MALY - ECOLI - GREMLIN Contacts

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MALY - Protein MalY

UniProt:	P23256	Sequences: MFDFSKVVDRHGTWCTQWDYVADRFGTADLLPFTISDMDFATAPCIIEALNQRLMHGVFGYSRWKNDEFLAAIAHWFSTQHYTAIDSQTVVYGPSVIYMVSELIRQWSETGEGVVIHTPAYDAFYKAIEGNQRTVMPVALEKQADGWFCDMGKLEAVLAKPECKIMLLCSPQNPTGKVWTCDELEIMADLCERHGVRVISDEIHMDMVWGEQPHIPWSNVARGDWALLTSGSKSFNIPALTGAYGIIENSSSRDAYLSALKGRDGLSSPSVLALTAHIAAYQQGAPWLDALRIYLKDNLTYIADKMNAAFPELNWQIPQSTYLAWLDLRPLNIDDNALQKALIEQEKVAIMPGYTYGEEGRGFVRLNAGCPRSKLEKGVAGLINAIRAVR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10564
Length:	390 (347)
Sequences:	43595 (30070)
Seq/√Len:	1614.2

ECOLI - MALY ALAC YBDL ALAA AVTA YJIR YDCR HIS8
BACSU - CBL MTNE AAT1 PATA YUGH AAT2 YISV YDEF YDFD YHDI AAT3 YDEL YCXD GABR HIS8
HALSA - Q9HQK2 Q9HRX4 Q9HRM6 Q9HQW2 HIS8 Q9HPL0
SULSO - AAT Y104 Q97TY7 Q97YX5 HIS8 Q97ZX4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
51_N	55_M	3.049	1.00
93_G	99_M	3.046	1.00
155_E	193_R	3.032	1.00
346_E	384_N	3.014	1.00
113_G	134_T	2.873	1.00
296_K	300_T	2.776	1.00
181_C	185_E	2.747	1.00
301_Y	376_E	2.728	1.00
112_E	164_K	2.728	1.00
314_N	327_D	2.686	1.00
72_A	282_Q	2.632	1.00
377_K	381_G	2.617	1.00
341_A	345_Q	2.611	1.00
297_D	372_R	2.532	1.00
44_P	48_E	2.418	1.00
108_S	133_R	2.411	1.00
68_E	278_I	2.309	1.00
78_S	84_A	2.295	1.00
247_I	253_R	2.263	1.00
101_S	105_R	2.211	1.00
305_K	379_V	2.185	1.00
242_G	277_H	2.129	1.00
377_K	380_A	2.101	1.00
180_T	183_E	2.090	1.00
185_E	189_D	2.067	1.00
334_D	337_A	2.035	1.00
48_E	52_Q	2.018	1.00
141_E	183_E	1.956	1.00
152_G	186_I	1.943	1.00
128_I	133_R	1.918	1.00
71_A	75_H	1.896	1.00
195_G	224_D	1.882	1.00
33_F	378_G	1.877	1.00
305_K	308_A	1.872	1.00
75_H	282_Q	1.846	1.00
304_D	308_A	1.824	1.00
155_E	186_I	1.806	1.00
113_G	136_M	1.804	1.00
153_K	157_V	1.804	1.00
103_L	226_A	1.788	1.00
191_C	198_V	1.786	1.00
71_A	87_S	1.776	1.00
303_A	307_N	1.775	1.00
148_F	183_E	1.774	1.00
192_E	223_G	1.750	1.00
307_N	315_W	1.741	1.00
165_I	199_I	1.733	1.00
300_T	304_D	1.725	1.00
74_A	87_S	1.704	1.00
305_K	380_A	1.695	1.00
301_Y	305_K	1.685	1.00
203_I	230_S	1.684	1.00
199_I	228_L	1.681	1.00
150_D	153_K	1.674	1.00
103_L	199_I	1.665	1.00
305_K	383_I	1.659	1.00
303_A	317_I	1.650	1.00
