SDHD - BACSU - GREMLIN Contacts

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SDHD - Probable D-serine dehydratase

UniProt:	P54555	Sequences: MSVHSEVLHALLKDPFIQKLIDAEPVFWANSGKKEGPLPRADEWATEIAEAEKRMQRFAPYIAEVFPETKGAKGIIESPLFEVQHMKGKLEAAYQQPFPGRWLLKCDHELPISGSIKARGGIYEVLKYAENLALQEGMLQETDDYRILQEERFTGFFSRYSIAVGSTGNLGLSIGIIGAALGFRVTVHMSADAKQWKKDLLRQKGVTVMEYETDYSEAVNEGRRQAEQDPFCYFIDDEHSRQLFLGYAVAASRLKTQLDCMNIKPSLETPLFVYLPCGVGGGPGGVAFGLKLLYGDDVHVFFAEPTHSPCMLLGLYSGLHEKISVQDIGLDNQTAADGLAVGRPSGFVGKLIEPLLSGCYTVEDNTLYTLLHMLAVSEDKYLEPSALAGMFGPVQLFSTEEGRRYAQKYKMEHAVHVVWGTGGSMVPKDEMAAYNRIGADLLKKRNEK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	448 (341)
Sequences:	2199 (1313)
Seq/√Len:	71.1

ECOLI - SDHD ILVA DPAL TRPB TDCB CYSK CYSM DCYD
BACSU - SDHD ILVA TRPB THRC CYSM CYSK MCCA
HALSA - Q9HNH6 Q9HMQ7 Q9HRU4 TRPB Q9HNH0 Q9HQ70
SULSO - Q980P1 TRPB1 TRPB2 Q97ZL6 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
178_G	185_V	6.013	1.00
195_Q	199_D	5.832	1.00
82_E	101_R	4.462	1.00
188_H	225_Q	4.025	1.00
299_H	358_G	3.894	1.00
221_E	224_R	3.718	1.00
254_L	417_V	3.660	1.00
80_L	417_V	3.140	1.00
184_R	207_T	3.138	1.00
366_T	395_Q	3.104	1.00
309_P	313_L	2.996	1.00
272_F	301_F	2.817	1.00
306_T	363_E	2.779	1.00
224_R	228_Q	2.630	1.00
164_V	187_V	2.604	1.00
335_A	368_Y	2.571	1.00
86_M	390_M	2.562	1.00
315_L	359_C	2.458	1.00
250_A	419_W	2.444	1.00
82_E	103_L	2.428	1.00
161_S	186_T	2.383	1.00
386_A	420_G	2.288	1.00
390_M	418_V	2.228	1.00
193_A	196_W	2.219	1.00
81_F	106_C	2.207	1.00
391_F	395_Q	2.166	1.00
127_K	242_Q	2.110	1.00
163_A	232_C	2.110	1.00
371_L	387_L	2.032	1.00
198_K	208_V	1.995	1.00
273_V	290_L	1.989	1.00
213_T	216_S	1.958	1.00
287_A	300_V	1.931	1.00
101_R	415_V	1.924	1.00
86_M	102_W	1.899	1.00
423_G	426_V	1.893	1.00
275_L	282_G	1.874	1.00
382_L	387_L	1.861	1.00
186_T	207_T	1.852	1.00
389_G	418_V	1.845	1.00
166_S	171_G	1.841	1.00
382_L	386_A	1.836	1.00
165_G	222_G	1.832	1.00
191_A	212_E	1.824	1.00
251_A	290_L	1.808	1.00
272_F	299_H	1.806	1.00
386_A	389_G	1.794	1.00
395_Q	399_T	1.775	1.00
268_E	415_V	1.774	1.00
386_A	421_T	1.774	1.00
307_H	331_D	1.766	1.00
224_R	227_E	1.765	1.00
428_K	432_A	1.754	1.00
432_A	436_R	1.722	1.00
216_S	219_V	1.658	1.00
362_V	391_F	1.652	0.99
303_A	360_Y	1.649	0.99
313_L	316_Y	1.624	0.99
51_A	60_P	1.597	0.99
221_E	225_Q	1.595	0.99
255_K	293_L	1.589	0.99
375_A	381_Y	1.586	0.99
116_I	282_G	1.581	0.99
83_V	86_M	1.575	0.99
161_S	184_R	1.571	0.99
89_K	373_M	1.568	0.99
258_L	417_V	1.567	0.99
411_M	414_A	1.562	0.99
99_P	416_H	1.561	0.99
363_E	366_T	1.551	0.99
48_I	292_L	1.541	0.99
199_D	203_Q	1.529	0.99
254_L	419_W	1.527	0.99
255_K	259_D	1.515	0.99
