SDHD - ECOLI - GREMLIN Contacts

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SDHD - D-serine dehydratase

UniProt:	P00926	Sequences: MENAKMNSLIAQYPLVKDLVALKETTWFNPGTTSLAEGLPYVGLTEQDVQDAHARLSRFAPYLAKAFPETAATGGIIESELVAIPAMQKRLEKEYQQPISGQLLLKKDSHLPISGSIKARGGIYEVLAHAEKLALEAGLLTLDDDYSKLLSPEFKQFFSQYSIAVGSTGNLGLSIGIMSARIGFKVTVHMSADARAWKKAKLRSHGVTVVEYEQDYGVAVEEGRKAAQSDPNCFFIDDENSRTLFLGYSVAGQRLKAQFAQQGRIVDADNPLFVYLPCGVGGGPGGVAFGLKLAFGDHVHCFFAEPTHSPCMLLGVHTGLHDQISVQDIGIDNLTAADGLAVGRASGFVGRAMERLLDGFYTLSDQTMYDMLGWLAQEEGIRLEPSALAGMAGPQRVCASVSYQQMHGFSAEQLRNTTHLVWATGGGMVPEEEMNQYLAKGR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10249
Length:	442 (335)
Sequences:	3360 (1816)
Seq/√Len:	99.2

ECOLI - SDHD ILVA DPAL TRPB TDCB CYSK CYSM DCYD
BACSU - SDHD ILVA TRPB THRC CYSM CYSK MCCA
HALSA - Q9HMQ7 Q9HRU4 Q9HNH6 TRPB Q9HNH0 Q9HQ70
SULSO - TRPB1 Q980P1 Q97ZL6 TRPB2 Q97ZT5 Q980F2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
255_L	420_L	4.607	1.00
300_H	359_G	4.393	1.00
179_S	186_V	4.378	1.00
189_H	226_A	3.706	1.00
367_T	396_R	3.510	1.00
83_A	102_Q	3.474	1.00
273_F	302_F	3.384	1.00
196_A	200_A	3.140	1.00
81_L	420_L	3.077	1.00
53_H	246_L	2.906	1.00
269_D	418_T	2.863	1.00
274_V	287_V	2.860	1.00
191_S	195_R	2.717	1.00
249_S	253_Q	2.598	1.00
83_A	88_Q	2.585	1.00
185_K	208_T	2.574	1.00
234_F	285_G	2.562	1.00
90_R	374_W	2.533	1.00
102_Q	263_G	2.501	1.00
287_V	422_W	2.429	1.00
187_T	208_T	2.371	1.00
222_E	225_K	2.363	1.00
73_T	262_Q	2.267	1.00
273_F	300_H	2.215	1.00
187_T	210_V	2.206	1.00
162_S	185_K	2.131	1.00
414_L	417_T	2.099	1.00
126_V	163_I	2.095	1.00
252_G	290_G	2.032	1.00
83_A	104_L	2.031	1.00
165_V	188_V	1.997	1.00
232_N	236_I	1.990	1.00
162_S	187_T	1.982	1.00
259_F	420_L	1.964	1.00
105_L	375_L	1.929	1.00
307_T	364_S	1.924	1.00
85_P	89_K	1.923	1.00
86_A	89_K	1.920	1.00
56_L	131_E	1.893	1.00
274_V	301_C	1.858	1.00
255_L	287_V	1.856	1.00
257_A	261_Q	1.832	1.00
239_E	242_R	1.819	1.00
287_V	301_C	1.816	1.00
162_S	226_A	1.808	1.00
226_A	230_D	1.801	1.00
214_Q	217_G	1.788	1.00
391_M	421_V	1.782	1.00
387_A	423_A	1.764	1.00
401_V	417_T	1.757	1.00
87_M	391_M	1.724	1.00
336_A	369_Y	1.712	1.00
232_N	235_F	1.706	1.00
69_E	73_T	1.688	1.00
102_Q	418_T	1.686	1.00
225_K	229_S	1.685	1.00
304_A	393_G	1.669	1.00
316_V	353_M	1.658	1.00
387_A	424_T	1.636	1.00
251_A	422_W	1.610	1.00
192_A	213_E	1.598	1.00
114_S	177_I	1.585	1.00
364_S	367_T	1.571	1.00
304_A	361_Y	1.570	1.00
302_F	359_G	1.566	1.00
203_R	208_T	1.551	1.00
372_L	388_L	1.549	1.00
91_L	395_Q	1.548	1.00
252_G	287_V	1.539	1.00
62_Y	66_A	1.530	1.00
79_S	112_P	1.517	1.00
52_A	55_R	1.505	1.00
