IDH - ECOLI - GREMLIN Contacts

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IDH - Isocitrate dehydrogenase [NADP]

UniProt:	P08200	Sequences: MESKVVVPAQGKKITLQNGKLNVPENPIIPYIEGDGIGVDVTPAMLKVVDAAVEKAYKGERKISWMEIYTGEKSTQVYGQDVWLPAETLDLIREYRVAIKGPLTTPVGGGIRSLNVALRQELDLYICLRPVRYYQGTPSPVKHPELTDMVIFRENSEDIYAGIEWKADSADAEKVIKFLREEMGVKKIRFPEHCGIGIKPCSEEGTKRLVRAAIEYAIANDRDSVTLVHKGNIMKFTEGAFKDWGYQLAREEFGGELIDGGPWLKVKNPNTGKEIVIKDVIADAFLQQILLRPAEYDVIACMNLNGDYISDALAAQVGGIGIAPGANIGDECALFEATHGTAPKYAGQDKVNPGSIILSAEMMLRHMGWTEAADLIVKGMEGAINAKTVTYDFERLMDGAKLLKCSEFGDAIIENM	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10489
Length:	416 (339)
Sequences:	6984 (3060)
Seq/√Len:	166.2

ECOLI - IDH DMLA LEU3
BACSU - IDH TTUC LEU3
HALSA - Q9HNZ7
SULSO - Q97WN0 LEU3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
218_I	274_E	4.380	1.00
210_V	245_G	3.134	1.00
44_A	409_G	3.052	1.00
211_R	215_E	2.880	1.00
28_I	64_S	2.786	1.00
47_K	410_D	2.749	1.00
284_A	288_Q	2.678	1.00
211_R	251_E	2.640	1.00
365_R	377_V	2.596	1.00
386_A	415_N	2.562	1.00
50_D	65_W	2.455	1.00
86_A	90_D	2.404	1.00
42_T	356_I	2.354	1.00
203_E	207_K	2.302	1.00
382_G	415_N	2.275	1.00
411_A	414_E	2.265	1.00
31_Y	46_L	2.230	1.00
44_A	47_K	2.185	1.00
365_R	374_D	2.170	1.00
226_T	278_K	2.167	1.00
80_Q	86_A	2.123	1.00
59_G	375_L	2.109	1.00
68_I	91_L	2.072	1.00
69_Y	77_V	2.026	1.00
224_S	278_K	2.026	1.00
46_L	67_E	1.993	1.00
245_G	277_I	1.992	1.00
150_V	216_Y	1.990	1.00
354_G	412_I	1.986	1.00
207_K	247_Q	1.969	1.00
30_P	91_L	1.967	1.00
93_R	122_L	1.947	1.00
358_L	380_M	1.940	1.00
207_K	244_W	1.914	1.00
369_W	372_A	1.910	1.00
224_S	276_V	1.898	1.00
215_E	253_F	1.894	1.00
210_V	300_A	1.893	1.00
388_T	403_L	1.844	1.00
349_D	406_S	1.837	1.00
374_D	378_K	1.835	1.00
349_D	404_K	1.816	1.00
74_S	85_P	1.815	1.00
357_I	412_I	1.815	1.00
292_R	295_E	1.812	1.00
383_A	415_N	1.805	1.00
37_I	351_V	1.795	1.00
211_R	253_F	1.794	1.00
388_T	411_A	1.755	1.00
90_D	94_E	1.755	1.00
39_V	43_P	1.744	1.00
361_E	377_V	1.739	1.00
246_Y	279_D	1.735	1.00
207_K	211_R	1.734	1.00
203_E	247_Q	1.717	1.00
409_G	413_I	1.705	1.00
228_V	285_F	1.682	1.00
244_W	247_Q	1.663	1.00
370_T	374_D	1.655	1.00
93_R	121_E	1.630	1.00
132_R	381_E	1.624	1.00
192_E	204_E	1.613	1.00
26_N	64_S	1.578	1.00
135_Q	385_N	1.570	1.00
52_A	376_I	1.563	1.00
199_K	302_M	1.552	1.00
166_K	243_D	1.546	1.00
128_L	150_V	1.545	1.00
410_D	414_E	1.541	1.00
90_D	93_R	1.516	1.00
30_P	95_Y	1.503	1.00
27_P	369_W	1.499	1.00
26_N	62_K	1.498	1.00
73_K	77_V	1.493	1.00
45_M	360_A	1.486	1.00
211_R	248_L	1.485	1.00
404_K	407_E	1.477	1.00
