YVBX - BACSU - GREMLIN Contacts

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YVBX - Uncharacterized glycosylase YvbX

UniProt:	O32258	Sequences: MKKWLIIAVSLAIAIVLFMYTKGEAKAAGMTVGYTTGDTASYNSLTKYHTYMNAIATDTFAFEKNGQIIGDAPTKQLTYAKKKKIKTWAVISNYNDAIYDFDGDLASRVMSNKTAKKRFTDQLITLAKKHSYYGINIDFEAVNPEDRAAYSNFIQYVSQALNKKHIKTMVSVPAKSADDKNDDWSWPYDYAKIGKYADFVQVMTYDEHGIWGEPGSVASTNWIKSSLQFSVKKIKANKVIMGIPAYGYDWDVKDGSTSTIREWNELKSLIKKQKAKPAFNKKSGSMTFSYVDKKKHKHVVWYENEKTVQTKSHLAKQYKIAGVSVYALGNESESFWKAIRKGTK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	344 (292)
Sequences:	5687 (4175)
Seq/√Len:	244.3

BACSU - YVBX YAAH YDHD YKVQ
HALSA - Q9HR84 Q9HR83

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
116_K	156_Y	3.311	1.00
158_S	162_N	3.055	1.00
189_D	192_K	2.945	1.00
128_K	164_K	2.929	1.00
224_K	228_Q	2.883	1.00
121_D	160_A	2.849	1.00
125_T	129_K	2.585	1.00
170_V	197_A	2.498	1.00
112_N	115_A	2.494	1.00
284_G	310_T	2.440	1.00
120_T	156_Y	2.422	1.00
60_F	89_A	2.414	1.00
224_K	314_L	2.341	1.00
155_Q	196_Y	2.274	1.00
315_A	323_V	2.252	1.00
286_M	304_N	2.218	1.00
286_M	307_T	2.156	1.00
137_I	154_I	2.149	1.00
123_L	135_I	2.126	1.00
107_S	146_D	2.102	1.00
117_K	121_D	2.087	1.00
228_Q	318_Y	2.087	1.00
194_G	235_K	2.035	1.00
236_A	319_K	2.028	1.00
146_D	149_A	2.024	1.00
154_I	193_I	2.021	1.00
277_P	304_N	1.972	1.00
227_L	320_I	1.962	1.00
218_A	244_P	1.959	1.00
202_V	227_L	1.924	1.00
221_N	224_K	1.903	1.00
243_I	308_V	1.892	1.00
33_G	52_M	1.861	1.00
231_V	236_A	1.850	1.00
117_K	156_Y	1.807	1.00
30_M	240_I	1.803	1.00
223_I	241_M	1.798	1.00
313_H	317_Q	1.786	1.00
303_E	311_K	1.757	1.00
194_G	200_V	1.752	1.00
280_N	283_S	1.720	1.00
281_K	284_G	1.675	1.00
86_K	133_Y	1.674	1.00
120_T	160_A	1.670	1.00
120_T	157_V	1.665	1.00
63_E	67_Q	1.628	1.00
30_M	321_A	1.622	1.00
127_A	166_I	1.618	1.00
117_K	160_A	1.613	1.00
309_Q	313_H	1.609	1.00
151_S	192_K	1.590	1.00
310_T	313_H	1.590	1.00
158_S	168_T	1.588	1.00
263_W	266_L	1.561	1.00
251_D	298_H	1.552	1.00
172_V	230_S	1.541	1.00
151_S	189_D	1.539	1.00
110_M	153_F	1.535	1.00
243_I	323_V	1.530	1.00
208_H	212_G	1.525	1.00
79_Y	83_K	1.508	1.00
124_I	160_A	1.504	1.00
207_E	219_S	1.474	1.00
88_W	169_M	1.473	1.00
277_P	302_Y	1.465	1.00
45_L	75_K	1.464	1.00
155_Q	192_K	1.446	1.00
74_T	78_T	1.437	1.00