113_G	163_C	1.631	1.00
113_G	159_A	1.628	1.00
96_V	228_L	1.623	1.00
67_D	71_A	1.608	1.00
118_T	137_P	1.605	1.00
52_Q	279_A	1.589	1.00
186_I	189_D	1.572	1.00
153_K	156_A	1.564	1.00
341_A	385_A	1.563	1.00
113_G	162_E	1.554	1.00
114_V	128_I	1.552	1.00
302_I	324_A	1.551	1.00
335_D	354_Y	1.528	1.00
371_P	374_K	1.514	1.00
72_A	75_H	1.512	1.00
350_I	364_V	1.504	1.00
85_I	246_I	1.495	1.00
104_I	128_I	1.489	1.00
68_E	282_Q	1.487	1.00
125_Y	129_E	1.483	1.00
47_I	51_N	1.481	1.00
77_F	246_I	1.461	1.00
73_I	244_Y	1.455	1.00
189_D	193_R	1.455	1.00
340_K	344_E	1.451	1.00
301_Y	372_R	1.437	1.00
182_D	185_E	1.434	1.00
155_E	194_H	1.418	1.00
191_C	196_V	1.410	1.00
89_T	249_N	1.408	1.00
337_A	341_A	1.396	1.00
308_A	383_I	1.394	1.00
325_W	353_G	1.390	1.00
302_I	379_V	1.388	1.00
226_A	247_I	1.378	1.00
346_E	381_G	1.378	1.00
245_G	256_Y	1.375	1.00
118_T	139_A	1.367	1.00
231_G	277_H	1.364	1.00
289_D	293_I	1.363	1.00
151_M	190_L	1.363	1.00
303_A	324_A	1.361	1.00
270_S	273_A	1.357	1.00
158_L	190_L	1.351	1.00
88_Q	249_N	1.339	1.00
380_A	384_N	1.332	1.00
307_N	317_I	1.321	1.00
151_M	186_I	1.316	1.00
73_I	92_Y	1.313	1.00
139_A	153_K	1.310	1.00
303_A	315_W	1.308	1.00
72_A	278_I	1.307	1.00
190_L	194_H	1.306	1.00
376_E	380_A	1.305	1.00
50_L	54_L	1.303	1.00
181_C	215_I	1.301	1.00
159_A	163_C	1.300	1.00
294_Y	297_D	1.288	1.00
337_A	340_K	1.286	1.00
104_I	167_L	1.283	1.00
91_V	253_R	1.274	1.00
334_D	361_R	1.241	1.00
115_V	163_C	1.241	1.00
47_I	55_M	1.240	1.00
50_L	276_A	1.238	1.00
289_D	292_R	1.233	1.00
293_I	296_K	1.229	1.00
49_A	279_A	1.228	1.00
190_L	196_V	1.226	1.00
326_L	366_L	1.222	1.00
183_E	186_I	1.222	1.00
48_E	51_N	1.218	1.00
141_E	150_D	1.215	1.00
189_D	192_E	1.209	1.00
116_I	135_V	1.204	1.00
305_K	376_E	1.203	1.00
75_H	79_T	1.199	1.00
73_I	90_V	1.193	1.00
299_L	303_A	1.188	1.00
104_I	108_S	1.186	1.00
125_Y	137_P	1.185	1.00
294_Y	372_R	1.185	1.00
65_K	70_L	1.171	1.00
77_F	244_Y	1.169	1.00
327_D	363_F	1.166	1.00
229_T	244_Y	1.165	1.00
68_E	275_T	1.161	1.00
28_A	347_K	1.161	1.00
115_V	138_V	1.160	1.00
94_P	98_Y	1.153	1.00
216_P	219_N	1.147	1.00
339_Q	350_I	1.143	1.00
155_E	159_A	1.130	1.00
70_L	74_A	1.126	1.00
294_Y	298_N	1.118	1.00
105_R	131_N	1.117	1.00
327_D	362_G	1.115	1.00
