YKVY - BACSU - GREMLIN Contacts

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YKVY - Putative dipeptidase YkvY

UniProt:	O31689	Sequences: MNRIQRVSSWLKEAGHTAAFIHTKENVFYLTGFYTEPHERLMGLFIFQEEEPFFVCPGMEAGQARNAGWNHEIIGYADHENPWELIEKALKKRNISIHMLAVEKDSISLSRAEQLKHATGGAQFVSAEETLNQFRLIKDDNEIRLLKEAAKLADYGVEVGTAALREGISEVEVLAQIEYELKKKGIQGMSFSTMVLFGEKSGQPHGNPGTATLKKGDFVLFDLGVILDGYCSDITRTFAYKTINPKQEAIYETVLQAEKAAIEASKPGVRIGDLDLTARGIIEKAGYGDYFPHRLGHGLGISVHEYPSMSQANDTLLQEGMVYTIEPGIYVPEIGGVRIEDDVHVTKDGAVALTQYPKDLIIL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	363 (339)
Sequences:	11008 (8050)
Seq/√Len:	437.2

ECOLI - YPDF AMPP PEPQ MAP1
BACSU - YKVY YQHT MAP11 MAP12
HALSA - Q9HRF6 Q9HQC0 Q9HMB3 Q9HP03
SULSO - Q981D7 Q980E9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
147_K	351_V	5.215	1.00
319_E	347_K	4.348	1.00
265_S	345_V	3.202	1.00
143_I	344_H	3.073	1.00
246_K	334_I	2.790	1.00
252_E	256_Q	2.574	1.00
148_E	151_K	2.501	1.00
155_Y	184_K	2.461	1.00
25_E	302_S	2.415	1.00
159_V	180_E	2.415	1.00
246_K	249_A	2.344	1.00
179_Y	183_K	2.343	1.00
260_A	281_I	2.342	1.00
244_N	247_Q	2.341	1.00
176_Q	179_Y	2.340	1.00
270_R	273_D	2.290	1.00
169_S	212_T	2.253	1.00
137_I	318_Q	2.244	1.00
275_D	279_R	2.242	1.00
259_K	263_E	2.237	1.00
16_H	101_A	2.230	1.00
245_P	249_A	2.215	1.00
199_E	211_A	2.201	1.00
146_L	322_V	2.185	1.00
272_G	314_D	2.174	1.00
261_A	278_A	2.156	1.00
280_G	284_K	2.148	1.00
264_A	277_T	2.133	1.00
113_E	116_K	2.112	1.00
299_L	342_D	2.102	1.00
99_M	123_Q	2.023	1.00
253_T	285_A	2.005	1.00
147_K	151_K	1.975	1.00
215_K	241_K	1.971	1.00
145_L	228_D	1.946	1.00
260_A	263_E	1.901	1.00
10_W	13_E	1.901	1.00
163_A	176_Q	1.889	1.00
214_K	217_D	1.888	1.00
213_L	240_Y	1.856	1.00
178_E	182_K	1.808	1.00
85_L	88_K	1.797	1.00
250_I	335_G	1.774	1.00
248_E	252_E	1.757	1.00
346_T	351_V	1.708	1.00
250_I	337_V	1.697	1.00
180_E	183_K	1.680	1.00
270_R	316_L	1.678	1.00
211_A	217_D	1.674	1.00
325_I	343_V	1.674	1.00
218_F	247_Q	1.669	1.00
276_L	280_G	1.668	1.00
256_Q	260_A	1.651	1.00
254_V	337_V	1.636	1.00
239_A	243_I	1.621	1.00
161_T	238_F	1.618	1.00
262_I	343_V	1.600	1.00
180_E	184_K	1.590	1.00
169_S	172_E	1.586	1.00
281_I	285_A	1.582	1.00
99_M	125_V	1.579	1.00
47_F	50_E	1.577	1.00
255_L	259_K	1.563	1.00
266_K	269_V	1.552	1.00
282_I	329_I	1.550	1.00
63_Q	67_A	1.525	1.00
195_V	219_V	1.523	1.00
154_D	356_Y	1.518	1.00
318_Q	321_M	1.518	1.00
190_S	231_C	1.517	1.00
171_V	210_T	1.517	1.00
261_A	274_L	1.461	1.00
175_A	179_Y	1.458	1.00
55_V	89_A	1.454	1.00
57_P	60_E	1.450	1.00
31_T	45_F	1.449	1.00
222_D	233_D	1.447	1.00
324_T	342_D	1.428	1.00
