PEPQ - ECOLI - GREMLIN Contacts

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PEPQ - Xaa-Pro dipeptidase

UniProt:	P21165	Sequences: MESLASLYKNHIATLQERTRDALARFKLDALLIHSGELFNVFLDDHPYPFKVNPQFKAWVPVTQVPNCWLLVDGVNKPKLWFYLPVDYWHNVEPLPTSFWTEDVEVIALPKADGIGSLLPAARGNIGYIGPVPERALQLGIEASNINPKGVIDYLHYYRSFKTEYELACMREAQKMAVNGHRAAEEAFRSGMSEFDINIAYLTATGHRDTDVPYSNIVALNEHAAVLHYTKLDHQAPEEMRSFLLDAGAEYNGYAADLTRTWSAKSDNDYAQLVKDVNDEQLALIATMKAGVSYVDYHIQFHQRIAKLLRKHQIITDMSEEAMVENDLTGPFMPHGIGHPLGLQVHDVAGFMQDDSGTHLAAPAKYPYLRCTRILQPGMVLTIEPGIYFIESLLAPWREGQFSKHFNWQKIEALKPFGGIRIEDNVVIHENNVENMTRDLKLA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10698
Length:	443 (339)
Sequences:	5695 (4063)
Seq/√Len:	220.7

ECOLI - PEPQ AMPP YPDF
BACSU - YQHT YKVY MAP11
HALSA - Q9HRF6 Q9HQC0 Q9HMB3
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
171_R	434_E	6.462	1.00
377_P	430_E	5.305	1.00
288_M	428_I	5.100	1.00
167_L	427_V	3.484	1.00
275_K	279_D	3.317	1.00
239_E	265_K	2.952	1.00
293_S	296_D	2.951	1.00
276_D	308_L	2.756	1.00
172_E	175_K	2.653	1.00
171_R	175_K	2.583	1.00
269_D	272_Q	2.582	1.00
273_L	420_I	2.578	1.00
283_A	286_A	2.476	1.00
283_A	304_R	2.469	1.00
287_T	300_Q	2.431	1.00
295_V	372_T	2.401	1.00
282_L	286_A	2.379	1.00
268_N	272_Q	2.351	1.00
170_M	380_V	2.318	1.00
298_H	302_H	2.298	1.00
179_N	208_R	2.270	1.00
183_A	204_A	2.166	1.00
161_F	376_Q	2.166	1.00
54_P	344_Q	2.153	1.00
269_D	392_S	2.053	1.00
271_A	275_K	2.050	1.00
238_E	241_R	2.042	1.00
341_L	425_N	2.029	1.00
203_T	207_H	2.016	1.00
139_L	142_E	1.992	1.00
213_P	255_A	1.964	1.00
279_D	308_L	1.940	1.00
114_G	117_S	1.926	1.00
305_I	387_I	1.925	1.00
267_D	270_Y	1.894	1.00
277_V	420_I	1.868	1.00
178_V	440_L	1.865	1.00
284_L	297_Y	1.854	1.00
285_I	426_V	1.846	1.00
427_V	436_M	1.839	1.00
196_D	207_H	1.799	1.00
293_S	374_I	1.792	1.00
169_C	252_N	1.757	1.00
200_A	203_T	1.751	1.00
279_D	283_A	1.724	1.00
426_V	435_N	1.705	1.00
125_N	147_N	1.688	1.00
190_S	239_E	1.671	1.00
41_V	46_H	1.664	1.00
284_L	301_F	1.664	1.00
280_E	304_R	1.663	1.00
193_S	235_Q	1.655	1.00
183_A	186_E	1.642	1.00
242_S	261_T	1.628	1.00
193_S	196_D	1.623	1.00
289_K	292_V	1.609	1.00
236_A	264_A	1.602	1.00
55_Q	156_H	1.590	1.00
288_M	383_I	1.565	1.00
61_P	70_L	1.523	1.00
204_A	208_R	1.522	1.00
118_L	121_A	1.519	1.00
177_A	258_L	1.506	1.00
199_I	203_T	1.505	1.00
126_I	129_I	1.504	1.00
170_M	174_Q	1.497	1.00
246_D	257_D	1.495	1.00
257_D	423_E	1.493	1.00
182_R	186_E	1.481	1.00
204_A	207_H	1.480	1.00
292_V	296_D	1.480	1.00
429_H	434_E	1.467	1.00
60_V	158_Y	1.458	1.00
283_A	300_Q	1.447	1.00
279_D	307_K	1.441	1.00
197_I	243_F	1.438	1.00