278_I	282_Q	1.114	1.00
181_C	220_V	1.112	1.00
366_L	378_G	1.112	1.00
166_M	196_V	1.110	1.00
293_I	297_D	1.110	1.00
79_T	285_A	1.108	1.00
52_Q	56_H	1.106	1.00
108_S	114_V	1.102	1.00
210_G	319_Q	1.102	1.00
226_A	245_G	1.094	1.00
182_D	186_I	1.093	1.00
86_D	89_T	1.086	1.00
342_L	382_L	1.085	1.00
335_D	362_G	1.082	1.00
67_D	87_S	1.079	1.00
372_R	376_E	1.078	1.00
279_A	282_Q	1.078	1.00
44_P	47_I	1.077	1.00
128_I	135_V	1.074	1.00
45_C	283_Q	1.073	1.00
107_W	165_I	1.073	1.00
155_E	190_L	1.072	1.00
329_R	362_G	1.066	1.00
110_T	132_Q	1.065	1.00
198_V	217_W	1.063	1.00
68_E	71_A	1.052	1.00
98_Y	261_K	1.050	1.00
74_A	86_D	1.043	1.00
188_A	225_W	1.041	1.00
336_N	354_Y	1.041	1.00
74_A	90_V	1.038	1.00
298_N	301_Y	1.036	1.00
197_R	226_A	1.026	1.00
99_M	245_G	1.023	1.00
188_A	198_V	1.018	1.00
99_M	228_L	1.013	1.00
185_E	220_V	1.012	1.00
107_W	197_R	1.009	1.00
67_D	70_L	1.005	1.00
338_L	364_V	0.998	1.00
47_I	54_L	0.996	1.00
86_D	249_N	0.996	1.00
69_F	92_Y	0.991	1.00
370_C	374_K	0.991	1.00
299_L	368_A	0.990	1.00
120_A	169_C	0.983	1.00
138_V	157_V	0.981	1.00
255_A	259_A	0.978	1.00
342_L	350_I	0.970	1.00
181_C	219_N	0.969	1.00
152_G	156_A	0.968	1.00
158_L	163_C	0.961	1.00
197_R	224_D	0.957	1.00
89_T	253_R	0.955	1.00
49_A	52_Q	0.954	1.00
114_V	165_I	0.954	1.00
124_F	167_L	0.952	1.00
374_K	377_K	0.951	1.00
94_P	270_S	0.947	1.00
300_T	317_I	0.947	1.00
109_E	112_E	0.947	1.00
103_L	256_Y	0.944	1.00
91_V	256_Y	0.944	1.00
204_H	323_L	0.933	1.00
158_L	196_V	0.931	1.00
149_C	183_E	0.930	1.00
106_Q	256_Y	0.928	1.00
90_V	246_I	0.924	1.00
258_S	261_K	0.923	1.00
304_D	307_N	0.921	1.00
141_E	153_K	0.920	1.00
29_D	347_K	0.911	1.00
218_S	227_L	0.907	1.00
279_A	283_Q	0.906	1.00
228_L	245_G	0.905	1.00
129_E	135_V	0.904	1.00
301_Y	304_D	0.900	1.00
302_I	375_L	0.894	1.00
217_W	225_W	0.893	1.00
341_A	346_E	0.892	1.00
76_W	206_D	0.890	1.00
290_A	293_I	0.887	1.00
208_V	211_E	0.885	1.00
304_D	376_E	0.884	1.00
97_I	123_A	0.883	1.00
302_I	305_K	0.880	1.00
208_V	214_H	0.879	1.00
340_K	345_Q	0.879	1.00
181_C	213_P	0.872	1.00
38_M	295_L	0.870	1.00
83_T	218_S	0.869	1.00
159_A	194_H	0.866	1.00
33_F	375_L	0.864	1.00
49_A	53_R	0.858	1.00
96_V	203_I	0.858	1.00
348_V	382_L	0.858	1.00
202_E	227_L	0.855	1.00