85_H	88_G	1.514	0.99
308_S	332_N	1.513	0.99
61_Y	65_V	1.507	0.99
360_Y	392_G	1.488	0.99
429_D	432_A	1.488	0.99
199_D	202_R	1.480	0.99
251_A	289_G	1.478	0.99
102_W	418_V	1.460	0.99
382_L	420_G	1.455	0.99
213_T	219_V	1.412	0.98
214_D	217_E	1.411	0.98
82_E	87_K	1.410	0.98
311_M	314_G	1.401	0.98
376_V	435_N	1.382	0.98
366_T	391_F	1.375	0.98
163_A	211_Y	1.367	0.98
214_D	219_V	1.366	0.98
274_Y	301_F	1.364	0.98
370_L	391_F	1.358	0.98
86_M	374_L	1.343	0.98
366_T	369_T	1.328	0.98
319_L	323_I	1.325	0.98
388_A	392_G	1.319	0.98
226_A	232_C	1.317	0.97
202_R	207_T	1.311	0.97
186_T	209_M	1.309	0.97
121_G	173_S	1.307	0.97
286_V	419_W	1.306	0.97
160_Y	225_Q	1.305	0.97
99_P	102_W	1.289	0.97
250_A	282_G	1.288	0.97
277_C	302_F	1.285	0.97
90_L	394_V	1.278	0.97
106_C	109_E	1.261	0.97
49_A	53_K	1.259	0.97
374_L	382_L	1.257	0.97
400_E	410_K	1.256	0.97
269_T	296_D	1.251	0.97
310_C	344_P	1.236	0.96
301_F	358_G	1.236	0.96
396_L	399_T	1.233	0.96
370_L	390_M	1.229	0.96
273_V	286_V	1.218	0.96
198_K	210_E	1.216	0.96
251_A	286_V	1.207	0.96
84_Q	87_K	1.199	0.96
81_F	108_H	1.197	0.96
297_D	357_S	1.186	0.95
352_I	356_L	1.184	0.95
175_G	187_V	1.183	0.95
350_K	354_P	1.177	0.95
89_K	377_S	1.174	0.95
322_K	325_V	1.169	0.95
229_D	232_C	1.162	0.95
166_S	383_E	1.152	0.95
167_T	197_K	1.142	0.94
158_S	233_Y	1.141	0.94
284_G	348_V	1.140	0.94
215_Y	282_G	1.138	0.94
395_Q	398_S	1.138	0.94
200_L	204_K	1.137	0.94
374_L	390_M	1.133	0.94
179_A	204_K	1.111	0.93
325_V	330_L	1.104	0.93
262_N	268_E	1.091	0.93
197_K	383_E	1.091	0.93
311_M	359_C	1.067	0.92
303_A	387_L	1.060	0.92
47_E	288_F	1.045	0.91
215_Y	310_C	1.040	0.91
159_R	231_F	1.040	0.91
223_R	227_E	1.029	0.90
336_A	367_L	1.026	0.90
197_K	337_D	1.021	0.90
196_W	427_P	1.020	0.90
49_A	52_E	1.015	0.90
113_S	425_M	1.010	0.90
262_N	415_V	1.010	0.90
256_T	260_C	1.008	0.89
423_G	427_P	1.000	0.89
269_T	415_V	0.998	0.89
302_F	359_C	0.998	0.89
252_S	256_T	0.997	0.89
213_T	217_E	0.995	0.89
373_M	377_S	0.994	0.89
113_S	176_I	0.991	0.89
273_V	298_V	0.991	0.89
187_V	332_N	0.985	0.88
303_A	392_G	0.983	0.88
200_L	381_Y	0.981	0.88
77_E	256_T	0.980	0.88
309_P	416_H	0.979	0.88
88_G	412_E	0.976	0.88
393_P	418_V	0.976	0.88
90_L	393_P	0.969	0.88
50_E	54_R	0.968	0.88
198_K	202_R	0.967	0.87
334_T	340_A	0.966	0.87
103_L	415_V	0.965	0.87
84_Q	88_G	0.962	0.87
313_L	317_S	0.958	0.87
308_S	311_M	0.956	0.87
69_T	249_V	0.952	0.87
223_R	234_F	0.945	0.86
277_C	311_M	0.935	0.86
57_R	60_P	0.932	0.85
313_L	318_G	0.932	0.85
225_Q	228_Q	0.931	0.85
101_R	262_N	0.929	0.85
286_V	417_V	0.927	0.85
232_C	284_G	0.922	0.85
79_P	109_E	0.921	0.85
49_A	252_S	0.918	0.85
363_E	412_E	0.913	0.84
383_E	422_G	0.909	0.84