344_H	353_L	1.424	1.00
44_L	47_F	1.412	1.00
136_L	321_M	1.406	1.00
158_E	162_A	1.405	1.00
166_E	215_K	1.398	1.00
233_D	340_E	1.391	1.00
218_F	239_A	1.391	1.00
173_V	213_L	1.391	1.00
197_F	211_A	1.389	1.00
10_W	14_A	1.372	1.00
159_V	184_K	1.372	1.00
258_E	262_I	1.368	1.00
140_D	144_R	1.363	1.00
226_I	231_C	1.363	1.00
159_V	162_A	1.357	1.00
144_R	148_E	1.344	1.00
250_I	331_V	1.322	1.00
17_T	98_H	1.320	1.00
12_K	49_E	1.303	1.00
28_F	229_G	1.302	1.00
257_A	281_I	1.302	1.00
269_V	273_D	1.296	1.00
176_Q	180_E	1.291	1.00
197_F	213_L	1.287	1.00
61_A	65_R	1.287	1.00
267_P	319_E	1.278	1.00
16_H	125_V	1.275	1.00
278_A	295_L	1.272	1.00
43_G	47_F	1.263	1.00
30_L	134_F	1.237	1.00
251_Y	339_I	1.235	1.00
249_A	285_A	1.233	1.00
222_D	340_E	1.229	1.00
173_V	219_V	1.224	1.00
245_P	248_E	1.221	1.00
172_E	183_K	1.219	1.00
283_E	288_G	1.216	1.00
256_Q	285_A	1.207	1.00
258_E	341_D	1.204	1.00
317_L	323_Y	1.203	1.00
260_A	277_T	1.201	1.00
174_L	178_E	1.197	1.00
273_D	276_L	1.192	1.00
272_G	276_L	1.189	1.00
262_I	352_A	1.188	1.00
317_L	345_V	1.180	1.00
146_L	150_A	1.174	1.00
137_I	321_M	1.172	1.00
148_E	227_L	1.168	1.00
153_A	234_I	1.167	1.00
81_N	84_E	1.160	1.00
112_A	116_K	1.157	1.00
152_L	229_G	1.154	1.00
157_V	234_I	1.151	1.00
256_Q	284_K	1.149	1.00
256_Q	281_I	1.145	1.00
17_T	99_M	1.144	1.00
133_Q	318_Q	1.142	1.00
249_A	252_E	1.133	1.00
141_N	145_L	1.132	1.00
151_K	155_Y	1.130	1.00
109_L	112_A	1.129	1.00
249_A	253_T	1.120	1.00
265_S	274_L	1.119	1.00
11_L	16_H	1.100	1.00
176_Q	183_K	1.097	1.00
218_F	237_T	1.082	1.00
269_V	277_T	1.079	1.00
261_A	277_T	1.077	1.00
152_L	186_I	1.076	1.00
141_N	144_R	1.073	1.00
168_I	172_E	1.069	1.00
264_A	269_V	1.069	1.00
346_T	349_G	1.067	1.00
159_V	176_Q	1.065	1.00
322_V	344_H	1.064	1.00
262_I	325_I	1.063	1.00
26_N	103_E	1.059	1.00
144_R	147_K	1.059	1.00
253_T	281_I	1.056	1.00
197_F	217_D	1.056	1.00
150_A	154_D	1.055	1.00
320_G	344_H	1.055	1.00
159_V	183_K	1.048	1.00
343_V	352_A	1.045	1.00
283_E	286_G	1.045	1.00
88_K	92_K	1.045	1.00
332_P	335_G	1.041	1.00
87_E	91_K	1.040	1.00
196_L	206_G	1.039	1.00
89_A	92_K	1.033	1.00
168_I	176_Q	1.026	1.00
198_G	217_D	1.022	1.00
178_E	193_T	1.020	1.00
246_K	331_V	1.019	1.00
30_L	131_L	1.019	1.00
331_V	334_I	1.012	1.00
147_K	344_H	1.012	1.00
275_D	295_L	1.011	1.00
257_A	282_I	1.010	1.00
265_S	325_I	1.007	1.00
260_A	264_A	1.005	1.00
178_E	189_M	1.004	1.00
21_I	30_L	1.003	1.00
76_Y	80_E	1.003	1.00
171_V	175_A	1.003	1.00
101_A	127_A	0.996	1.00
221_F	238_F	0.995	1.00
109_L	113_E	0.993	1.00
253_T	256_Q	0.991	1.00
211_A	214_K	0.986	1.00
127_A	130_T	0.979	1.00
75_G	80_E	0.974	1.00