111_S	149_A	1.437	1.00
73_P	77_L	1.434	1.00
216_S	285_S	1.433	1.00
156_Y	160_A	1.432	1.00
249_D	298_H	1.430	1.00
204_T	241_M	1.421	1.00
240_I	321_A	1.402	1.00
113_K	117_K	1.398	1.00
32_V	56_A	1.398	1.00
88_W	167_K	1.394	1.00
227_L	241_M	1.387	1.00
154_I	197_A	1.375	1.00
148_A	189_D	1.324	1.00
245_A	325_V	1.310	1.00
120_T	124_I	1.307	1.00
279_F	307_T	1.300	1.00
155_Q	159_Q	1.299	1.00
70_G	73_P	1.294	1.00
224_K	318_Y	1.294	1.00
262_E	330_N	1.291	1.00
192_K	195_K	1.290	1.00
229_F	233_K	1.290	1.00
197_A	200_V	1.266	1.00
75_K	78_T	1.265	1.00
279_F	310_T	1.262	1.00
201_Q	324_S	1.262	1.00
228_Q	232_K	1.253	1.00
73_P	76_Q	1.250	1.00
140_E	203_M	1.248	1.00
161_L	166_I	1.246	1.00
194_G	238_K	1.243	1.00
30_M	199_F	1.235	1.00
231_V	318_Y	1.230	1.00
152_N	155_Q	1.227	1.00
171_S	203_M	1.226	1.00
249_D	300_V	1.221	1.00
56_A	90_V	1.214	1.00
170_V	193_I	1.212	1.00
224_K	317_Q	1.210	1.00
279_F	306_K	1.209	1.00
231_V	320_I	1.198	1.00
194_G	234_I	1.194	1.00
89_A	126_L	1.189	1.00
279_F	304_N	1.187	1.00
72_A	75_K	1.187	1.00
128_K	166_I	1.180	1.00
138_D	203_M	1.173	1.00
127_A	135_I	1.173	1.00
71_D	74_T	1.170	1.00
121_D	125_T	1.166	1.00
79_Y	85_I	1.163	1.00
137_I	157_V	1.151	1.00
199_F	240_I	1.151	1.00
43_N	46_T	1.149	1.00
154_I	196_Y	1.148	1.00
116_K	152_N	1.145	1.00
76_Q	87_T	1.136	1.00
67_Q	118_R	1.135	1.00
143_N	146_D	1.134	1.00
275_A	288_F	1.130	1.00
190_Y	234_I	1.122	1.00
54_A	88_W	1.120	1.00
266_L	270_I	1.117	1.00
34_Y	171_S	1.117	1.00
109_V	115_A	1.114	1.00
56_A	201_Q	1.108	1.00
172_V	200_V	1.106	1.00
33_G	325_V	1.104	1.00
205_Y	242_G	1.102	1.00
235_K	238_K	1.098	1.00
74_T	77_L	1.095	1.00
88_W	134_G	1.095	1.00
200_V	234_I	1.092	1.00
199_F	321_A	1.089	1.00
314_L	318_Y	1.088	1.00
207_E	223_I	1.086	1.00
147_R	189_D	1.072	1.00
277_P	306_K	1.067	1.00
247_G	300_V	1.059	1.00
312_S	323_V	1.055	1.00
29_G	316_K	1.054	1.00
237_N	321_A	1.049	1.00
33_G	328_L	1.046	1.00
70_G	78_T	1.041	1.00
156_Y	159_Q	1.039	1.00
110_M	139_F	1.038	1.00
151_S	196_Y	1.037	1.00
148_A	152_N	1.032	1.00
113_K	152_N	1.032	1.00
136_N	169_M	1.027	1.00
327_A	330_N	1.026	1.00
191_A	195_K	1.024	1.00
61_A	96_D	1.022	1.00
207_E	226_S	1.015	1.00
206_D	248_Y	0.999	1.00
136_N	171_S	0.996	1.00
263_W	267_K	0.993	1.00
247_G	302_Y	0.990	1.00
79_Y	82_K	0.982	1.00