373_M	394_V	0.905	0.84
167_T	383_E	0.902	0.84
244_F	284_G	0.898	0.83
274_Y	303_A	0.895	0.83
172_L	200_L	0.889	0.83
226_A	233_Y	0.889	0.83
372_H	433_A	0.885	0.82
272_F	414_A	0.884	0.82
163_A	226_A	0.880	0.82
369_T	436_R	0.878	0.82
254_L	258_L	0.876	0.82
309_P	361_T	0.876	0.82
89_K	376_V	0.876	0.82
381_Y	431_M	0.875	0.82
430_E	433_A	0.871	0.81
104_L	374_L	0.869	0.81
410_K	414_A	0.866	0.81
301_F	360_Y	0.864	0.81
104_L	420_G	0.863	0.81
332_N	340_A	0.860	0.81
91_E	413_H	0.859	0.80
273_V	300_V	0.858	0.80
113_S	118_A	0.857	0.80
217_E	220_N	0.857	0.80
52_E	245_L	0.856	0.80
287_A	355_L	0.856	0.80
193_A	337_D	0.854	0.80
255_K	290_L	0.851	0.80
325_V	329_G	0.850	0.80
211_Y	218_A	0.850	0.80
269_T	298_V	0.848	0.80
368_Y	433_A	0.846	0.79
282_G	286_V	0.844	0.79
166_S	197_K	0.844	0.79
66_F	256_T	0.841	0.79
162_I	178_G	0.840	0.79
69_T	181_L	0.826	0.78
311_M	315_L	0.824	0.78
274_Y	392_G	0.824	0.78
299_H	357_S	0.823	0.78
372_H	376_V	0.822	0.77
259_D	262_N	0.822	0.77
220_N	224_R	0.822	0.77
186_T	232_C	0.821	0.77
307_H	333_Q	0.817	0.77
365_N	369_T	0.816	0.77
59_A	63_A	0.815	0.77
362_V	388_A	0.813	0.77
215_Y	219_V	0.812	0.77
102_W	397_F	0.807	0.76
103_L	258_L	0.800	0.76
302_F	356_L	0.798	0.75
291_K	357_S	0.798	0.75
80_L	258_L	0.793	0.75
193_A	281_G	0.793	0.75
163_A	225_Q	0.791	0.75
120_G	246_G	0.790	0.75
362_V	367_L	0.784	0.74
91_E	412_E	0.781	0.74
172_L	201_L	0.780	0.74
252_S	289_G	0.779	0.74
336_A	422_G	0.779	0.74
68_E	72_A	0.774	0.73
375_A	435_N	0.767	0.72
161_S	178_G	0.766	0.72
170_L	247_Y	0.765	0.72
366_T	370_L	0.764	0.72
312_L	359_C	0.763	0.72
50_E	53_K	0.757	0.71
237_D	247_Y	0.754	0.71
81_F	380_K	0.752	0.71
197_K	385_S	0.752	0.71
103_L	262_N	0.751	0.71
189_M	348_V	0.748	0.71
301_F	353_E	0.748	0.71
268_E	398_S	0.747	0.70
170_L	243_L	0.745	0.70
390_M	393_P	0.742	0.70
170_L	237_D	0.742	0.70
199_D	431_M	0.742	0.70
125_V	162_I	0.741	0.70
291_K	295_G	0.740	0.70
258_L	262_N	0.740	0.70
162_I	235_I	0.739	0.70
250_A	286_V	0.739	0.70
190_S	193_A	0.738	0.69
106_C	420_G	0.736	0.69
387_L	390_M	0.733	0.69
189_M	208_V	0.732	0.69
247_Y	279_V	0.731	0.69
301_F	357_S	0.730	0.69
375_A	431_M	0.730	0.69
100_G	415_V	0.729	0.69
189_M	338_G	0.728	0.68
118_A	176_I	0.724	0.68
301_F	396_L	0.724	0.68
189_M	210_E	0.724	0.68
80_L	83_V	0.723	0.68
293_L	390_M	0.722	0.68
99_P	397_F	0.720	0.68
254_L	286_V	0.720	0.68
393_P	416_H	0.719	0.67
314_G	317_S	0.719	0.67
285_G	348_V	0.718	0.67
163_A	222_G	0.717	0.67
366_T	373_M	0.716	0.67
272_F	411_M	0.715	0.67
170_L	240_S	0.714	0.67
275_L	287_A	0.712	0.67
87_K	99_P	0.709	0.66
303_A	388_A	0.709	0.66
159_R	184_R	0.709	0.66
88_G	260_C	0.705	0.66
116_I	286_V	0.705	0.66
372_H	434_Y	0.703	0.66