326_V	330_G	1.501	1.00
374_W	395_Q	1.495	1.00
259_F	418_T	1.491	1.00
316_V	360_F	1.487	1.00
326_V	331_I	1.487	1.00
310_P	318_T	1.474	1.00
272_L	417_T	1.472	1.00
292_K	358_D	1.471	1.00
310_P	314_L	1.469	1.00
392_A	396_R	1.466	1.00
361_Y	393_G	1.449	1.00
164_A	233_C	1.444	1.00
167_S	172_G	1.425	1.00
63_L	66_A	1.424	1.00
194_A	211_E	1.388	0.99
93_K	101_G	1.383	0.99
274_V	291_L	1.372	0.99
52_A	61_P	1.367	0.99
351_R	355_R	1.367	0.99
397_V	400_S	1.366	0.99
82_V	107_K	1.360	0.99
394_P	421_V	1.333	0.99
371_M	392_A	1.332	0.99
130_A	184_F	1.323	0.99
433_E	436_Q	1.314	0.99
275_Y	302_F	1.313	0.99
163_I	179_S	1.304	0.99
60_A	64_A	1.296	0.99
85_P	88_Q	1.295	0.99
383_L	388_L	1.284	0.99
215_D	218_V	1.274	0.99
321_H	324_I	1.270	0.99
128_A	243_T	1.270	0.99
276_L	283_G	1.266	0.99
303_F	360_F	1.266	0.99
104_L	263_G	1.263	0.99
259_F	263_G	1.262	0.99
273_F	401_V	1.252	0.99
70_T	182_I	1.252	0.99
199_K	209_V	1.232	0.99
273_F	419_H	1.229	0.99
191_S	214_Q	1.229	0.99
90_R	378_E	1.220	0.99
401_V	414_L	1.213	0.99
84_I	87_M	1.212	0.99
255_L	422_W	1.205	0.99
390_G	421_V	1.198	0.98
256_K	260_A	1.195	0.98
78_E	257_A	1.194	0.98
376_A	382_R	1.194	0.98
51_D	55_R	1.194	0.98
275_Y	394_P	1.193	0.98
220_V	235_F	1.191	0.98
191_S	194_A	1.191	0.98
263_G	418_T	1.188	0.98
373_G	377_Q	1.187	0.98
221_E	225_K	1.181	0.98
200_A	204_S	1.178	0.98
60_A	63_L	1.173	0.98
91_L	399_A	1.162	0.98
166_G	223_G	1.160	0.98
252_G	291_L	1.159	0.98
225_K	228_Q	1.157	0.98
75_G	112_P	1.131	0.98
363_L	392_A	1.125	0.98
371_M	391_M	1.121	0.98
93_K	103_L	1.113	0.98
164_A	226_A	1.110	0.97
114_S	119_A	1.107	0.97
54_A	58_R	1.096	0.97
396_R	399_A	1.095	0.97
91_L	394_P	1.091	0.97
367_T	392_A	1.084	0.97
50_Q	54_A	1.072	0.97
177_I	205_H	1.072	0.97
366_Q	370_D	1.071	0.97
82_V	109_S	1.067	0.97
369_Y	385_P	1.066	0.97
278_C	303_F	1.064	0.97
102_Q	416_N	1.063	0.97
383_L	387_A	1.062	0.97
263_G	269_D	1.061	0.97
87_M	374_W	1.060	0.97
393_G	397_V	1.049	0.96
226_A	229_S	1.047	0.96
191_S	213_E	1.046	0.96
194_A	203_R	1.035	0.96
104_L	259_F	1.033	0.96
302_F	397_V	1.028	0.96
375_L	391_M	1.026	0.96
387_A	390_G	1.024	0.96
288_A	301_C	1.013	0.96
201_K	205_H	1.012	0.96
275_Y	304_A	1.009	0.96
396_R	400_S	1.005	0.95
308_H	332_D	1.000	0.95
349_V	360_F	0.994	0.95
87_M	103_L	0.993	0.95
273_F	417_T	0.988	0.95
259_F	268_A	0.988	0.95
117_I	283_G	0.987	0.95
222_E	226_A	0.984	0.95
192_A	214_Q	0.978	0.95
273_F	414_L	0.978	0.95
249_S	290_G	0.953	0.94
91_L	374_W	0.949	0.94
350_G	353_M	0.936	0.93
47_Q	50_Q	0.934	0.93
173_L	201_K	0.934	0.93
56_L	59_F	0.932	0.93
431_E	435_N	0.932	0.93
270_N	299_V	0.932	0.93
53_H	57_S	0.932	0.93