222_E	234_H	1.429	1.00
304_R	308_L	1.422	1.00
303_Q	307_K	1.408	1.00
300_Q	304_R	1.397	1.00
69_W	72_V	1.396	1.00
376_Q	379_M	1.393	1.00
43_L	46_H	1.383	1.00
130_G	139_L	1.379	1.00
202_L	206_G	1.378	1.00
280_E	305_I	1.366	1.00
198_N	202_L	1.363	1.00
380_V	427_V	1.362	1.00
284_L	300_Q	1.356	1.00
250_E	255_A	1.344	1.00
299_I	303_Q	1.329	1.00
281_Q	285_I	1.328	1.00
134_E	137_L	1.319	1.00
301_F	333_M	1.317	1.00
78_P	108_A	1.317	1.00
220_L	234_H	1.316	1.00
187_A	200_A	1.313	1.00
378_G	427_V	1.309	1.00
285_I	435_N	1.309	1.00
295_V	299_I	1.308	1.00
127_G	131_P	1.305	1.00
301_F	337_I	1.297	1.00
290_A	377_P	1.295	1.00
161_F	379_M	1.285	1.00
84_L	87_D	1.284	1.00
268_N	271_A	1.280	1.00
296_D	299_I	1.274	1.00
288_M	433_V	1.273	1.00
58_A	253_G	1.273	1.00
177_A	256_A	1.272	1.00
246_D	423_E	1.263	1.00
341_L	380_V	1.263	1.00
287_T	292_V	1.259	1.00
133_P	138_Q	1.256	1.00
165_Y	169_C	1.252	1.00
300_Q	303_Q	1.251	1.00
135_R	138_Q	1.250	1.00
172_E	251_Y	1.240	1.00
183_A	200_A	1.235	1.00
306_A	315_I	1.232	1.00
175_K	439_D	1.229	1.00
160_S	379_M	1.227	1.00
220_L	236_A	1.225	1.00
41_V	45_D	1.222	1.00
179_N	182_R	1.220	1.00
288_M	297_Y	1.219	1.00
375_L	381_L	1.217	1.00
383_I	426_V	1.212	1.00
429_H	432_N	1.208	1.00
74_G	77_K	1.206	1.00
41_V	44_D	1.180	1.00
127_G	130_G	1.177	1.00
279_D	304_R	1.175	1.00
185_E	262_W	1.172	1.00
281_Q	424_D	1.170	1.00
242_S	263_S	1.159	1.00
138_Q	142_E	1.156	1.00
174_Q	437_T	1.154	1.00
283_A	287_T	1.150	1.00
188_F	197_I	1.126	1.00
53_N	56_F	1.120	1.00
290_A	433_V	1.116	1.00
125_N	149_K	1.112	1.00
79_K	106_V	1.103	1.00
292_V	300_Q	1.102	1.00
290_A	428_I	1.098	1.00
45_D	127_G	1.087	1.00
60_V	155_L	1.085	1.00
273_L	389_F	1.083	1.00
427_V	434_E	1.083	1.00
290_A	429_H	1.080	1.00
288_M	426_V	1.077	1.00
164_E	168_A	1.069	1.00
235_Q	238_E	1.066	1.00
234_H	241_R	1.064	1.00
192_M	196_D	1.057	1.00
278_N	282_L	1.057	1.00
188_F	262_W	1.056	1.00
51_K	250_E	1.039	1.00
110_P	114_G	1.033	1.00
123_R	129_I	1.029	1.00
276_D	304_R	1.027	1.00
99_F	103_D	1.025	1.00
169_C	251_Y	1.024	1.00
272_Q	275_K	1.017	1.00
178_V	439_D	1.014	1.00
165_Y	168_A	1.006	1.00
384_E	423_E	0.996	1.00
171_R	427_V	0.995	1.00
242_S	270_Y	0.995	1.00
99_F	102_E	0.986	1.00
297_Y	375_L	0.970	1.00
249_A	256_A	0.970	1.00
278_N	422_I	0.966	1.00
169_C	172_E	0.963	1.00
69_W	115_I	0.955	1.00
285_I	433_V	0.953	1.00
101_T	105_E	0.951	1.00
243_F	264_A	0.951	1.00
151_V	154_Y	0.949	1.00
221_N	241_R	0.946	1.00
223_H	234_H	0.945	1.00
189_R	192_M	0.944	1.00
292_V	297_Y	0.937	1.00
181_H	262_W	0.937	1.00
287_T	290_A	0.934	1.00
298_H	337_I	0.934	1.00
45_D	50_F	0.931	1.00
157_Y	373_R	0.929	1.00
297_Y	300_Q	0.927	1.00