277_T	280_G	0.973	1.00
265_S	343_V	0.972	1.00
150_A	342_D	0.969	1.00
186_I	225_V	0.965	1.00
47_F	52_P	0.964	1.00
253_T	282_I	0.959	1.00
323_Y	345_V	0.957	1.00
274_L	277_T	0.954	1.00
299_L	322_V	0.954	1.00
89_A	93_R	0.949	1.00
26_N	132_N	0.947	1.00
156_G	180_E	0.945	1.00
200_K	206_G	0.941	1.00
219_V	240_Y	0.940	1.00
164_L	238_F	0.939	1.00
154_D	355_Q	0.937	1.00
51_E	72_E	0.936	1.00
274_L	317_L	0.936	1.00
272_G	312_A	0.936	1.00
11_L	18_A	0.934	1.00
189_M	193_T	0.931	1.00
74_I	78_D	0.927	1.00
200_K	203_Q	0.922	1.00
157_V	238_F	0.918	1.00
81_N	85_L	0.910	1.00
173_V	195_V	0.907	1.00
158_E	356_Y	0.906	1.00
148_E	152_L	0.903	1.00
140_D	346_T	0.900	1.00
192_S	207_N	0.898	1.00
145_L	148_E	0.896	1.00
177_I	181_L	0.896	1.00
164_L	173_V	0.896	1.00
280_G	283_E	0.895	1.00
201_S	220_L	0.894	1.00
165_R	168_I	0.889	1.00
310_S	313_N	0.884	1.00
159_V	163_A	0.883	1.00
252_E	255_L	0.882	1.00
21_I	131_L	0.879	1.00
264_A	274_L	0.878	1.00
148_E	228_D	0.878	1.00
113_E	117_H	0.877	1.00
277_T	281_I	0.875	1.00
271_I	317_L	0.875	1.00
269_V	274_L	0.874	1.00
246_K	250_I	0.871	1.00
267_P	346_T	0.871	1.00
343_V	350_A	0.871	1.00
200_K	211_A	0.868	1.00
19_A	127_A	0.863	1.00
104_K	113_E	0.863	1.00
181_L	225_V	0.860	1.00
298_G	307_P	0.859	1.00
153_A	232_S	0.855	1.00
42_M	46_I	0.854	1.00
255_L	339_I	0.851	1.00
344_H	351_V	0.851	1.00
155_Y	158_E	0.850	1.00
196_L	201_S	0.848	1.00
43_G	46_I	0.847	1.00
239_A	247_Q	0.845	1.00
298_G	305_E	0.845	1.00
27_V	43_G	0.845	1.00
77_A	80_E	0.836	1.00
143_I	147_K	0.833	1.00
278_A	291_F	0.832	1.00
262_I	350_A	0.831	1.00
261_A	325_I	0.827	1.00
265_S	350_A	0.824	1.00
345_V	350_A	0.823	1.00
290_Y	332_P	0.806	1.00
150_A	354_T	0.806	1.00
267_P	347_K	0.803	1.00
162_A	166_E	0.801	1.00
257_A	261_A	0.800	1.00
270_R	314_D	0.799	1.00
29_Y	134_F	0.799	1.00
133_Q	315_T	0.798	1.00
166_E	240_Y	0.796	1.00
28_F	301_I	0.793	1.00
10_W	133_Q	0.793	1.00
260_A	278_A	0.787	1.00
152_L	227_L	0.786	1.00
88_K	91_K	0.784	1.00
130_T	133_Q	0.783	1.00
54_F	64_A	0.781	1.00
168_I	173_V	0.779	1.00
243_I	248_E	0.779	1.00
282_I	287_Y	0.778	1.00
136_L	318_Q	0.778	1.00
42_M	45_F	0.773	1.00
309_M	323_Y	0.773	1.00
102_V	109_L	0.771	1.00
267_P	318_Q	0.771	1.00
12_K	48_Q	0.771	1.00
142_E	230_Y	0.770	1.00
236_R	341_D	0.768	1.00
346_T	350_A	0.768	1.00
251_Y	255_L	0.766	1.00
326_E	340_E	0.765	1.00
42_M	47_F	0.764	1.00
68_G	72_E	0.764	1.00
315_T	318_Q	0.762	1.00
204_P	293_H	0.757	1.00
150_A	353_L	0.757	1.00
222_D	326_E	0.757	1.00
163_A	180_E	0.756	1.00
197_F	240_Y	0.755	1.00
281_I	284_K	0.754	1.00
299_L	324_T	0.753	1.00
177_I	221_F	0.753	1.00
170_E	200_K	0.751	1.00
