YCBU - BACSU - GREMLIN Contacts

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YCBU - Uncharacterized aminotransferase YcbU

UniProt:	P42253	Sequences: MEHLPEQYRQLFPTLQTHTMLASCSQSALAEPVSRAIQDYYDSLLYKGTNWKEAIEKTEFARNEFAKLIGAEPDEVAIVPSVSDALVSVASSLTAFGKKHVVYTDMDFPAVPHVWQAHSDYTVSVIPSIDGVLPLEQYETHISDETVLTCVPHVHYRDGYVQDIKAIAEISQRKGSLLFVDAYQSAGHIPIDVKEWGVDMLAAGTRKYLLGIPGVAFLYVRKELADALKPKASAWFGRESGFDGAYAKVARRFQTGTPAFISVYAAAAALSLLNHIGVSHIRDHVKTICADAVQYAAEKGLQLAAAQGGIQPGMVAIRDERASETAGLLKKKKVICAPRENVIRLAPHFYNTKEEMRHAIDEIAAKTIHK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	370 (327)
Sequences:	34842 (23960)
Seq/√Len:	1325.0

ECOLI - CSDA SUFS ISCS SERC DCEB DCEA LTAE
BACSU - YCBU SUFS ISCS ISCS1 PUCG ISCS2 SERC
HALSA - Q9HR11 CSD MFNA Q9HMR6 Q9HHV3
SULSO - Q97WK1 Q97VM5 Q97ZK0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
168_A	178_L	3.414	1.00
291_D	357_R	3.375	1.00
100_H	124_S	3.311	1.00
295_Y	360_I	3.298	1.00
291_D	353_K	3.255	1.00
153_H	185_S	2.963	1.00
163_D	166_A	2.828	1.00
64_E	271_S	2.745	1.00
139_E	170_I	2.716	1.00
192_D	195_E	2.573	1.00
105_D	127_P	2.558	1.00
139_E	173_R	2.517	1.00
100_H	122_T	2.506	1.00
182_A	201_L	2.446	1.00
171_S	176_S	2.372	1.00
268_A	271_S	2.371	1.00
203_A	217_F	2.345	1.00
100_H	143_S	2.315	1.00
291_D	295_Y	2.291	1.00
137_Q	140_T	2.257	1.00
259_A	262_S	2.249	1.00
149_T	171_S	2.240	1.00
332_K	365_A	2.140	1.00
295_Y	357_R	2.120	1.00
358_H	362_E	2.050	1.00
332_K	362_E	2.002	1.00
168_A	172_Q	2.002	1.00
137_Q	141_H	1.981	1.00
70_G	192_D	1.971	1.00
302_Q	318_R	1.953	1.00
284_H	288_I	1.951	1.00
100_H	146_T	1.940	1.00
31_E	35_R	1.932	1.00
124_S	141_H	1.903	1.00
38_Q	42_D	1.902	1.00
295_Y	298_E	1.877	1.00
134_P	137_Q	1.828	1.00
80_P	84_D	1.825	1.00
34_S	38_Q	1.822	1.00
151_V	167_I	1.811	1.00
345_L	359_A	1.808	1.00
100_H	145_E	1.773	1.00
287_T	353_K	1.771	1.00
64_E	267_A	1.771	1.00
127_P	137_Q	1.747	1.00
328_L	366_K	1.735	1.00
165_K	195_E	1.729	1.00
171_S	178_L	1.726	1.00
169_E	173_R	1.723	1.00
67_K	274_N	1.713	1.00
165_K	169_E	1.710	1.00
170_I	174_K	1.693	1.00
128_S	132_V	1.662	1.00
302_Q	320_E	1.641	1.00
39_D	43_S	1.617	1.00
180_V	198_V	1.605	1.00
135_L	170_I	1.604	1.00
304_A	318_R	1.586	1.00
172_Q	197_G	1.580	1.00
99_K	147_V	1.578	1.00
86_L	110_A	1.576	1.00
328_L	332_K	1.561	1.00
64_E	274_N	1.555	1.00
166_A	169_E	1.545	1.00
89_V	200_M	1.537	1.00
292_A	347_P	1.534	1.00
35_R	39_D	1.526	1.00
327_G	331_K	1.514	1.00
75_E	222_K	1.508	1.00
79_V	85_A	1.495	1.00
286_K	290_A	1.477	1.00
139_E	174_K	1.475	1.00