201_Y	245_L	0.925	0.99
224_A	419_G	0.922	0.99
192_M	200_A	0.919	0.99
184_A	245_L	0.918	0.99
41_V	47_P	0.918	0.99
175_K	179_N	0.913	0.99
220_L	264_A	0.911	0.99
168_A	171_R	0.909	0.99
257_D	339_H	0.909	0.99
284_L	287_T	0.909	0.99
273_L	276_D	0.907	0.99
289_K	433_V	0.904	0.99
127_G	132_V	0.900	0.99
340_P	347_D	0.900	0.99
297_Y	337_I	0.899	0.99
133_P	140_G	0.898	0.99
339_H	423_E	0.896	0.99
81_W	91_N	0.896	0.99
59_W	158_Y	0.888	0.99
167_L	380_V	0.887	0.99
102_E	105_E	0.887	0.99
126_I	131_P	0.887	0.99
355_D	373_R	0.887	0.99
245_L	262_W	0.884	0.99
68_C	72_V	0.884	0.99
134_E	138_Q	0.882	0.99
234_H	238_E	0.882	0.99
172_E	252_N	0.880	0.99
137_L	140_G	0.878	0.99
275_K	278_N	0.875	0.99
428_I	433_V	0.873	0.99
201_Y	205_T	0.871	0.99
222_E	225_A	0.867	0.99
51_K	56_F	0.864	0.99
164_E	378_G	0.862	0.99
194_E	223_H	0.862	0.99
195_F	233_D	0.856	0.99
174_Q	425_N	0.854	0.99
116_G	120_P	0.852	0.99
40_N	48_Y	0.850	0.99
240_M	264_A	0.848	0.99
133_P	139_L	0.846	0.99
223_H	226_V	0.846	0.99
51_K	54_P	0.845	0.99
183_A	187_A	0.845	0.99
274_V	422_I	0.845	0.99
177_A	180_G	0.842	0.99
280_E	284_L	0.841	0.99
173_A	177_A	0.835	0.99
305_I	333_M	0.834	0.99
170_M	341_L	0.831	0.99
137_L	141_I	0.830	0.99
426_V	433_V	0.828	0.99
56_F	68_C	0.828	0.99
388_Y	421_R	0.825	0.99
202_L	216_N	0.824	0.99
289_K	431_N	0.824	0.99
290_A	430_E	0.822	0.99
129_I	132_V	0.821	0.99
82_F	118_L	0.817	0.99
214_Y	248_G	0.817	0.99
200_A	207_H	0.817	0.99
192_M	197_I	0.814	0.99
246_D	384_E	0.814	0.99
128_Y	131_P	0.813	0.99
202_L	212_V	0.813	0.99
284_L	337_I	0.812	0.99
58_A	343_L	0.810	0.99
296_D	300_Q	0.807	0.99
174_Q	178_V	0.806	0.99
166_E	254_Y	0.802	0.99
276_D	305_I	0.793	0.98
374_I	377_P	0.792	0.98
294_Y	338_G	0.787	0.98
70_L	79_K	0.787	0.98
157_Y	376_Q	0.786	0.98
223_H	229_Y	0.780	0.98
69_W	73_D	0.773	0.98
55_Q	59_W	0.772	0.98
240_M	265_K	0.772	0.98
40_N	46_H	0.770	0.98
174_Q	256_A	0.770	0.98
272_Q	276_D	0.769	0.98
228_H	346_H	0.769	0.98
200_A	204_A	0.766	0.98
212_V	216_N	0.766	0.98
138_Q	141_I	0.765	0.98
302_H	333_M	0.762	0.98
123_R	127_G	0.760	0.98
73_D	80_L	0.759	0.98
382_T	425_N	0.758	0.98
303_Q	306_A	0.757	0.98
285_I	383_I	0.753	0.98
257_D	384_E	0.753	0.98
274_V	278_N	0.750	0.98
98_S	101_T	0.747	0.98
44_D	47_P	0.746	0.98
193_S	236_A	0.746	0.98
288_M	375_L	0.746	0.98
335_H	346_H	0.745	0.98
222_E	391_E	0.744	0.98
94_P	99_F	0.743	0.98
340_P	349_A	0.741	0.98
133_P	137_L	0.741	0.98
94_P	104_V	0.740	0.98
70_L	73_D	0.740	0.98
283_A	301_F	0.740	0.98
135_R	139_L	0.736	0.97
123_R	131_P	0.736	0.97
144_S	148_P	0.733	0.97
280_E	283_A	0.733	0.97
246_D	259_T	0.732	0.97
50_F	60_V	0.730	0.97