209_M	273_V	0.702	0.66
81_F	378_E	0.700	0.65
103_L	261_M	0.699	0.65
309_P	318_G	0.699	0.65
171_G	280_G	0.696	0.65
215_Y	279_V	0.694	0.65
288_F	292_L	0.693	0.65
273_V	417_V	0.693	0.65
121_G	174_I	0.692	0.65
311_M	349_G	0.692	0.65
176_I	204_K	0.692	0.65
256_T	259_D	0.690	0.64
380_K	420_G	0.687	0.64
304_E	339_L	0.687	0.64
352_I	359_C	0.685	0.64
252_S	292_L	0.685	0.64
352_I	357_S	0.681	0.63
63_A	379_D	0.681	0.63
314_G	393_P	0.681	0.63
370_L	387_L	0.680	0.63
87_K	91_E	0.679	0.63
53_K	56_Q	0.677	0.63
368_Y	384_P	0.677	0.63
154_T	436_R	0.677	0.63
375_A	379_D	0.676	0.63
308_S	312_L	0.676	0.63
78_S	187_V	0.676	0.63
110_L	118_A	0.674	0.62
75_I	253_R	0.674	0.62
77_E	253_R	0.674	0.62
309_P	317_S	0.672	0.62
287_A	356_L	0.672	0.62
115_S	236_D	0.671	0.62
306_T	309_P	0.670	0.62
78_S	286_V	0.670	0.62
71_G	261_M	0.669	0.62
262_N	267_L	0.669	0.62
237_D	279_V	0.667	0.62
115_S	213_T	0.664	0.61
300_V	356_L	0.663	0.61
78_S	115_S	0.661	0.61
396_L	400_E	0.661	0.61
178_G	315_L	0.659	0.61
398_S	401_E	0.659	0.61
161_S	244_F	0.653	0.60
208_V	363_E	0.653	0.60
314_G	318_G	0.652	0.60
224_R	259_D	0.650	0.60
166_S	336_A	0.649	0.60
382_L	390_M	0.649	0.60
167_T	215_Y	0.647	0.59
272_F	416_H	0.646	0.59
85_H	436_R	0.644	0.59
167_T	385_S	0.643	0.59
309_P	316_Y	0.643	0.59
270_P	417_V	0.643	0.59
88_G	207_T	0.643	0.59
360_Y	428_K	0.642	0.59
185_V	204_K	0.641	0.59
173_S	249_V	0.641	0.59
426_V	429_D	0.640	0.58
245_L	288_F	0.640	0.58
89_K	398_S	0.639	0.58
113_S	172_L	0.638	0.58
367_L	371_L	0.637	0.58
362_V	392_G	0.636	0.58
385_S	389_G	0.636	0.58
90_L	377_S	0.635	0.58
156_F	160_Y	0.634	0.58
269_T	299_H	0.634	0.58
104_L	249_V	0.634	0.58
369_T	372_H	0.634	0.58
167_T	338_G	0.634	0.58
307_H	364_D	0.631	0.57
128_Y	233_Y	0.631	0.57
315_L	318_G	0.628	0.57
80_L	261_M	0.626	0.57
268_E	413_H	0.623	0.56
273_V	291_K	0.622	0.56
91_E	99_P	0.620	0.56
63_A	73_K	0.618	0.56
86_M	100_G	0.616	0.56
312_L	316_Y	0.615	0.56
278_G	338_G	0.615	0.56
351_L	354_P	0.614	0.55
47_E	54_R	0.613	0.55
277_C	421_T	0.612	0.55
66_F	70_K	0.612	0.55
252_S	293_L	0.610	0.55
195_Q	202_R	0.604	0.54
394_V	398_S	0.601	0.54
52_E	56_Q	0.600	0.54
179_A	182_G	0.600	0.54
167_T	337_D	0.596	0.53
107_D	243_L	0.595	0.53
362_V	395_Q	0.594	0.53
125_V	174_I	0.594	0.53
384_P	422_G	0.593	0.53
319_L	322_K	0.591	0.53
189_M	193_A	0.591	0.53
88_G	252_S	0.591	0.53
428_K	431_M	0.588	0.52
290_L	355_L	0.587	0.52
225_Q	229_D	0.587	0.52
63_A	70_K	0.586	0.52
430_E	434_Y	0.586	0.52
99_P	412_E	0.586	0.52
91_E	231_F	0.585	0.52
82_E	306_T	0.584	0.52
258_L	270_P	0.583	0.52
250_A	254_L	0.581	0.51
371_L	384_P	0.580	0.51
228_Q	412_E	0.580	0.51
99_P	401_E	0.579	0.51
111_P	176_I	0.579	0.51