290_A	294_Q	1.455	1.00
31_E	42_D	1.453	1.00
135_L	166_A	1.453	1.00
151_V	178_L	1.448	1.00
198_V	201_L	1.445	1.00
60_F	64_E	1.437	1.00
142_I	170_I	1.419	1.00
172_Q	199_D	1.417	1.00
295_Y	364_A	1.417	1.00
82_V	183_Y	1.416	1.00
34_S	42_D	1.414	1.00
170_I	173_R	1.413	1.00
283_D	287_T	1.412	1.00
279_S	283_D	1.402	1.00
293_V	315_V	1.385	1.00
36_A	268_A	1.374	1.00
289_C	293_V	1.370	1.00
282_R	286_K	1.368	1.00
35_R	38_Q	1.367	1.00
148_L	179_F	1.366	1.00
353_K	357_R	1.361	1.00
60_F	267_A	1.359	1.00
93_L	177_L	1.344	1.00
65_F	217_F	1.332	1.00
293_V	297_A	1.330	1.00
205_T	266_A	1.329	1.00
37_I	265_A	1.326	1.00
328_L	331_K	1.323	1.00
63_N	67_K	1.314	1.00
352_T	355_E	1.300	1.00
72_E	222_K	1.293	1.00
86_L	179_F	1.293	1.00
36_A	39_D	1.291	1.00
139_E	143_S	1.288	1.00
292_A	356_M	1.284	1.00
105_D	125_V	1.283	1.00
91_S	233_S	1.264	1.00
117_A	233_S	1.263	1.00
63_N	66_A	1.263	1.00
44_L	53_E	1.257	1.00
164_I	180_V	1.256	1.00
362_E	365_A	1.255	1.00
168_A	197_G	1.252	1.00
169_E	197_G	1.248	1.00
126_I	141_H	1.248	1.00
212_I	265_A	1.238	1.00
358_H	361_D	1.224	1.00
200_M	220_V	1.210	1.00
61_A	267_A	1.209	1.00
179_F	202_A	1.201	1.00
30_A	272_L	1.198	1.00
103_Y	115_W	1.198	1.00
154_V	311_Q	1.195	1.00
334_V	358_H	1.194	1.00
143_S	174_K	1.190	1.00
32_P	272_L	1.181	1.00
99_K	145_E	1.170	1.00
64_E	67_K	1.170	1.00
277_G	280_H	1.163	1.00
136_E	139_E	1.163	1.00
267_A	271_S	1.159	1.00
136_E	140_T	1.156	1.00
112_P	125_V	1.154	1.00
284_H	287_T	1.150	1.00
102_V	146_T	1.149	1.00
297_A	307_Q	1.134	1.00
324_E	328_L	1.134	1.00
102_V	141_H	1.133	1.00
113_H	116_Q	1.124	1.00
360_I	364_A	1.116	1.00
103_Y	125_V	1.107	1.00
135_L	139_E	1.102	1.00
298_E	364_A	1.093	1.00
186_A	203_A	1.084	1.00
294_Q	297_A	1.084	1.00
151_V	164_I	1.082	1.00
85_A	202_A	1.082	1.00
154_V	185_S	1.081	1.00
210_L	348_H	1.079	1.00
143_S	146_T	1.077	1.00
139_E	166_A	1.071	1.00
138_Y	149_T	1.069	1.00
288_I	356_M	1.068	1.00
56_E	60_F	1.064	1.00
138_Y	167_I	1.060	1.00
336_C	343_I	1.060	1.00
96_F	99_K	1.059	1.00
63_N	73_P	1.058	1.00
288_I	353_K	1.056	1.00
149_T	176_S	1.051	1.00
191_I	195_E	1.050	1.00
161_V	189_I	1.048	1.00
95_A	98_K	1.048	1.00
68_L	186_A	1.042	1.00
74_D	222_K	1.038	1.00
98_K	147_V	1.037	1.00
354_E	357_R	1.030	1.00
57_K	264_Y	1.026	1.00
209_L	266_A	1.026	1.00
311_Q	314_M	1.018	1.00
153_H	201_L	1.013	1.00
294_Q	298_E	1.010	1.00
323_S	327_G	1.003	1.00
357_R	361_D	1.001	1.00
326_A	338_P	0.999	1.00
271_S	275_H	0.991	1.00
361_D	365_A	0.981	1.00
34_S	41_Y	0.980	1.00
95_A	99_K	0.978	1.00
70_G	194_K	0.977	1.00
111_V	150_C	0.972	1.00