117_S	121_A	0.730	0.97
64_Q	253_G	0.729	0.97
136_A	139_L	0.728	0.97
339_H	384_E	0.725	0.97
124_G	127_G	0.724	0.97
215_S	230_T	0.720	0.97
88_Y	92_V	0.720	0.97
184_A	200_A	0.719	0.97
290_A	434_E	0.715	0.97
63_T	68_C	0.713	0.97
280_E	301_F	0.712	0.97
40_N	45_D	0.710	0.97
47_P	50_F	0.708	0.97
67_N	84_L	0.708	0.97
259_T	423_E	0.708	0.97
168_A	172_E	0.706	0.97
388_Y	419_G	0.705	0.97
162_K	166_E	0.705	0.97
224_A	244_L	0.704	0.97
123_R	126_I	0.701	0.97
386_G	419_G	0.701	0.97
114_G	118_L	0.699	0.97
126_I	130_G	0.698	0.97
117_S	120_P	0.697	0.96
287_T	296_D	0.697	0.96
177_A	440_L	0.696	0.96
178_V	438_R	0.693	0.96
246_D	339_H	0.691	0.96
167_L	171_R	0.688	0.96
52_V	56_F	0.687	0.96
128_Y	132_V	0.684	0.96
174_Q	436_M	0.681	0.96
190_S	264_A	0.681	0.96
103_D	106_V	0.680	0.96
180_G	205_T	0.680	0.96
219_A	224_A	0.680	0.96
134_E	140_G	0.679	0.96
133_P	136_A	0.679	0.96
228_H	419_G	0.678	0.96
128_Y	135_R	0.676	0.96
135_R	141_I	0.675	0.96
73_D	77_K	0.674	0.96
179_N	204_A	0.674	0.96
68_C	73_D	0.671	0.96
290_A	376_Q	0.670	0.96
226_V	229_Y	0.670	0.96
59_W	62_V	0.669	0.96
380_V	436_M	0.666	0.95
294_Y	375_L	0.665	0.95
290_A	432_N	0.664	0.95
178_V	182_R	0.663	0.95
183_A	208_R	0.660	0.95
228_H	388_Y	0.659	0.95
335_H	421_R	0.658	0.95
125_N	130_G	0.658	0.95
218_V	245_L	0.656	0.95
124_G	130_G	0.654	0.95
113_D	117_S	0.652	0.95
198_N	210_T	0.648	0.95
287_T	297_Y	0.648	0.95
172_E	176_M	0.648	0.95
73_D	79_K	0.647	0.95
228_H	335_H	0.646	0.95
125_N	128_Y	0.646	0.95
269_D	273_L	0.646	0.95
46_H	215_S	0.644	0.95
40_N	47_P	0.643	0.95
101_T	106_V	0.643	0.95
101_T	104_V	0.640	0.94
85_P	113_D	0.640	0.94
241_R	270_Y	0.636	0.94
140_G	143_A	0.636	0.94
386_G	421_R	0.634	0.94
220_L	241_R	0.634	0.94
136_A	140_G	0.634	0.94
314_I	389_F	0.634	0.94
219_A	229_Y	0.633	0.94
212_V	215_S	0.633	0.94
176_M	249_A	0.631	0.94
384_E	388_Y	0.629	0.94
202_L	211_D	0.628	0.94
134_E	139_L	0.628	0.94
340_P	379_M	0.627	0.94
277_V	386_G	0.626	0.94
260_R	424_D	0.625	0.94
156_H	348_V	0.623	0.94
304_R	307_K	0.622	0.93
181_H	247_A	0.621	0.93
195_F	199_I	0.618	0.93
425_N	437_T	0.616	0.93
263_S	266_S	0.614	0.93
124_G	128_Y	0.613	0.93
384_E	421_R	0.612	0.93
98_S	102_E	0.611	0.93
182_R	439_D	0.608	0.93
129_I	134_E	0.604	0.92
201_Y	247_A	0.604	0.92
224_A	242_S	0.604	0.92
377_P	429_H	0.602	0.92
214_Y	256_A	0.601	0.92
187_A	204_A	0.599	0.92
332_F	390_I	0.598	0.92
294_Y	297_Y	0.598	0.92
183_A	201_Y	0.598	0.92
263_S	270_Y	0.598	0.92
255_A	345_V	0.597	0.92
71_L	82_F	0.592	0.92
346_H	385_P	0.591	0.92
197_I	218_V	0.591	0.92
199_I	206_G	0.590	0.92
174_Q	258_L	0.589	0.92
429_H	433_V	0.589	0.92
52_V	55_Q	0.586	0.91
197_I	236_A	0.586	0.91