89_L	121_E	1.473	1.00
66_M	94_E	1.472	1.00
365_R	373_A	1.472	1.00
125_Y	330_D	1.468	1.00
117_A	121_E	1.451	1.00
290_L	312_A	1.448	1.00
214_I	249_A	1.443	1.00
65_W	360_A	1.443	1.00
61_R	369_W	1.433	1.00
32_I	70_T	1.432	1.00
47_K	413_I	1.430	1.00
53_V	63_I	1.427	1.00
49_V	63_I	1.411	1.00
30_P	68_I	1.405	1.00
349_D	405_C	1.403	1.00
227_L	245_G	1.399	1.00
152_F	212_A	1.398	1.00
46_L	50_D	1.388	1.00
51_A	413_I	1.380	1.00
66_M	95_Y	1.366	1.00
215_E	219_A	1.365	1.00
61_R	372_A	1.349	1.00
248_L	251_E	1.349	1.00
45_M	99_I	1.348	1.00
222_R	297_D	1.341	1.00
151_I	310_S	1.338	1.00
69_Y	78_Y	1.334	1.00
84_L	89_L	1.330	1.00
136_G	385_N	1.330	1.00
33_E	67_E	1.323	1.00
193_H	203_E	1.306	1.00
365_R	370_T	1.282	1.00
286_L	309_I	1.278	1.00
350_K	391_Y	1.266	1.00
152_F	216_Y	1.263	1.00
354_G	408_F	1.249	1.00
240_A	244_W	1.236	1.00
383_A	411_A	1.235	1.00
363_M	367_M	1.233	1.00
223_D	297_D	1.231	1.00
227_L	279_D	1.231	1.00
280_V	288_Q	1.231	1.00
215_E	218_I	1.228	1.00
105_T	108_G	1.227	1.00
403_L	411_A	1.225	1.00
46_L	65_W	1.224	1.00
27_P	367_M	1.220	1.00
210_V	248_L	1.215	1.00
408_F	412_I	1.215	1.00
45_M	356_I	1.212	1.00
69_Y	74_S	1.211	1.00
378_K	382_G	1.195	1.00
197_G	236_F	1.193	1.00
28_I	66_M	1.187	1.00
66_M	91_L	1.182	1.00
280_V	284_A	1.169	1.00
92_I	98_A	1.163	1.00
247_Q	250_R	1.160	1.00
199_K	236_F	1.158	1.00
246_Y	250_R	1.147	1.00
280_V	296_Y	1.144	1.00
364_L	372_A	1.138	1.00
403_L	407_E	1.138	1.00
151_I	313_L	1.127	1.00
289_I	299_I	1.118	1.00
243_D	247_Q	1.117	1.00
31_Y	67_E	1.112	1.00
48_V	376_I	1.105	1.00
207_K	248_L	1.105	1.00
203_E	244_W	1.103	1.00
149_M	289_I	1.102	1.00
280_V	285_F	1.101	1.00
74_S	78_Y	1.089	1.00
407_E	410_D	1.085	1.00
218_I	223_D	1.080	1.00
55_K	375_L	1.079	1.00
49_V	360_A	1.078	1.00
30_P	92_I	1.076	1.00
78_Y	87_E	1.076	1.00
214_I	253_F	1.075	1.00
349_D	407_E	1.071	0.99
123_D	208_R	1.071	0.99
214_I	275_I	1.069	0.99
286_L	312_A	1.069	0.99
146_L	294_A	1.064	0.99
128_L	152_F	1.060	0.99
99_I	360_A	1.058	0.99
345_Y	351_V	1.058	0.99
206_T	210_V	1.046	0.99
47_K	406_S	1.044	0.99
225_V	277_I	1.040	0.99
132_R	148_D	1.038	0.99
195_G	240_A	1.038	0.99
220_N	297_D	1.026	0.99
282_A	308_Y	1.025	0.99
52_A	372_A	1.014	0.99
231_G	242_K	1.010	0.99
382_G	386_A	0.997	0.99
201_C	302_M	0.990	0.99
45_M	357_I	0.990	0.99
53_V	61_R	0.990	0.99
207_K	251_E	0.989	0.99
159_I	199_K	0.986	0.99
204_E	207_K	0.979	0.99
218_I	275_I	0.978	0.99
159_I	302_M	0.978	0.99
164_E	198_I	0.975	0.99
288_Q	295_E	0.975	0.99
44_A	406_S	0.974	0.99
228_V	282_A	0.973	0.99
391_Y	402_L	0.970	0.99
100_K	115_N	0.970	0.99
216_Y	220_N	0.965	0.99
47_K	409_G	0.960	0.99