192_A	195_R	0.931	0.93
160_Q	234_F	0.929	0.93
432_E	436_Q	0.926	0.93
275_Y	393_G	0.921	0.93
93_K	398_C	0.918	0.93
214_Q	218_V	0.916	0.93
88_Q	101_G	0.913	0.93
220_V	224_R	0.910	0.92
47_Q	51_D	0.907	0.92
75_G	79_S	0.905	0.92
57_S	246_L	0.904	0.92
300_H	358_D	0.900	0.92
104_L	418_T	0.900	0.92
49_V	293_L	0.889	0.92
126_V	182_I	0.889	0.92
432_E	435_N	0.888	0.91
255_L	291_L	0.884	0.91
363_L	396_R	0.881	0.91
70_T	181_R	0.878	0.91
218_V	221_E	0.877	0.91
259_F	269_D	0.871	0.91
201_K	382_R	0.870	0.91
130_A	182_I	0.861	0.90
318_T	321_H	0.859	0.90
373_G	434_M	0.852	0.90
85_P	181_R	0.851	0.90
382_R	434_M	0.850	0.90
256_K	296_G	0.850	0.90
54_A	242_R	0.848	0.89
320_L	324_I	0.845	0.89
92_E	415_R	0.844	0.89
269_D	416_N	0.842	0.89
122_G	174_S	0.842	0.89
263_G	268_A	0.839	0.89
375_L	383_L	0.838	0.89
200_A	203_R	0.835	0.89
54_A	57_S	0.835	0.89
260_A	263_G	0.834	0.89
253_Q	290_G	0.830	0.88
122_G	178_M	0.829	0.88
167_S	384_E	0.827	0.88
302_F	358_D	0.827	0.88
314_L	319_G	0.822	0.88
370_D	374_W	0.821	0.88
52_A	56_L	0.815	0.88
251_A	283_G	0.815	0.88
199_K	211_E	0.815	0.88
314_L	317_H	0.813	0.87
260_A	270_N	0.813	0.87
309_S	333_N	0.812	0.87
81_L	259_F	0.807	0.87
195_R	433_E	0.806	0.87
93_K	419_H	0.805	0.87
394_P	419_H	0.800	0.87
302_F	393_G	0.800	0.87
389_A	393_G	0.798	0.86
311_C	345_A	0.796	0.86
374_W	378_E	0.795	0.86
92_E	416_N	0.794	0.86
119_A	177_I	0.794	0.86
200_A	431_E	0.793	0.86
285_G	349_V	0.792	0.86
79_S	116_S	0.790	0.86
304_A	362_T	0.789	0.86
71_A	75_G	0.786	0.86
273_F	397_V	0.785	0.86
230_D	233_C	0.784	0.85
70_T	123_I	0.783	0.85
103_L	398_C	0.783	0.85
59_F	62_Y	0.778	0.85
235_F	238_D	0.778	0.85
312_M	360_F	0.777	0.85
198_K	384_E	0.776	0.85
418_T	422_W	0.774	0.85
256_K	291_L	0.773	0.85
397_V	401_V	0.771	0.84
316_V	321_H	0.769	0.84
274_V	420_L	0.765	0.84
175_I	179_S	0.765	0.84
227_A	233_C	0.760	0.84
188_V	220_V	0.759	0.84
108_D	424_T	0.757	0.83
86_A	378_E	0.753	0.83
50_Q	53_H	0.751	0.83
364_S	396_R	0.750	0.83
270_N	291_L	0.750	0.83
285_G	289_F	0.749	0.83
364_S	415_R	0.748	0.83
309_S	312_M	0.748	0.83
325_S	330_G	0.748	0.83
114_S	428_M	0.747	0.83
312_M	315_G	0.746	0.83
271_P	420_L	0.743	0.82
376_A	434_M	0.741	0.82
367_T	370_D	0.741	0.82
363_L	393_G	0.740	0.82
216_Y	283_G	0.739	0.82
200_A	435_N	0.734	0.81
168_T	198_K	0.727	0.81
372_L	434_M	0.726	0.81
278_C	312_M	0.725	0.81
275_Y	397_V	0.725	0.81
161_Y	185_K	0.725	0.81
224_R	228_Q	0.724	0.81
83_A	263_G	0.716	0.80
101_G	419_H	0.715	0.80
246_L	249_S	0.715	0.80
388_L	391_M	0.715	0.80
57_S	60_A	0.714	0.80
289_F	293_L	0.710	0.79
93_K	401_V	0.710	0.79
180_A	205_H	0.709	0.79
191_S	332_D	0.708	0.79