73_P	78_T	0.981	1.00
108_R	115_A	0.980	1.00
234_I	239_V	0.978	1.00
135_I	168_T	0.974	1.00
72_A	77_L	0.964	1.00
159_Q	196_Y	0.961	1.00
279_F	284_G	0.957	1.00
124_I	128_K	0.954	1.00
241_M	315_A	0.932	1.00
71_D	75_K	0.932	1.00
236_A	320_I	0.930	1.00
304_N	307_T	0.930	1.00
203_M	246_Y	0.930	1.00
229_F	232_K	0.926	1.00
77_L	87_T	0.920	1.00
312_S	315_A	0.916	1.00
217_V	301_W	0.915	1.00
32_V	324_S	0.914	1.00
52_M	328_L	0.908	1.00
54_A	167_K	0.904	1.00
291_V	296_H	0.901	1.00
54_A	86_K	0.896	1.00
313_H	316_K	0.895	1.00
82_K	85_I	0.893	1.00
152_N	156_Y	0.892	1.00
140_E	171_S	0.891	1.00
306_K	310_T	0.889	1.00
265_E	268_S	0.889	1.00
277_P	288_F	0.887	1.00
162_N	165_H	0.885	1.00
147_R	187_P	0.882	1.00
150_Y	170_V	0.875	0.99
153_F	157_V	0.875	0.99
70_G	74_T	0.875	0.99
158_S	196_Y	0.875	0.99
264_N	267_K	0.874	0.99
126_L	130_H	0.868	0.99
303_E	307_T	0.867	0.99
49_H	85_I	0.865	0.99
206_D	246_Y	0.859	0.99
147_R	151_S	0.858	0.99
111_S	115_A	0.856	0.99
87_T	133_Y	0.855	0.99
241_M	320_I	0.854	0.99
227_L	239_V	0.853	0.99
247_G	266_L	0.853	0.99
115_A	118_R	0.849	0.99
109_V	119_F	0.845	0.99
169_M	201_Q	0.842	0.99
104_D	108_R	0.838	0.99
81_K	133_Y	0.831	0.99
49_H	82_K	0.831	0.99
40_A	262_E	0.826	0.99
217_V	248_Y	0.825	0.99
252_V	299_V	0.825	0.99
56_A	88_W	0.823	0.99
201_Q	240_I	0.823	0.99
190_Y	230_S	0.823	0.99
47_K	328_L	0.823	0.99
214_P	299_V	0.820	0.99
175_K	183_D	0.817	0.99
157_V	161_L	0.817	0.99
30_M	54_A	0.815	0.99
208_H	215_G	0.813	0.99
220_T	284_G	0.813	0.99
63_E	66_G	0.811	0.99
89_A	132_Y	0.803	0.99
140_E	205_Y	0.801	0.99
136_N	201_Q	0.799	0.99
203_M	326_Y	0.798	0.99
32_V	199_F	0.798	0.99
248_Y	260_I	0.797	0.99
118_R	121_D	0.794	0.99
184_W	187_P	0.792	0.99
307_T	310_T	0.790	0.99
108_R	143_N	0.783	0.99
124_I	164_K	0.779	0.99
118_R	122_Q	0.775	0.99
193_I	200_V	0.773	0.99
58_D	90_V	0.771	0.99
107_S	149_A	0.771	0.99
160_A	163_K	0.769	0.99
267_K	332_S	0.769	0.99
154_I	170_V	0.759	0.99
161_L	168_T	0.758	0.99
110_M	149_A	0.757	0.98
48_Y	51_Y	0.756	0.98
314_L	320_I	0.755	0.98
138_D	246_Y	0.752	0.98
160_A	164_K	0.748	0.98
261_R	265_E	0.748	0.98
72_A	78_T	0.747	0.98
70_G	75_K	0.747	0.98
109_V	112_N	0.744	0.98
49_H	52_M	0.743	0.98
50_T	82_K	0.741	0.98
107_S	111_S	0.739	0.98
108_R	111_S	0.737	0.98
278_A	287_T	0.734	0.98
266_L	302_Y	0.733	0.98