350_K	402_L	0.960	0.99
87_E	90_D	0.959	0.99
126_I	209_L	0.956	0.99
354_G	384_I	0.948	0.99
245_G	300_A	0.947	0.99
107_V	110_G	0.946	0.99
218_I	253_F	0.943	0.99
132_R	377_V	0.941	0.99
155_N	327_N	0.939	0.99
135_Q	145_E	0.932	0.99
85_P	88_T	0.932	0.99
225_V	248_L	0.926	0.99
158_D	199_K	0.925	0.99
278_K	295_E	0.925	0.99
48_V	357_I	0.924	0.99
28_I	94_E	0.923	0.99
329_G	332_C	0.922	0.98
194_C	200_P	0.921	0.98
31_Y	42_T	0.920	0.98
74_S	88_T	0.920	0.98
52_A	360_A	0.920	0.98
247_Q	251_E	0.918	0.98
358_L	377_V	0.917	0.98
225_V	298_V	0.916	0.98
51_A	54_E	0.914	0.98
48_V	413_I	0.913	0.98
354_G	380_M	0.909	0.98
291_L	315_A	0.907	0.98
40_D	347_G	0.904	0.98
149_M	313_L	0.903	0.98
80_Q	117_A	0.902	0.98
44_A	349_D	0.901	0.98
229_H	242_K	0.899	0.98
33_E	43_P	0.893	0.98
214_I	225_V	0.891	0.98
41_V	101_G	0.890	0.98
53_V	62_K	0.887	0.98
384_I	389_V	0.886	0.98
134_Y	381_E	0.886	0.98
238_E	305_N	0.884	0.98
374_D	377_V	0.877	0.98
201_C	206_T	0.877	0.98
213_A	225_V	0.874	0.98
70_T	118_L	0.872	0.98
345_Y	391_Y	0.870	0.98
361_E	365_R	0.868	0.98
41_V	356_I	0.866	0.98
337_A	356_I	0.864	0.98
68_I	88_T	0.858	0.98
68_I	95_Y	0.853	0.97
91_L	95_Y	0.850	0.97
345_Y	350_K	0.848	0.97
158_D	302_M	0.847	0.97
249_A	277_I	0.846	0.97
288_Q	292_R	0.844	0.97
357_I	380_M	0.844	0.97
44_A	410_D	0.838	0.97
55_K	59_G	0.837	0.97
136_G	381_E	0.833	0.97
372_A	375_L	0.833	0.97
128_L	212_A	0.833	0.97
87_E	91_L	0.832	0.97
144_P	294_A	0.825	0.97
131_V	313_L	0.823	0.97
76_Q	105_T	0.822	0.97
225_V	300_A	0.821	0.97
227_L	277_I	0.817	0.97
382_G	385_N	0.817	0.97
42_T	101_G	0.815	0.97
360_A	363_M	0.815	0.97
379_G	383_A	0.813	0.97
194_C	202_S	0.813	0.97
344_K	391_Y	0.811	0.97
97_V	367_M	0.810	0.97
231_G	281_I	0.809	0.97
70_T	114_L	0.806	0.96
226_T	280_V	0.798	0.96
225_V	249_A	0.795	0.96
225_V	275_I	0.793	0.96
123_D	156_S	0.792	0.96
151_I	309_I	0.791	0.96
126_I	212_A	0.789	0.96
50_D	53_V	0.789	0.96
45_M	49_V	0.787	0.96
32_I	92_I	0.786	0.96
348_Q	391_Y	0.784	0.96
383_A	412_I	0.784	0.96
411_A	415_N	0.783	0.96
229_H	279_D	0.781	0.96
102_P	339_H	0.780	0.96
135_Q	381_E	0.779	0.96
282_A	302_M	0.779	0.96
165_W	196_I	0.778	0.96
108_G	111_I	0.777	0.96
127_C	338_T	0.776	0.96
31_Y	65_W	0.774	0.96
43_P	47_K	0.774	0.96
52_A	61_R	0.773	0.96
159_I	304_L	0.772	0.96
75_T	83_W	0.770	0.95
213_A	300_A	0.769	0.95
131_V	317_V	0.768	0.95
69_Y	73_K	0.768	0.95
246_Y	277_I	0.763	0.95
63_I	360_A	0.763	0.95
171_D	191_P	0.760	0.95
244_W	248_L	0.760	0.95
378_K	381_E	0.759	0.95
210_V	277_I	0.759	0.95
403_L	408_F	0.756	0.95
168_D	194_C	0.754	0.95
249_A	273_K	0.751	0.95
391_Y	404_K	0.750	0.95
49_V	364_L	0.750	0.95