103_L	421_V	0.707	0.79
308_H	365_D	0.706	0.79
81_L	262_Q	0.704	0.79
316_V	354_E	0.703	0.79
393_G	396_R	0.700	0.78
321_H	350_G	0.699	0.78
63_L	67_F	0.699	0.78
321_H	354_E	0.697	0.78
109_S	424_T	0.696	0.78
383_L	423_A	0.696	0.78
302_F	361_Y	0.696	0.78
59_F	63_L	0.691	0.77
313_L	360_F	0.691	0.77
126_V	175_I	0.687	0.77
101_G	394_P	0.687	0.77
189_H	222_E	0.684	0.77
260_A	269_D	0.682	0.77
220_V	333_N	0.680	0.76
186_V	207_V	0.677	0.76
370_D	395_Q	0.677	0.76
304_A	363_L	0.677	0.76
224_R	235_F	0.677	0.76
168_T	384_E	0.675	0.76
315_G	344_R	0.673	0.76
187_T	233_C	0.670	0.75
128_A	131_E	0.668	0.75
204_S	373_G	0.667	0.75
89_K	378_E	0.666	0.75
198_K	338_D	0.666	0.75
114_S	205_H	0.665	0.75
129_H	240_N	0.664	0.75
51_D	54_A	0.663	0.74
238_D	242_R	0.662	0.74
58_R	63_L	0.662	0.74
304_A	388_L	0.659	0.74
400_S	414_L	0.658	0.74
361_Y	396_R	0.656	0.74
175_I	188_V	0.655	0.74
163_I	184_F	0.655	0.74
286_G	349_V	0.654	0.73
315_G	318_T	0.651	0.73
116_S	122_G	0.650	0.73
309_S	314_L	0.648	0.73
253_Q	293_L	0.648	0.73
164_A	189_H	0.647	0.73
57_S	242_R	0.644	0.72
256_K	290_G	0.643	0.72
370_D	399_A	0.643	0.72
298_H	358_D	0.643	0.72
107_K	423_A	0.640	0.72
62_Y	65_K	0.640	0.72
162_S	233_C	0.640	0.72
202_L	207_V	0.639	0.72
256_K	293_L	0.639	0.72
363_L	368_M	0.638	0.72
287_V	420_L	0.637	0.72
237_D	248_Y	0.635	0.71
164_A	212_Y	0.634	0.71
353_M	357_L	0.632	0.71
203_R	435_N	0.631	0.71
278_C	345_A	0.629	0.71
381_I	423_A	0.629	0.71
320_L	323_Q	0.629	0.71
160_Q	232_N	0.628	0.70
88_Q	93_K	0.628	0.70
88_Q	102_Q	0.626	0.70
307_T	362_T	0.623	0.70
400_S	415_R	0.622	0.70
310_P	315_G	0.621	0.70
130_A	161_Y	0.619	0.69
179_S	187_T	0.619	0.69
58_R	61_P	0.618	0.69
178_M	182_I	0.617	0.69
220_V	433_E	0.616	0.69
93_K	415_R	0.616	0.69
303_F	357_L	0.614	0.69
105_L	423_A	0.613	0.69
67_F	71_A	0.613	0.69
325_S	331_I	0.611	0.68
129_H	234_F	0.611	0.68
292_K	352_A	0.611	0.68
129_H	163_I	0.611	0.68
394_P	398_C	0.609	0.68
248_Y	387_A	0.606	0.68
395_Q	399_A	0.604	0.68
245_F	285_G	0.603	0.67
67_F	257_A	0.603	0.67
315_G	319_G	0.602	0.67
337_A	425_G	0.601	0.67
220_V	240_N	0.600	0.67
253_Q	257_A	0.598	0.67
75_G	123_I	0.598	0.67
172_G	281_G	0.598	0.67
61_P	66_A	0.596	0.66
367_T	371_M	0.596	0.66
375_L	423_A	0.595	0.66
50_Q	242_R	0.594	0.66
70_T	73_T	0.594	0.66
245_F	346_S	0.593	0.66
64_A	71_A	0.590	0.66
101_G	416_N	0.589	0.66
56_L	61_P	0.588	0.65
376_A	383_L	0.583	0.65
120_R	248_Y	0.582	0.65
337_A	368_M	0.582	0.65
167_S	198_K	0.582	0.65
384_E	425_G	0.581	0.65
75_G	119_A	0.581	0.65
173_L	202_L	0.581	0.65
314_L	323_Q	0.579	0.64
171_L	244_L	0.578	0.64
87_M	375_L	0.577	0.64
171_L	248_Y	0.576	0.64