151_M	187_M	0.854	1.00
313_L	328_L	0.854	1.00
96_V	230_S	0.849	1.00
197_R	252_S	0.848	1.00
301_Y	379_V	0.845	1.00
108_S	165_I	0.845	1.00
299_L	318_P	0.841	1.00
313_L	326_L	0.840	1.00
29_D	377_K	0.839	1.00
40_F	294_Y	0.838	1.00
151_M	183_E	0.835	1.00
52_Q	55_M	0.834	1.00
336_N	340_K	0.833	1.00
152_G	155_E	0.833	1.00
76_W	235_F	0.832	1.00
163_C	196_V	0.825	1.00
97_I	121_Y	0.822	1.00
115_V	166_M	0.818	1.00
290_A	294_Y	0.818	1.00
275_T	278_I	0.814	1.00
217_W	220_V	0.813	1.00
69_F	73_I	0.811	1.00
192_E	224_D	0.810	1.00
350_I	366_L	0.807	1.00
104_I	165_I	0.807	1.00
95_S	241_T	0.807	1.00
286_P	290_A	0.807	1.00
93_G	245_G	0.805	1.00
314_N	329_R	0.804	1.00
45_C	48_E	0.803	1.00
115_V	157_V	0.803	1.00
98_Y	266_L	0.802	1.00
154_L	166_M	0.796	1.00
66_N	70_L	0.795	1.00
114_V	133_R	0.794	1.00
209_W	296_K	0.792	1.00
215_I	219_N	0.790	1.00
348_V	381_G	0.788	1.00
48_E	55_M	0.788	1.00
242_G	269_P	0.783	1.00
297_D	300_T	0.780	1.00
206_D	234_S	0.777	1.00
242_G	273_A	0.775	1.00
117_H	138_V	0.772	1.00
76_W	81_H	0.771	1.00
106_Q	260_L	0.770	1.00
328_L	364_V	0.767	1.00
45_C	279_A	0.764	1.00
338_L	385_A	0.759	1.00
32_P	37_D	0.752	1.00
75_H	78_S	0.751	1.00
151_M	155_E	0.751	1.00
117_H	149_C	0.749	1.00
286_P	289_D	0.744	1.00
346_E	385_A	0.744	1.00
118_T	359_E	0.743	1.00
336_N	352_P	0.741	1.00
98_Y	102_E	0.739	1.00
348_V	378_G	0.738	1.00
66_N	274_L	0.735	1.00
140_L	172_Q	0.734	1.00
53_R	276_A	0.732	1.00
373_S	376_E	0.730	1.00
41_A	47_I	0.730	1.00
231_G	244_Y	0.727	1.00
115_V	154_L	0.727	1.00
150_D	183_E	0.726	1.00
117_H	172_Q	0.726	1.00
285_A	289_D	0.725	1.00
287_W	291_L	0.724	1.00
298_N	371_P	0.723	1.00
247_I	256_Y	0.723	1.00
27_T	347_K	0.722	1.00
108_S	112_E	0.722	1.00
339_Q	352_P	0.722	1.00
218_S	221_A	0.722	1.00
91_V	245_G	0.721	1.00
136_M	159_A	0.714	1.00
226_A	252_S	0.711	1.00
335_D	352_P	0.710	1.00
300_T	303_A	0.710	1.00
136_M	163_C	0.709	1.00
254_D	259_A	0.707	1.00
51_N	54_L	0.707	1.00
74_A	85_I	0.704	1.00
50_L	272_L	0.703	1.00
302_I	368_A	0.701	1.00
116_I	128_I	0.697	1.00
113_G	164_K	0.693	1.00
173_N	204_H	0.693	1.00
58_V	275_T	0.689	1.00
142_K	314_N	0.689	1.00
163_C	166_M	0.689	1.00
291_L	295_L	0.687	1.00
287_W	290_A	0.686	1.00
210_G	299_L	0.685	1.00
311_P	383_I	0.684	1.00