192_D	196_W	0.970	1.00
130_D	306_A	0.966	1.00
106_M	162_Q	0.963	1.00
280_H	284_H	0.955	1.00
334_V	359_A	0.951	1.00
326_A	330_K	0.949	1.00
91_S	117_A	0.942	1.00
295_Y	361_D	0.940	1.00
277_G	281_I	0.939	1.00
313_G	316_A	0.938	1.00
76_V	219_Y	0.938	1.00
271_S	274_N	0.936	1.00
150_C	179_F	0.935	1.00
185_S	201_L	0.934	1.00
101_V	115_W	0.933	1.00
354_E	358_H	0.931	1.00
291_D	356_M	0.924	1.00
293_V	303_L	0.921	1.00
193_V	219_Y	0.919	1.00
280_H	283_D	0.918	1.00
153_H	196_W	0.918	1.00
300_G	320_E	0.915	1.00
289_C	315_V	0.913	1.00
177_L	200_M	0.913	1.00
58_T	263_V	0.912	1.00
329_L	336_C	0.912	1.00
190_P	193_V	0.911	1.00
268_A	272_L	0.910	1.00
199_D	221_R	0.906	1.00
66_A	71_A	0.904	1.00
153_H	164_I	0.902	1.00
72_E	75_E	0.902	1.00
94_T	121_Y	0.902	1.00
142_I	174_K	0.901	1.00
32_P	35_R	0.901	1.00
190_P	279_S	0.901	1.00
324_E	327_G	0.898	1.00
122_T	143_S	0.898	1.00
44_L	47_K	0.897	1.00
172_Q	178_L	0.895	1.00
292_A	359_A	0.892	1.00
177_L	224_L	0.889	1.00
171_S	175_G	0.884	1.00
90_A	115_W	0.884	1.00
47_K	50_N	0.884	1.00
347_P	356_M	0.881	1.00
281_I	285_V	0.876	1.00
334_V	362_E	0.875	1.00
68_L	270_L	0.875	1.00
128_S	134_P	0.873	1.00
61_A	64_E	0.869	1.00
336_C	345_L	0.865	1.00
317_I	345_L	0.861	1.00
325_T	366_K	0.860	1.00
142_I	146_T	0.859	1.00
154_V	312_P	0.858	1.00
193_V	196_W	0.848	1.00
326_A	336_C	0.847	1.00
311_Q	315_V	0.845	1.00
179_F	200_M	0.843	1.00
190_P	194_K	0.842	1.00
200_M	224_L	0.840	1.00
69_I	203_A	0.840	1.00
112_P	116_Q	0.838	1.00
351_N	355_E	0.831	1.00
351_N	356_M	0.829	1.00
281_I	349_F	0.825	1.00
135_L	138_Y	0.818	1.00
348_H	351_N	0.815	1.00
296_A	317_I	0.815	1.00
93_L	200_M	0.813	1.00
37_I	41_Y	0.812	1.00
152_P	156_Y	0.807	1.00
327_G	330_K	0.806	1.00
31_E	34_S	0.805	1.00
191_I	194_K	0.800	1.00
229_K	233_S	0.794	1.00
205_T	215_V	0.791	1.00
221_R	224_L	0.788	1.00
69_I	219_Y	0.785	1.00
234_A	238_R	0.785	1.00
142_I	176_S	0.784	1.00
292_A	315_V	0.780	1.00
89_V	179_F	0.775	1.00
72_E	194_K	0.774	1.00
215_V	262_S	0.770	1.00
53_E	56_E	0.769	1.00
287_T	291_D	0.766	1.00
235_W	238_R	0.765	1.00
104_T	107_D	0.763	1.00
149_T	167_I	0.762	1.00
60_F	271_S	0.759	1.00
234_A	237_G	0.756	1.00
171_S	174_K	0.751	1.00
46_Y	50_N	0.749	1.00
281_I	284_H	0.748	1.00
304_A	316_A	0.747	1.00
65_F	270_L	0.741	1.00
168_A	196_W	0.741	1.00
292_A	345_L	0.740	1.00
190_P	195_E	0.735	1.00
127_P	141_H	0.733	1.00
115_W	123_V	0.732	1.00
211_G	215_V	0.731	1.00
292_A	296_A	0.730	1.00
103_Y	123_V	0.730	1.00
59_E	63_N	0.729	1.00
197_G	221_R	0.728	1.00
60_F	63_N	0.726	1.00