338_G	385_S	0.578	0.51
115_S	164_V	0.578	0.51
108_H	215_Y	0.578	0.51
303_A	434_Y	0.577	0.51
69_T	72_A	0.576	0.51
83_V	104_L	0.576	0.51
184_R	228_Q	0.576	0.51
77_E	257_Q	0.576	0.51
189_M	251_A	0.576	0.51
314_G	349_G	0.571	0.50
164_V	174_I	0.570	0.50
79_P	106_C	0.569	0.50
247_Y	386_A	0.567	0.50
341_V	386_A	0.567	0.50
90_L	373_M	0.567	0.50
245_L	248_A	0.564	0.49
296_D	412_E	0.563	0.49
400_E	414_A	0.562	0.49
110_L	113_S	0.561	0.49
269_T	417_V	0.561	0.49
236_D	243_L	0.561	0.49
248_A	252_S	0.561	0.49
117_K	169_N	0.555	0.48
167_T	172_L	0.552	0.48
122_I	177_I	0.551	0.48
167_T	170_L	0.551	0.48
369_T	398_S	0.550	0.48
126_L	181_L	0.549	0.47
86_M	373_M	0.548	0.47
255_K	292_L	0.548	0.47
61_Y	180_A	0.547	0.47
88_G	401_E	0.546	0.47
105_K	253_R	0.546	0.47
59_A	67_P	0.546	0.47
342_G	364_D	0.545	0.47
363_E	395_Q	0.545	0.47
155_G	159_R	0.544	0.47
385_S	388_A	0.544	0.47
54_R	58_F	0.543	0.47
201_L	206_V	0.543	0.47
99_P	393_P	0.542	0.47
216_S	279_V	0.541	0.46
369_T	394_V	0.541	0.46
277_C	345_S	0.540	0.46
336_A	383_E	0.539	0.46
258_L	268_E	0.538	0.46
62_I	69_T	0.538	0.46
234_F	237_D	0.538	0.46
286_V	291_K	0.538	0.46
81_F	84_Q	0.535	0.46
189_M	201_L	0.532	0.45
391_F	396_L	0.531	0.45
255_K	289_G	0.531	0.45
308_S	342_G	0.531	0.45
274_Y	393_P	0.530	0.45
187_V	339_L	0.529	0.45
108_H	382_L	0.528	0.45
171_G	338_G	0.528	0.45
305_P	385_S	0.527	0.45
53_K	82_E	0.526	0.45
67_P	155_G	0.526	0.45
87_K	100_G	0.525	0.45
100_G	413_H	0.523	0.44
308_S	314_G	0.522	0.44
85_H	377_S	0.521	0.44
85_H	155_G	0.521	0.44
48_I	55_M	0.520	0.44
54_R	57_R	0.520	0.44
124_E	337_D	0.519	0.44
194_K	429_D	0.519	0.44
368_Y	372_H	0.517	0.44
81_F	103_L	0.516	0.43
73_K	179_A	0.516	0.43
69_T	122_I	0.516	0.43
83_V	87_K	0.515	0.43
335_A	430_E	0.514	0.43
312_L	361_T	0.512	0.43
248_A	288_F	0.511	0.43
377_S	384_P	0.510	0.43
118_A	235_I	0.509	0.43
121_G	166_S	0.509	0.43
85_H	227_E	0.509	0.43
170_L	279_V	0.507	0.42
384_P	387_L	0.507	0.42
244_F	345_S	0.505	0.42
217_E	221_E	0.505	0.42
127_K	156_F	0.504	0.42
335_A	425_M	0.503	0.42
194_K	335_A	0.502	0.42
400_E	413_H	0.502	0.42
387_L	391_F	0.501	0.42
74_G	78_S	0.501	0.42
170_L	236_D	0.500	0.42

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	0.9576	100	0.27	Contact Map
1tdjA	2	0.7545	100	0.401	Contact Map
2gn0A	2	0.7344	100	0.431	Contact Map
4d9iA	2	0.8371	100	0.431	Contact Map
1v71A	2	0.7098	100	0.432	Contact Map
2zsjA	2	0.7433	100	0.438	Contact Map
1e5xA	2	0.8259	100	0.438	Contact Map
2rkbA	2	0.7031	100	0.441	Contact Map
3aeyA	2	0.7411	100	0.441	Contact Map
2d1fA	2	0.7478	100	0.441	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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