150_Y	154_I	0.731	0.98
275_A	291_V	0.728	0.98
270_I	288_F	0.724	0.98
249_D	261_R	0.724	0.98
243_I	325_V	0.721	0.98
69_I	74_T	0.720	0.98
86_K	167_K	0.720	0.98
172_V	190_Y	0.720	0.98
108_R	112_N	0.719	0.98
44_S	47_K	0.719	0.98
267_K	270_I	0.719	0.98
228_Q	231_V	0.719	0.98
149_A	152_N	0.718	0.98
259_T	269_L	0.714	0.98
269_L	288_F	0.709	0.98
59_T	140_E	0.709	0.98
58_D	326_Y	0.709	0.98
220_T	224_K	0.708	0.98
290_Y	296_H	0.706	0.98
220_T	314_L	0.706	0.98
193_I	197_A	0.706	0.98
116_K	149_A	0.706	0.98
262_E	265_E	0.704	0.98
70_G	77_L	0.704	0.98
190_Y	233_K	0.703	0.98
245_A	308_V	0.703	0.98
60_F	130_H	0.703	0.98
204_T	240_I	0.702	0.98
240_I	324_S	0.700	0.97
80_A	84_K	0.698	0.97
123_L	157_V	0.698	0.97
261_R	266_L	0.695	0.97
227_L	314_L	0.695	0.97
218_A	303_E	0.694	0.97
29_G	319_K	0.692	0.97
77_L	81_K	0.691	0.97
69_I	73_P	0.691	0.97
256_S	299_V	0.690	0.97
262_E	266_L	0.690	0.97
312_S	316_K	0.682	0.97
54_A	199_F	0.678	0.97
148_A	192_K	0.677	0.97
308_V	312_S	0.675	0.97
31_T	323_V	0.672	0.97
71_D	76_Q	0.670	0.97
288_F	300_V	0.666	0.97
56_A	199_F	0.665	0.97
286_M	302_Y	0.664	0.97
174_A	226_S	0.664	0.97
281_K	306_K	0.661	0.96
167_K	199_F	0.653	0.96
124_I	166_I	0.652	0.96
59_T	90_V	0.652	0.96
32_V	240_I	0.651	0.96
145_E	149_A	0.650	0.96
119_F	123_L	0.648	0.96
116_K	120_T	0.648	0.96
254_D	257_T	0.647	0.96
124_I	161_L	0.647	0.96
109_V	120_T	0.644	0.96
200_V	230_S	0.643	0.96
216_S	280_N	0.643	0.96
138_D	171_S	0.642	0.96
125_T	128_K	0.640	0.96
173_P	187_P	0.639	0.96
227_L	231_V	0.637	0.96
127_A	131_S	0.635	0.96
124_I	127_A	0.634	0.96
270_I	273_Q	0.634	0.96
79_Y	87_T	0.633	0.95
251_D	296_H	0.633	0.95
94_Y	141_A	0.632	0.95
135_I	161_L	0.632	0.95
62_F	109_V	0.632	0.95
173_P	188_Y	0.630	0.95
113_K	156_Y	0.627	0.95
120_T	152_N	0.627	0.95
202_V	230_S	0.622	0.95
123_L	127_A	0.621	0.95
291_V	297_K	0.620	0.95
111_S	145_E	0.615	0.95
306_K	309_Q	0.613	0.95
52_M	55_I	0.612	0.95
106_A	110_M	0.612	0.95
231_V	239_V	0.610	0.95
67_Q	122_Q	0.609	0.94
140_E	326_Y	0.608	0.94
169_M	199_F	0.607	0.94
268_S	272_K	0.607	0.94
260_I	266_L	0.606	0.94
167_K	198_D	0.606	0.94
151_S	155_Q	0.604	0.94
42_Y	328_L	0.604	0.94
60_F	91_I	0.603	0.94
279_F	286_M	0.600	0.94
91_I	119_F	0.596	0.94
230_S	239_V	0.596	0.94
55_I	328_L	0.595	0.94
236_A	321_A	0.594	0.94
