q	0.725	0.88
154_V	164_V	0.723	0.88
311_R	314_L	0.723	0.88
87_D	400_S	0.722	0.88
225_R	231_L	0.722	0.88
275_L	353_T	0.722	0.88
239_A	276_A	0.722	0.88
246_M	250_G	0.720	0.88
234_A	351_T	0.718	0.88
33_E	37_A	0.718	0.88
42_V	207_S	0.714	0.87
314_L	322_I	0.711	0.87
402_R	405_K	0.708	0.87
239_A	337_V	0.707	0.87
218_E	222_A	0.706	0.87
112_D	191_D	0.703	0.87
171_S	179_N	0.701	0.86
276_A	341_L	0.700	0.86
301_T	305_G	0.698	0.86
96_L	129_M	0.696	0.86
194_Y	201_G	0.695	0.86
234_A	390_D	0.688	0.85
306_V	311_R	0.687	0.85
248_A	251_A	0.684	0.85
178_I	198_S	0.684	0.85
86_E	379_T	0.683	0.85
407_L	411_I	0.681	0.85
187_T	190_A	0.680	0.85
79_V	393_G	0.678	0.84
67_L	224_S	0.678	0.84
281_G	324_E	0.677	0.84
239_A	298_S	0.676	0.84
250_G	340_E	0.674	0.84
255_S	272_V	0.673	0.84
106_A	193_H	0.672	0.84
284_L	295_N	0.672	0.84
83_L	399_V	0.672	0.84
73_L	76_R	0.671	0.84
198_S	310_A	0.671	0.84
51_D	55_Q	0.670	0.84
383_V	386_L	0.668	0.84
54_R	222_A	0.666	0.83
68_T	71_P	0.666	0.83
282_S	326_H	0.666	0.83
85_R	88_L	0.665	0.83
233_A	394_P	0.660	0.83
282_S	286_V	0.660	0.83
284_L	337_V	0.659	0.83
145_T	171_S	0.657	0.83
157_M	162_A	0.656	0.82
307_L	314_L	0.656	0.82
184_D	187_T	0.655	0.82
106_A	114_I	0.654	0.82
394_P	398_N	0.654	0.82
224_S	227_Q	0.653	0.82
211_D	214_A	0.648	0.82
221_R	231_L	0.646	0.82
195_V	201_G	0.646	0.82
34_L	254_G	0.646	0.82
298_S	302_G	0.645	0.81
192_T	197_G	0.644	0.81
36_D	39_E	0.644	0.81
315_L	323_V	0.643	0.81
231_L	252_F	0.643	0.81
42_V	50_V	0.642	0.81
179_N	182_M	0.642	0.81
176_E	180_E	0.642	0.81
145_T	324_E	0.641	0.81
254_G	270_P	0.638	0.81
154_V	158_R	0.637	0.81
105_L	108_Y	0.636	0.81
196_I	201_G	0.634	0.80
89_L	96_L	0.633	0.80
303_T	316_Q	0.632	0.80
194_Y	199_V	0.630	0.80
216_I	398_N	0.630	0.80
81_V	386_L	0.629	0.80
272_V	349_R	0.629	0.80
298_S	310_A	0.628	0.80
78_G	391_G	0.626	0.79
280_G	286_V	0.624	0.79
193_H	196_I	0.623	0.79
282_S	325_S	0.621	0.79
359_A	362_A	0.621	0.79
307_L	310_A	0.620	0.79
379_T	382_A	0.620	0.79
156_R	407_L	0.619	0.79
316_Q	321_Q	0.616	0.78
221_R	254_G	0.616	0.78
225_R	229_G	0.614	0.78
38_Y	207_S	0.614	0.78
55_Q	58_R	0.613	0.78
154_V	166_P	0.613	0.78
211_D	250_G	0.611	0.78
41_Y	50_V	0.611	0.78
248_A	396_V	0.606	0.77
355_V	388_Q	0.604	0.77
385_A	388_Q	0.604	0.77
295_N	303_T	0.603	0.77
79_V	395_V	0.601	0.77
298_S	303_T	0.601	0.77
40_R	43_L	0.598	0.76
115_V	193_H	0.598	0.76
342_A	345_V	0.597	0.76
221_R	251_A	0.597	0.76
364_F	377_L	0.595	0.76
67_L	228_L	0.594	0.76
377_L	410_V	0.594	0.76
107_K	112_D	0.594	0.76
77_H	370_D	0.592	0.76
129_M	133_A	0.590	0.75
97_N	215_I	0.589	0.75
361_L	410_V	0.589	0.75
155_F	408_D	0.585	0.75
218_E	250_G	0.584	0.75
142_M	157_M	0.580	0.74
106_A	136_M	0.580	0.74
179_N	321_Q	0.579	0.74
304_E	346_D	0.579	0.74
107_K	136_M	0.577	0.74
166_P	169_V	0.577	0.74
113_R	141_Y	0.575	0.74
91_G	160_H	0.575	0.74
34_L	196_I	0.573	0.73