118_T	357_G	0.681	1.00
215_I	220_V	0.681	1.00
318_P	321_T	0.679	1.00
126_K	129_E	0.678	1.00
172_Q	175_T	0.677	1.00
158_L	194_H	0.677	1.00
167_L	199_I	0.676	1.00
70_L	87_S	0.674	1.00
261_K	266_L	0.674	1.00
305_K	311_P	0.672	1.00
102_E	256_Y	0.672	1.00
166_M	191_C	0.672	1.00
72_A	281_Y	0.671	1.00
142_K	327_D	0.671	1.00
124_F	128_I	0.665	1.00
301_Y	375_L	0.664	1.00
36_S	204_H	0.664	1.00
104_I	133_R	0.654	1.00
103_L	228_L	0.654	1.00
92_Y	242_G	0.653	1.00
339_Q	364_V	0.650	1.00
29_D	374_K	0.650	1.00
234_S	288_L	0.650	1.00
353_G	363_F	0.647	1.00
42_T	45_C	0.647	1.00
100_V	127_A	0.646	1.00
154_L	190_L	0.646	1.00
326_L	363_F	0.643	1.00
353_G	356_Y	0.643	1.00
136_M	157_V	0.642	1.00
202_E	216_P	0.639	1.00
297_D	301_Y	0.638	1.00
192_E	222_R	0.638	1.00
288_L	292_R	0.638	1.00
39_D	298_N	0.637	1.00
101_S	265_G	0.637	1.00
111_G	134_T	0.637	1.00
302_I	366_L	0.634	1.00
333_I	338_L	0.633	1.00
200_S	227_L	0.632	1.00
92_Y	274_L	0.632	1.00
212_Q	319_Q	0.632	1.00
116_I	125_Y	0.628	1.00
104_I	131_N	0.623	1.00
148_F	180_T	0.620	1.00
101_S	131_N	0.619	1.00
89_T	248_E	0.619	1.00
138_V	153_K	0.618	1.00
97_I	267_S	0.617	1.00
141_E	148_F	0.616	1.00
170_S	202_E	0.616	1.00
235_F	285_A	0.616	1.00
27_T	30_L	0.614	1.00
325_W	363_F	0.613	1.00
308_A	376_E	0.613	1.00
43_A	46_I	0.611	1.00
209_W	368_A	0.608	1.00
210_G	296_K	0.606	1.00
380_A	383_I	0.605	1.00
76_W	205_M	0.605	1.00
81_H	205_M	0.604	1.00
221_A	224_D	0.604	1.00
31_L	377_K	0.603	1.00
191_C	195_G	0.603	1.00
49_A	276_A	0.602	1.00
338_L	342_L	0.598	1.00
292_R	296_K	0.597	1.00
247_I	252_S	0.596	1.00
113_G	161_P	0.595	1.00
184_L	217_W	0.591	1.00
42_T	46_I	0.589	1.00
168_L	184_L	0.589	1.00
45_C	287_W	0.588	1.00
91_V	247_I	0.587	1.00
250_S	254_D	0.587	1.00
36_S	323_L	0.586	1.00
271_V	275_T	0.585	1.00
177_K	319_Q	0.584	1.00
276_A	279_A	0.583	1.00
179_W	183_E	0.583	1.00
69_F	277_H	0.583	1.00
207_M	292_R	0.583	1.00
65_K	258_S	0.581	1.00
381_G	384_N	0.580	1.00
101_S	127_A	0.579	1.00
77_F	227_L	0.578	1.00
209_W	299_L	0.578	1.00
45_C	286_P	0.578	1.00
335_D	339_Q	0.578	1.00
42_T	287_W	0.576	1.00
56_H	279_A	0.572	1.00
315_W	324_A	0.571	1.00
53_R	56_H	0.571	1.00
46_I	237_I	0.569	1.00
170_S	178_V	0.569	1.00
46_I	280_A	0.569	1.00
42_T	47_I	0.569	1.00
171_P	320_S	0.569	1.00