180_G	201_Y	0.585	0.91
276_D	279_D	0.583	0.91
346_H	421_R	0.583	0.91
301_F	305_I	0.583	0.91
177_A	247_A	0.581	0.91
72_V	79_K	0.580	0.91
242_S	420_I	0.580	0.91
382_T	385_P	0.579	0.91
123_R	128_Y	0.578	0.91
160_S	340_P	0.578	0.91
54_P	343_L	0.578	0.91
293_S	372_T	0.577	0.91
80_L	108_A	0.576	0.91
205_T	212_V	0.576	0.91
385_P	421_R	0.572	0.90
352_M	355_D	0.568	0.90
382_T	423_E	0.567	0.90
335_H	388_Y	0.567	0.90
193_S	233_D	0.563	0.90
70_L	106_V	0.563	0.90
259_T	386_G	0.563	0.90
160_S	376_Q	0.563	0.90
90_H	94_P	0.561	0.89
92_V	99_F	0.561	0.89
175_K	178_V	0.560	0.89
280_E	300_Q	0.559	0.89
348_V	351_F	0.559	0.89
298_H	336_G	0.559	0.89
122_A	131_P	0.559	0.89
188_F	243_F	0.558	0.89
48_Y	151_V	0.557	0.89
93_E	96_P	0.555	0.89
376_Q	430_E	0.554	0.89
299_I	302_H	0.553	0.89
259_T	421_R	0.553	0.89
297_Y	428_I	0.551	0.89
170_M	256_A	0.549	0.88
122_A	126_I	0.549	0.88
244_L	421_R	0.549	0.88
346_H	384_E	0.548	0.88
273_L	417_F	0.548	0.88
257_D	382_T	0.548	0.88
430_E	433_V	0.545	0.88
228_H	421_R	0.545	0.88
176_M	251_Y	0.543	0.88
205_T	249_A	0.543	0.88
229_Y	232_L	0.542	0.88
434_E	438_R	0.542	0.88
174_Q	177_A	0.541	0.88
295_V	354_D	0.541	0.88
85_P	111_K	0.538	0.87
124_G	129_I	0.538	0.87
228_H	386_G	0.535	0.87
257_D	346_H	0.534	0.87
99_F	104_V	0.532	0.87
333_M	336_G	0.530	0.87
167_L	436_M	0.529	0.87
431_N	434_E	0.529	0.87
168_A	175_K	0.527	0.86
261_T	420_I	0.527	0.86
180_G	204_A	0.522	0.86
100_W	104_V	0.521	0.86
128_Y	138_Q	0.520	0.86
80_L	110_P	0.520	0.86
381_L	428_I	0.520	0.86
259_T	384_E	0.519	0.86
73_D	76_N	0.518	0.85
298_H	333_M	0.518	0.85
244_L	259_T	0.517	0.85
120_P	145_N	0.517	0.85
377_P	433_V	0.517	0.85
273_L	387_I	0.516	0.85
276_D	280_E	0.515	0.85
139_L	143_A	0.515	0.85
122_A	128_Y	0.513	0.85
174_Q	435_N	0.511	0.85
248_G	257_D	0.509	0.84
131_P	134_E	0.508	0.84
160_S	373_R	0.507	0.84
157_Y	160_S	0.507	0.84
198_N	232_L	0.506	0.84
346_H	382_T	0.505	0.84
185_E	188_F	0.505	0.84
72_V	75_V	0.505	0.84
183_A	203_T	0.505	0.84
107_I	114_G	0.504	0.84
346_H	386_G	0.502	0.84
91_N	95_L	0.501	0.84
385_P	389_F	0.500	0.83
45_D	48_Y	0.500	0.83
266_S	271_A	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
2iw2A	2	0.9842	100	0.258	Contact Map
3l24A	2	0.9481	100	0.277	Contact Map
2v3zA	3	0.9029	100	0.281	Contact Map
4qr8A	2	0.9842	100	0.282	Contact Map
3rvaA	2	0.9797	100	0.284	Contact Map
3ig4A	4	0.8578	100	0.309	Contact Map
3q6dA	1	0.7856	100	0.339	Contact Map
4r60A	2	0.8307	100	0.342	Contact Map
2zsgA	2	0.781	100	0.345	Contact Map
1wn1A	2	0.7765	100	0.349	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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