66_G	118_R	0.593	0.94
248_Y	301_W	0.592	0.94
59_T	171_S	0.590	0.93
35_T	44_S	0.588	0.93
193_I	196_Y	0.582	0.93
117_K	159_Q	0.577	0.93
71_D	78_T	0.577	0.93
260_I	265_E	0.577	0.93
124_I	162_N	0.576	0.93
214_P	253_K	0.574	0.93
183_D	187_P	0.573	0.92
56_A	324_S	0.569	0.92
137_I	153_F	0.566	0.92
171_S	205_Y	0.566	0.92
93_N	96_D	0.566	0.92
62_F	105_L	0.563	0.92
96_D	106_A	0.560	0.92
225_S	229_F	0.559	0.92
191_A	194_G	0.558	0.91
106_A	139_F	0.554	0.91
303_E	308_V	0.554	0.91
216_S	283_S	0.554	0.91
96_D	105_L	0.553	0.91
267_K	271_K	0.551	0.91
155_Q	195_K	0.550	0.91
243_I	315_A	0.549	0.91
176_S	185_S	0.545	0.91
188_Y	193_I	0.545	0.91
325_V	328_L	0.544	0.90
107_S	143_N	0.542	0.90
62_F	68_I	0.541	0.90
173_P	185_S	0.540	0.90
81_K	87_T	0.539	0.90
243_I	312_S	0.539	0.90
208_H	217_V	0.538	0.90
240_I	244_P	0.538	0.90
66_G	109_V	0.537	0.90
154_I	158_S	0.537	0.90
236_A	318_Y	0.536	0.90
288_F	302_Y	0.533	0.90
215_G	250_W	0.531	0.89
203_M	206_D	0.530	0.89
270_I	277_P	0.530	0.89
212_G	215_G	0.529	0.89
35_T	57_T	0.529	0.89
70_G	76_Q	0.528	0.89
116_K	153_F	0.526	0.89
261_R	264_N	0.525	0.89
55_I	85_I	0.524	0.89
121_D	124_I	0.524	0.89
221_N	314_L	0.524	0.89
210_I	248_Y	0.521	0.88
264_N	268_S	0.521	0.88
260_I	263_W	0.518	0.88
192_K	196_Y	0.518	0.88
127_A	132_Y	0.517	0.88
205_Y	246_Y	0.517	0.88
174_A	207_E	0.515	0.88
261_R	269_L	0.514	0.88
112_N	149_A	0.513	0.88
90_V	93_N	0.512	0.88
32_V	169_M	0.510	0.87
135_I	157_V	0.510	0.87
139_F	153_F	0.506	0.87
147_R	193_I	0.505	0.87
81_K	84_K	0.505	0.87
30_M	53_N	0.504	0.87
241_M	314_L	0.503	0.87
69_I	75_K	0.503	0.87
136_N	242_G	0.503	0.87
141_A	203_M	0.501	0.86
60_F	126_L	0.500	0.86

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
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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
3w4rA	1	0.8779	100	0.191	Contact Map
4q6tA	1	0.9041	100	0.206	Contact Map
1itxA	1	0.9041	100	0.212	Contact Map
1edqA	1	0.9535	100	0.217	Contact Map
1w9pA	1	0.875	100	0.227	Contact Map
1goiA	2	0.8983	100	0.229	Contact Map
3arxA	1	0.9535	100	0.23	Contact Map
3oa5A	1	0.9535	100	0.234	Contact Map
1vf8A	1	0.8692	100	0.236	Contact Map
3g6mA	1	0.8692	100	0.236	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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