383_L	391_M	0.573	0.63
316_V	324_I	0.572	0.63
93_K	394_P	0.572	0.63
199_K	203_R	0.566	0.63
312_M	316_V	0.565	0.62
68_P	71_A	0.565	0.62
202_L	209_V	0.565	0.62
87_M	90_R	0.563	0.62
365_D	369_Y	0.563	0.62
278_C	424_T	0.563	0.62
233_C	236_I	0.563	0.62
119_A	181_R	0.560	0.62
274_V	299_V	0.557	0.61
48_D	289_F	0.557	0.61
289_F	348_F	0.556	0.61
86_A	379_E	0.554	0.61
308_H	334_L	0.551	0.60
90_R	377_Q	0.551	0.60
187_T	226_A	0.551	0.60
372_L	385_P	0.551	0.60
168_T	280_V	0.549	0.60
186_V	205_H	0.547	0.60
216_Y	280_V	0.547	0.60
89_K	261_Q	0.545	0.60
366_Q	369_Y	0.544	0.59
309_S	313_L	0.544	0.59
310_P	362_T	0.543	0.59
309_S	315_G	0.543	0.59
122_G	385_P	0.543	0.59
361_Y	400_S	0.542	0.59
288_A	356_L	0.542	0.59
243_T	247_G	0.540	0.59
84_I	105_L	0.540	0.59
186_V	415_R	0.539	0.59
89_K	253_Q	0.539	0.59
300_H	417_T	0.538	0.59
303_F	349_V	0.537	0.59
198_K	386_S	0.536	0.58
225_K	325_S	0.536	0.58
189_H	220_V	0.536	0.58
168_T	386_S	0.534	0.58
333_N	341_A	0.534	0.58
48_D	55_R	0.532	0.58
109_S	423_A	0.532	0.58
112_P	177_I	0.531	0.58
55_R	58_R	0.531	0.58
363_L	389_A	0.531	0.58
79_S	119_A	0.529	0.57
245_F	348_F	0.529	0.57
262_Q	268_A	0.528	0.57
82_V	85_P	0.528	0.57
180_A	377_Q	0.527	0.57
336_A	365_D	0.527	0.57
127_L	131_E	0.526	0.57
121_G	247_G	0.526	0.57
287_V	290_G	0.525	0.57
212_Y	219_A	0.525	0.57
89_K	229_S	0.525	0.57
68_P	72_A	0.523	0.57
49_V	53_H	0.520	0.56
374_W	400_S	0.518	0.56
69_E	85_P	0.517	0.56
273_F	400_S	0.517	0.56
316_V	320_L	0.517	0.56
168_T	216_Y	0.516	0.56
268_A	298_H	0.516	0.56
180_A	186_V	0.515	0.55
259_F	262_Q	0.515	0.55
60_A	68_P	0.515	0.55
255_L	259_F	0.514	0.55
237_D	244_L	0.512	0.55
166_G	283_G	0.510	0.55
398_C	401_V	0.510	0.55
194_A	282_G	0.509	0.55
61_P	64_A	0.509	0.55
58_R	68_P	0.508	0.54
307_T	365_D	0.507	0.54
310_P	419_H	0.506	0.54
171_L	241_S	0.505	0.54
220_V	233_C	0.504	0.54
123_I	178_M	0.503	0.54
370_D	373_G	0.503	0.54
105_L	387_A	0.503	0.54
292_K	301_C	0.503	0.54
304_A	389_A	0.503	0.54
270_N	296_G	0.502	0.54
299_V	357_L	0.502	0.54
168_T	339_G	0.502	0.54
312_M	323_Q	0.501	0.53
104_L	262_Q	0.500	0.53
269_D	272_L	0.500	0.53

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
3ss7X	1	0.9796	100	0.237	Contact Map
1tdjA	2	0.7421	100	0.399	Contact Map
1e5xA	2	0.819	100	0.419	Contact Map
2zsjA	2	0.7353	100	0.426	Contact Map
2d1fA	2	0.7376	100	0.427	Contact Map
1v71A	2	0.7195	100	0.428	Contact Map
3aeyA	2	0.7308	100	0.428	Contact Map
2gn0A	2	0.7421	100	0.43	Contact Map
2rkbA	2	0.7036	100	0.433	Contact Map
4h27A	1	0.7036	100	0.437	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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