212_A	216_Y	0.750	0.95
326_A	335_F	0.745	0.95
43_P	406_S	0.745	0.95
282_A	286_L	0.744	0.95
99_I	356_I	0.743	0.94
91_L	94_E	0.741	0.94
70_T	100_K	0.739	0.94
390_T	408_F	0.738	0.94
80_Q	87_E	0.736	0.94
228_V	309_I	0.736	0.94
289_I	313_L	0.735	0.94
324_P	362_M	0.735	0.94
112_R	117_A	0.734	0.94
219_A	368_G	0.734	0.94
72_E	105_T	0.731	0.94
72_E	76_Q	0.730	0.94
102_P	356_I	0.730	0.94
43_P	67_E	0.729	0.94
199_K	304_L	0.726	0.94
360_A	364_L	0.726	0.94
228_V	299_I	0.726	0.94
89_L	93_R	0.724	0.94
166_K	195_G	0.722	0.94
27_P	61_R	0.720	0.94
138_P	389_V	0.715	0.93
44_A	413_I	0.715	0.93
406_S	410_D	0.714	0.93
383_A	388_T	0.709	0.93
248_L	253_F	0.709	0.93
285_F	296_Y	0.707	0.93
148_D	297_D	0.700	0.93
243_D	250_R	0.700	0.93
344_K	351_V	0.700	0.93
214_I	277_I	0.699	0.92
50_D	54_E	0.697	0.92
138_P	393_F	0.691	0.92
133_Y	147_T	0.691	0.92
285_F	299_I	0.689	0.92
406_S	409_G	0.688	0.92
59_G	372_A	0.688	0.92
152_F	209_L	0.687	0.92
246_Y	249_A	0.687	0.92
124_L	334_L	0.686	0.92
76_Q	107_V	0.685	0.92
203_E	240_A	0.683	0.92
104_T	341_T	0.682	0.92
199_K	305_N	0.679	0.91
72_E	104_T	0.677	0.91
51_A	55_K	0.677	0.91
68_I	87_E	0.674	0.91
284_A	320_I	0.673	0.91
164_E	196_I	0.673	0.91
131_V	149_M	0.672	0.91
93_R	332_C	0.670	0.91
401_K	407_E	0.670	0.91
47_K	50_D	0.669	0.91
49_V	65_W	0.668	0.91
324_P	358_L	0.667	0.91
371_E	374_D	0.665	0.91
70_T	84_L	0.665	0.91
342_A	345_Y	0.662	0.90
157_E	205_G	0.656	0.90
44_A	357_I	0.655	0.90
143_H	146_L	0.654	0.90
410_D	413_I	0.653	0.90
150_V	220_N	0.651	0.90
84_L	118_L	0.651	0.90
242_K	246_Y	0.650	0.90
215_E	251_E	0.648	0.89
381_E	385_N	0.648	0.89
191_P	204_E	0.648	0.89
42_T	45_M	0.647	0.89
319_G	355_S	0.644	0.89
209_L	300_A	0.640	0.89
373_A	377_V	0.637	0.89
326_A	362_M	0.637	0.89
98_A	334_L	0.634	0.88
166_K	169_S	0.633	0.88
86_A	117_A	0.630	0.88
288_Q	291_L	0.630	0.88
383_A	408_F	0.629	0.88
149_M	316_Q	0.628	0.88
73_K	76_Q	0.627	0.88
170_A	194_C	0.624	0.88
375_L	379_G	0.623	0.87
357_I	376_I	0.620	0.87
229_H	281_I	0.619	0.87
80_Q	83_W	0.618	0.87
324_P	355_S	0.615	0.87
84_L	117_A	0.615	0.87
101_G	356_I	0.614	0.87
199_K	238_E	0.614	0.87
228_V	301_C	0.611	0.86
290_L	316_Q	0.610	0.86
351_V	391_Y	0.609	0.86
338_T	355_S	0.608	0.86
138_P	142_K	0.608	0.86
197_G	239_G	0.607	0.86
335_F	366_H	0.606	0.86
163_I	200_P	0.605	0.86
206_T	244_W	0.604	0.86
29_I	363_M	0.603	0.86
134_Y	358_L	0.603	0.86
212_A	330_D	0.602	0.86
114_L	117_A	0.602	0.86
29_I	63_I	0.600	0.85
328_I	366_H	0.597	0.85
193_H	243_D	0.596	0.85
147_T	294_A	0.596	0.85
74_S	84_L	0.595	0.85
123_D	204_E	0.591	0.85
150_V	298_V	0.589	0.84
227_L	241_F	0.588	0.84