101_V	148_L	0.723	1.00
325_T	363_I	0.720	1.00
109_P	113_H	0.720	1.00
267_A	270_L	0.717	1.00
57_K	60_F	0.717	1.00
43_S	47_K	0.715	1.00
30_A	33_V	0.714	1.00
108_F	156_Y	0.713	1.00
132_V	309_G	0.713	1.00
276_I	280_H	0.713	1.00
64_E	68_L	0.711	1.00
209_L	270_L	0.710	1.00
141_H	144_D	0.709	1.00
124_S	146_T	0.708	1.00
87_V	91_S	0.702	1.00
45_L	48_G	0.697	1.00
116_Q	125_V	0.697	1.00
44_L	48_G	0.695	1.00
236_F	239_E	0.693	1.00
177_L	199_D	0.692	1.00
165_K	196_W	0.688	1.00
91_S	231_K	0.687	1.00
166_A	170_I	0.687	1.00
205_T	211_G	0.687	1.00
132_V	162_Q	0.686	1.00
182_A	185_S	0.685	1.00
124_S	143_S	0.682	1.00
210_L	349_F	0.682	1.00
224_L	227_A	0.681	1.00
191_I	196_W	0.677	1.00
169_E	172_Q	0.676	1.00
315_V	318_R	0.676	1.00
222_K	226_D	0.676	1.00
153_H	180_V	0.676	1.00
359_A	363_I	0.675	1.00
71_A	219_Y	0.675	1.00
77_A	88_S	0.674	1.00
111_V	115_W	0.674	1.00
45_L	49_T	0.672	1.00
140_T	144_D	0.669	1.00
39_D	42_D	0.666	1.00
186_A	209_L	0.664	1.00
182_A	186_A	0.664	1.00
330_K	335_I	0.663	1.00
61_A	263_V	0.662	1.00
86_L	202_A	0.659	1.00
215_V	263_V	0.658	1.00
296_A	363_I	0.657	1.00
297_A	306_A	0.655	1.00
291_D	294_Q	0.653	1.00
361_D	364_A	0.652	1.00
126_I	137_Q	0.652	1.00
32_P	268_A	0.652	1.00
39_D	44_L	0.652	1.00
248_K	251_R	0.650	1.00
185_S	189_I	0.650	1.00
103_Y	107_D	0.649	1.00
153_H	191_I	0.642	1.00
114_V	118_H	0.641	1.00
71_A	75_E	0.641	1.00
32_P	275_H	0.640	1.00
67_K	70_G	0.639	1.00
293_V	307_Q	0.639	1.00
68_L	274_N	0.638	1.00
167_I	178_L	0.634	1.00
55_I	59_E	0.633	1.00
211_G	214_G	0.633	1.00
284_H	353_K	0.632	1.00
288_I	347_P	0.626	1.00
95_A	121_Y	0.626	1.00
222_K	225_A	0.626	1.00
288_I	292_A	0.625	1.00
292_A	360_I	0.624	1.00
115_W	150_C	0.623	1.00
138_Y	142_I	0.622	1.00
190_P	196_W	0.621	1.00
291_D	360_I	0.618	1.00
250_A	253_F	0.618	1.00
45_L	50_N	0.617	1.00
283_D	286_K	0.617	1.00
357_R	360_I	0.617	1.00
168_A	198_V	0.617	1.00
235_W	239_E	0.616	1.00
233_S	236_F	0.614	1.00
82_V	202_A	0.614	1.00
186_A	270_L	0.614	1.00
59_E	62_R	0.611	1.00
310_I	314_M	0.610	1.00
190_P	282_R	0.609	1.00
164_I	178_L	0.606	1.00
168_A	171_S	0.605	1.00
33_V	269_A	0.603	1.00
75_E	223_E	0.603	1.00
279_S	282_R	0.601	1.00
249_V	252_R	0.601	1.00
296_A	301_L	0.598	1.00
128_S	131_G	0.597	1.00
65_F	78_I	0.596	1.00
102_V	124_S	0.596	1.00
75_E	221_R	0.595	1.00
249_V	253_F	0.594	1.00
64_E	270_L	0.593	1.00
301_L	319_D	0.591	1.00
356_M	360_I	0.591	1.00
232_A	237_G	0.591	1.00
287_T	290_A	0.590	1.00
278_V	282_R	0.589	1.00
104_T	151_V	0.589	1.00
46_Y	49_T	0.588	1.00
165_K	191_I	0.586	1.00