112_E	162_E	0.568	1.00
216_P	227_L	0.567	1.00
116_I	137_P	0.566	1.00
45_C	285_A	0.566	1.00
232_S	241_T	0.565	1.00
342_L	385_A	0.563	1.00
139_A	157_V	0.563	1.00
296_K	299_L	0.560	1.00
103_L	165_I	0.559	1.00
223_G	250_S	0.558	1.00
275_T	279_A	0.556	1.00
179_W	184_L	0.556	1.00
335_D	364_V	0.555	1.00
306_M	326_L	0.554	1.00
299_L	317_I	0.553	1.00
63_R	67_D	0.551	1.00
108_S	164_K	0.547	1.00
335_D	361_R	0.547	1.00
168_L	171_P	0.546	1.00
149_C	154_L	0.545	1.00
159_A	162_E	0.544	1.00
104_I	127_A	0.543	1.00
156_A	159_A	0.542	1.00
205_M	229_T	0.542	1.00
231_G	281_Y	0.541	1.00
102_E	261_K	0.541	1.00
114_V	167_L	0.539	1.00
85_I	218_S	0.538	1.00
71_A	74_A	0.537	1.00
214_H	217_W	0.535	1.00
34_T	349_A	0.533	1.00
94_P	269_P	0.533	1.00
165_I	197_R	0.533	1.00
377_K	384_N	0.532	1.00
85_I	89_T	0.532	1.00
314_N	330_P	0.532	1.00
298_N	372_R	0.531	1.00
157_V	161_P	0.530	1.00
184_L	200_S	0.530	1.00
327_D	330_P	0.530	1.00
215_I	218_S	0.529	1.00
283_Q	286_P	0.529	1.00
139_A	150_D	0.527	1.00
307_N	314_N	0.527	1.00
371_P	376_E	0.527	1.00
71_A	282_Q	0.525	1.00
173_N	365_R	0.523	1.00
217_W	221_A	0.523	1.00
333_I	341_A	0.522	1.00
274_L	278_I	0.521	1.00
325_W	365_R	0.519	1.00
249_N	254_D	0.517	1.00
148_F	177_K	0.514	1.00
78_S	82_Y	0.514	1.00
109_E	164_K	0.512	1.00
343_I	349_A	0.511	1.00
166_M	198_V	0.511	1.00
298_N	374_K	0.510	1.00
32_P	35_I	0.510	1.00
127_A	131_N	0.509	1.00
30_L	349_A	0.509	1.00
192_E	221_A	0.508	1.00
379_V	383_I	0.508	1.00
245_G	253_R	0.508	1.00
159_A	193_R	0.508	1.00
99_M	243_A	0.507	1.00
31_L	381_G	0.507	1.00
207_M	295_L	0.505	1.00
305_K	375_L	0.504	1.00
154_L	187_M	0.503	1.00
188_A	221_A	0.503	1.00
328_L	333_I	0.502	1.00
68_E	72_A	0.500	1.00
95_S	243_A	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
1d2fA	2	0.9385	100	0.287	Contact Map
1c7nA	2	0.9949	100	0.288	Contact Map
3t32A	2	0.9154	100	0.296	Contact Map
3piuA	2	0.9333	100	0.297	Contact Map
3dzzA	2	0.9795	100	0.297	Contact Map
3b1dA	4	0.9821	100	0.301	Contact Map
3dydA	2	0.9359	100	0.302	Contact Map
4dq6A	2	0.9795	100	0.305	Contact Map
4my5A	2	0.9769	100	0.308	Contact Map
2x5dA	3	0.9462	100	0.309	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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