152_L	184_K	0.746	1.00
160_G	221_F	0.745	1.00
273_D	277_T	0.745	1.00
53_F	74_I	0.745	1.00
225_V	232_S	0.743	1.00
145_L	227_L	0.742	1.00
11_L	19_A	0.742	1.00
108_S	111_R	0.741	1.00
15_G	99_M	0.737	1.00
151_K	154_D	0.734	1.00
201_S	218_F	0.734	1.00
257_A	277_T	0.733	1.00
154_D	158_E	0.733	1.00
75_G	78_D	0.732	1.00
260_A	280_G	0.730	1.00
330_Y	338_R	0.728	1.00
216_G	242_T	0.728	1.00
150_A	232_S	0.728	1.00
158_E	357_P	0.723	1.00
107_I	112_A	0.723	1.00
79_H	82_P	0.722	1.00
105_D	108_S	0.720	1.00
266_K	350_A	0.720	1.00
31_T	52_P	0.719	1.00
250_I	253_T	0.712	1.00
313_N	316_L	0.711	1.00
233_D	297_H	0.710	1.00
156_G	181_L	0.709	1.00
175_A	182_K	0.708	1.00
199_E	333_E	0.707	1.00
216_G	240_Y	0.706	1.00
85_L	89_A	0.705	1.00
18_A	100_L	0.705	1.00
64_A	67_A	0.703	1.00
114_Q	117_H	0.701	1.00
250_I	287_Y	0.700	1.00
160_G	173_V	0.699	1.00
191_F	224_G	0.699	1.00
264_A	267_P	0.698	1.00
297_H	340_E	0.698	1.00
179_Y	182_K	0.698	1.00
82_P	85_L	0.696	1.00
110_S	114_Q	0.695	1.00
279_R	291_F	0.695	1.00
267_P	345_V	0.694	1.00
70_N	73_I	0.692	1.00
205_H	304_H	0.692	1.00
328_G	338_R	0.690	1.00
203_Q	206_G	0.689	1.00
140_D	320_G	0.688	1.00
62_G	66_N	0.686	1.00
243_I	247_Q	0.685	1.00
201_S	336_G	0.685	1.00
76_Y	79_H	0.684	1.00
172_E	175_A	0.681	1.00
157_V	160_G	0.676	1.00
177_I	223_L	0.675	1.00
319_E	346_T	0.675	1.00
217_D	247_Q	0.674	1.00
169_S	210_T	0.674	1.00
157_V	223_L	0.673	1.00
258_E	325_I	0.672	1.00
53_F	89_A	0.670	1.00
218_F	243_I	0.670	1.00
233_D	326_E	0.668	1.00
261_A	264_A	0.666	1.00
231_C	303_V	0.665	1.00
79_H	83_W	0.664	1.00
117_H	120_G	0.656	1.00
136_L	315_T	0.655	1.00
189_M	192_S	0.652	0.99
153_A	156_G	0.651	0.99
267_P	350_A	0.646	0.99
25_E	301_I	0.645	0.99
247_Q	334_I	0.645	0.99
152_L	225_V	0.644	0.99
26_N	131_L	0.642	0.99
18_A	45_F	0.640	0.99
107_I	111_R	0.637	0.99
150_A	234_I	0.636	0.99
261_A	295_L	0.636	0.99
156_G	177_I	0.632	0.99
104_K	126_S	0.631	0.99
316_L	319_E	0.630	0.99
97_I	100_L	0.630	0.99
291_F	294_R	0.630	0.99
48_Q	52_P	0.628	0.99
84_E	88_K	0.628	0.99
143_I	322_V	0.626	0.99
58_G	66_N	0.625	0.99
160_G	176_Q	0.622	0.99
195_V	221_F	0.621	0.99
352_A	355_Q	0.621	0.99
331_V	335_G	0.620	0.99
28_F	34_Y	0.620	0.99
265_S	317_L	0.620	0.99
274_L	295_L	0.619	0.99
14_A	17_T	0.618	0.99
259_K	262_I	0.617	0.99
73_I	76_Y	0.616	0.99
53_F	81_N	0.615	0.99
330_Y	336_G	0.613	0.99
153_A	223_L	0.610	0.99
149_A	153_A	0.605	0.99
24_K	27_V	0.605	0.99
164_L	219_V	0.600	0.99
133_Q	136_L	0.600	0.99
315_T	321_M	0.599	0.99
116_K	120_G	0.598	0.99
322_V	342_D	0.598	0.99
300_G	305_E	0.597	0.99
160_G	163_A	0.595	0.99
308_S	312_A	0.595	0.99