74_S	80_D	0.572	0.73
221_R	252_F	0.571	0.73
71_P	74_S	0.570	0.73
375_P	399_V	0.570	0.73
337_V	345_V	0.569	0.73
364_F	375_P	0.569	0.73
312_T	318_E	0.569	0.73
336_G	339_P	0.568	0.73
186_A	193_H	0.568	0.73
379_T	386_L	0.565	0.72
35_T	208_M	0.565	0.72
196_I	310_A	0.564	0.72
35_T	207_S	0.563	0.72
107_K	111_K	0.563	0.72
300_S	354_N	0.563	0.72
185_W	188_N	0.562	0.72
301_T	304_E	0.562	0.72
127_T	195_V	0.561	0.72
369_R	414_S	0.560	0.72
180_E	184_D	0.559	0.71
310_A	321_Q	0.559	0.71
299_L	302_G	0.554	0.71
237_A	244_N	0.553	0.71
36_D	41_Y	0.550	0.70
231_L	270_P	0.550	0.70
159_L	368_S	0.549	0.70
149_R	330_A	0.549	0.70
70_A	74_S	0.549	0.70
97_N	213_Q	0.549	0.70
96_L	133_A	0.548	0.70
191_D	197_G	0.546	0.70
253_V	274_L	0.545	0.70
360_A	380_S	0.545	0.70
375_P	383_V	0.544	0.69
284_L	297_A	0.543	0.69
222_A	225_R	0.543	0.69
147_V	167_V	0.543	0.69
66_P	88_L	0.542	0.69
214_A	250_G	0.540	0.69
200_V	312_T	0.539	0.69
131_C	137_P	0.539	0.69
356_D	388_Q	0.538	0.69
33_E	36_D	0.536	0.68
191_D	198_S	0.535	0.68
329_S	332_L	0.534	0.68
103_V	127_T	0.534	0.68
362_A	387_D	0.533	0.68
31_V	34_L	0.532	0.68
209_V	213_Q	0.532	0.68
304_E	342_A	0.531	0.68
297_A	302_G	0.530	0.67
55_Q	71_P	0.530	0.67
63_R	97_N	0.530	0.67
213_Q	379_T	0.529	0.67
53_F	215_I	0.528	0.67
188_N	192_T	0.528	0.67
40_R	48_G	0.527	0.67
199_V	248_A	0.524	0.67
245_T	349_R	0.524	0.67
56_R	59_S	0.524	0.67
367_L	375_P	0.524	0.67
308_H	335_A	0.524	0.67
42_V	47_D	0.523	0.66
47_D	50_V	0.522	0.66
147_V	168_T	0.521	0.66
140_I	196_I	0.520	0.66
332_L	378_E	0.520	0.66
69_H	228_L	0.520	0.66
103_V	137_P	0.519	0.66
220_L	251_A	0.519	0.66
87_D	379_T	0.518	0.66
43_L	47_D	0.518	0.66
127_T	138_C	0.517	0.66
281_G	357_D	0.517	0.66
32_E	39_E	0.517	0.66
79_V	392_D	0.517	0.66
61_G	96_L	0.517	0.66
147_V	413_A	0.516	0.65
310_A	319_T	0.514	0.65
140_I	178_I	0.513	0.65
178_I	195_V	0.513	0.65
58_R	64_P	0.513	0.65
89_L	409_T	0.512	0.65
178_I	310_A	0.512	0.65
332_L	381_H	0.511	0.65
298_S	336_G	0.511	0.65
163_D	166_P	0.511	0.65
345_V	349_R	0.509	0.64
182_M	195_V	0.509	0.64
83_L	383_V	0.508	0.64
124_G	157_M	0.508	0.64
73_L	79_V	0.508	0.64
275_L	350_I	0.508	0.64
117_E	241_G	0.504	0.64
192_T	198_S	0.503	0.63
60_F	100_L	0.503	0.63
169_V	176_E	0.502	0.63
284_L	287_D	0.502	0.63
252_F	255_S	0.501	0.63
89_L	129_M	0.501	0.63
296_S	301_T	0.500	0.63
279_A	322_I	0.500	0.63

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
2o2eA	2	0.7233	100	0.333	Contact Map
1x1qA	2	0.8884	100	0.334	Contact Map
4negA	2	0.7442	100	0.341	Contact Map
4ht3B	2	0.893	100	0.355	Contact Map
1v8zA	2	0.8791	100	0.372	Contact Map
1tdjA	2	0.7767	100	0.377	Contact Map
3ss7X	1	0.8488	100	0.379	Contact Map
2gn0A	2	0.7465	100	0.398	Contact Map
1v71A	2	0.7256	100	0.402	Contact Map
3iauA	1	0.8233	100	0.41	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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