165_K	197_G	0.585	1.00
312_P	315_V	0.583	1.00
102_V	126_I	0.583	1.00
296_A	360_I	0.582	1.00
40_Y	57_K	0.581	1.00
118_H	121_Y	0.580	1.00
285_V	313_G	0.578	1.00
44_L	49_T	0.577	1.00
89_V	218_L	0.577	1.00
312_P	316_A	0.577	1.00
168_A	180_V	0.576	1.00
314_M	318_R	0.576	1.00
82_V	86_L	0.574	1.00
103_Y	150_C	0.573	1.00
319_D	325_T	0.571	1.00
41_Y	261_I	0.571	1.00
31_E	38_Q	0.571	1.00
79_V	88_S	0.570	1.00
58_T	260_F	0.568	1.00
153_H	161_V	0.567	1.00
232_A	235_W	0.567	1.00
138_Y	170_I	0.566	1.00
292_A	295_Y	0.563	1.00
152_P	155_H	0.562	1.00
52_K	55_I	0.562	1.00
84_D	87_V	0.560	1.00
89_V	93_L	0.559	1.00
122_T	145_E	0.554	1.00
136_E	166_A	0.553	1.00
66_A	73_P	0.551	1.00
205_T	217_F	0.551	1.00
37_I	261_I	0.550	1.00
265_A	269_A	0.550	1.00
162_Q	167_I	0.550	1.00
152_P	162_Q	0.550	1.00
84_D	232_A	0.550	1.00
314_M	317_I	0.548	1.00
306_A	309_G	0.547	1.00
71_A	201_L	0.544	1.00
69_I	193_V	0.543	1.00
186_A	191_I	0.543	1.00
177_L	223_E	0.538	1.00
231_K	235_W	0.538	1.00
90_A	94_T	0.536	1.00
359_A	362_E	0.535	1.00
126_I	133_L	0.534	1.00
325_T	329_L	0.534	1.00
333_K	337_A	0.533	1.00
272_L	275_H	0.531	1.00
130_D	307_Q	0.529	1.00
293_V	311_Q	0.529	1.00
228_L	232_A	0.528	1.00
75_E	194_K	0.528	1.00
295_Y	356_M	0.526	1.00
318_R	321_R	0.526	1.00
201_L	219_Y	0.524	1.00
32_P	36_A	0.524	1.00
69_I	186_A	0.524	1.00
288_I	351_N	0.522	1.00
42_D	47_K	0.522	1.00
272_L	276_I	0.520	1.00
40_Y	264_Y	0.520	1.00
183_Y	204_G	0.519	1.00
87_V	117_A	0.519	1.00
299_K	364_A	0.519	1.00
135_L	167_I	0.518	1.00
310_I	313_G	0.517	1.00
35_R	42_D	0.515	1.00
336_C	359_A	0.514	1.00
36_A	40_Y	0.514	1.00
299_K	302_Q	0.513	1.00
314_M	320_E	0.513	1.00
30_A	349_F	0.512	1.00
113_H	117_A	0.512	1.00
316_A	320_E	0.511	1.00
290_A	293_V	0.510	1.00
146_T	176_S	0.510	1.00
264_Y	267_A	0.509	1.00
205_T	209_L	0.509	1.00
42_D	45_L	0.508	1.00
148_L	177_L	0.508	1.00
311_Q	316_A	0.508	1.00
170_I	176_S	0.507	1.00
312_P	317_I	0.507	1.00
40_Y	261_I	0.506	1.00
107_D	112_P	0.505	1.00
91_S	118_H	0.500	1.00
293_V	310_I	0.500	1.00

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
3e9kA	2	0.9946	100	0.338	Contact Map
1qz9A	2	0.9838	100	0.371	Contact Map
1eluA	2	0.9649	100	0.374	Contact Map
1kmjA	2	0.9892	100	0.376	Contact Map
1t3iA	2	0.9892	100	0.387	Contact Map
4lw2A	2	0.9892	100	0.391	Contact Map
4w91A	2	0.9919	100	0.393	Contact Map
4q75A	2	0.9946	100	0.396	Contact Map
3caiA	2	0.9514	100	0.4	Contact Map
3a9zA	2	0.9162	100	0.415	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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