268_G	318_Q	0.594	0.99
18_A	48_Q	0.593	0.99
235_T	340_E	0.593	0.99
83_W	86_I	0.590	0.99
253_T	287_Y	0.590	0.99
297_H	300_G	0.589	0.99
257_A	278_A	0.589	0.99
267_P	349_G	0.589	0.99
239_A	244_N	0.588	0.99
256_Q	259_K	0.586	0.99
201_S	239_A	0.586	0.99
253_T	329_I	0.585	0.99
144_R	151_K	0.584	0.99
58_G	292_P	0.582	0.99
49_E	52_P	0.582	0.99
11_L	14_A	0.581	0.99
244_N	334_I	0.574	0.99
82_P	90_L	0.571	0.99
234_I	342_D	0.570	0.99
164_L	240_Y	0.569	0.99
132_N	306_Y	0.567	0.99
65_R	68_G	0.566	0.99
293_H	304_H	0.565	0.99
22_H	25_E	0.565	0.99
157_V	161_T	0.564	0.99
257_A	260_A	0.564	0.99
64_A	68_G	0.564	0.99
188_G	192_S	0.562	0.98
10_W	134_F	0.559	0.98
268_G	316_L	0.559	0.98
222_D	297_H	0.559	0.98
284_K	287_Y	0.559	0.98
17_T	48_Q	0.556	0.98
201_S	204_P	0.556	0.98
155_Y	180_E	0.554	0.98
26_N	29_Y	0.553	0.98
71_H	75_G	0.550	0.98
27_V	31_T	0.550	0.98
282_I	288_G	0.549	0.98
173_V	221_F	0.548	0.98
275_D	294_R	0.547	0.98
215_K	242_T	0.545	0.98
75_G	79_H	0.545	0.98
68_G	71_H	0.544	0.98
351_V	355_Q	0.544	0.98
140_D	319_E	0.543	0.98
137_I	319_E	0.542	0.98
81_N	89_A	0.541	0.98
276_L	311_Q	0.540	0.98
266_K	348_D	0.539	0.98
138_K	142_E	0.535	0.98
56_C	61_A	0.532	0.98
166_E	214_K	0.531	0.98
153_A	224_G	0.531	0.98
154_D	354_T	0.529	0.98
231_C	301_I	0.529	0.98
76_Y	82_P	0.528	0.98
35_T	63_Q	0.528	0.98
253_T	257_A	0.528	0.98
54_F	68_G	0.527	0.98
33_F	63_Q	0.522	0.98
328_G	336_G	0.521	0.98
148_E	229_G	0.520	0.98
33_F	36_E	0.520	0.98
342_D	354_T	0.517	0.97
184_K	187_Q	0.516	0.97
108_S	112_A	0.515	0.97
171_V	187_Q	0.515	0.97
271_I	296_G	0.515	0.97
62_G	65_R	0.515	0.97
160_G	177_I	0.515	0.97
250_I	329_I	0.515	0.97
20_F	100_L	0.514	0.97
199_E	202_G	0.514	0.97
278_A	281_I	0.513	0.97
234_I	354_T	0.513	0.97
72_E	75_G	0.513	0.97
153_A	225_V	0.512	0.97
272_G	313_N	0.510	0.97
104_K	108_S	0.510	0.97
102_V	124_F	0.509	0.97
59_M	64_A	0.506	0.97
222_D	235_T	0.506	0.97
98_H	123_Q	0.506	0.97
271_I	315_T	0.506	0.97
348_D	351_V	0.505	0.97
156_G	225_V	0.503	0.97
82_P	86_I	0.503	0.97
155_Y	159_V	0.501	0.97
185_G	228_D	0.500	0.97
297_H	326_E	0.500	0.97

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
4fkcA	2	0.9917	100	0.128	Contact Map
1wn1A	2	0.9752	100	0.141	Contact Map
2zsgA	2	0.9752	100	0.143	Contact Map
3q6dA	1	0.9725	100	0.147	Contact Map
4r60A	2	0.989	100	0.155	Contact Map
4egeA	2	0.9835	100	0.165	Contact Map
1wy2A	2	0.9559	100	0.166	Contact Map
1kp0A	2	0.8871	100	0.19	Contact Map
1chmA	2	0.9917	100	0.192	Contact Map
3ig4A	4	0.9697	100	0.195	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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