69_Y	87_E	0.587	0.84
332_C	335_F	0.586	0.84
193_H	204_E	0.586	0.84
192_E	202_S	0.585	0.84
49_V	376_I	0.583	0.84
218_I	273_K	0.582	0.84
42_T	46_L	0.581	0.84
191_P	207_K	0.580	0.83
123_D	157_E	0.578	0.83
371_E	375_L	0.578	0.83
171_D	192_E	0.578	0.83
322_I	393_F	0.577	0.83
364_L	376_I	0.576	0.83
388_T	401_K	0.574	0.83
29_I	65_W	0.572	0.83
151_I	299_I	0.571	0.83
194_C	203_E	0.570	0.82
249_A	275_I	0.570	0.82
206_T	302_M	0.570	0.82
357_I	409_G	0.566	0.82
164_E	167_A	0.566	0.82
67_E	73_K	0.564	0.82
107_V	111_I	0.564	0.82
123_D	329_G	0.564	0.82
284_A	295_E	0.563	0.82
105_T	113_S	0.562	0.82
113_S	117_A	0.562	0.82
205_G	208_R	0.561	0.81
367_M	370_T	0.557	0.81
163_I	198_I	0.554	0.81
42_T	99_I	0.553	0.81
390_T	393_F	0.551	0.80
32_I	68_I	0.550	0.80
160_Y	336_E	0.549	0.80
389_V	393_F	0.547	0.80
92_I	118_L	0.547	0.80
125_Y	209_L	0.546	0.80
218_I	249_A	0.545	0.80
103_L	341_T	0.544	0.79
63_I	369_W	0.543	0.79
319_G	322_I	0.543	0.79
148_D	222_R	0.543	0.79
167_A	243_D	0.542	0.79
234_M	237_T	0.541	0.79
212_A	215_E	0.539	0.79
340_G	343_P	0.538	0.79
88_T	114_L	0.538	0.79
253_F	273_K	0.538	0.79
100_K	118_L	0.537	0.79
92_I	122_L	0.537	0.79
150_V	222_R	0.534	0.78
333_A	366_H	0.532	0.78
30_P	66_M	0.531	0.78
400_A	403_L	0.531	0.78
197_G	234_M	0.528	0.77
393_F	400_A	0.527	0.77
157_E	202_S	0.523	0.77
43_P	46_L	0.522	0.77
45_M	48_V	0.522	0.77
329_G	333_A	0.520	0.76
63_I	372_A	0.520	0.76
196_I	200_P	0.519	0.76
125_Y	212_A	0.518	0.76
210_V	244_W	0.518	0.76
349_D	410_D	0.517	0.76
68_I	85_P	0.517	0.76
215_E	248_L	0.517	0.76
328_I	333_A	0.516	0.76
388_T	408_F	0.515	0.76
92_I	95_Y	0.515	0.76
223_D	275_I	0.514	0.76
388_T	415_N	0.514	0.76
166_K	235_K	0.513	0.75
285_F	309_I	0.513	0.75
212_A	328_I	0.512	0.75
52_A	375_L	0.510	0.75
74_S	77_V	0.510	0.75
389_V	403_L	0.509	0.75
249_A	253_F	0.509	0.75
71_G	74_S	0.508	0.75
230_K	283_D	0.508	0.75
49_V	52_A	0.508	0.75
39_V	73_K	0.507	0.75
223_D	274_E	0.507	0.75
217_A	225_V	0.507	0.75
84_L	88_T	0.506	0.74
245_G	248_L	0.506	0.74
302_M	305_N	0.505	0.74
83_W	87_E	0.505	0.74
170_A	192_E	0.500	0.74

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
2d4vA	2	0.9952	100	0.086	Contact Map
3dmsA	2	0.988	100	0.099	Contact Map
2iv0A	2	0.9784	100	0.103	Contact Map
1hqsA	2	0.9784	100	0.114	Contact Map
2e0cA	2	0.9543	100	0.114	Contact Map
1tyoA	2	0.9856	100	0.115	Contact Map
3flkA	3	0.8197	100	0.148	Contact Map
2d1cA	2	0.8389	100	0.15	Contact Map
3blxB	1	0.8197	100	0.152	Contact Map
3u1hA	2	0.8053	100	0.155	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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