YDAM - ECOLI - GREMLIN Contacts

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YDAM - Probable diguanylate cyclase YdaM

UniProt:	P77302	Sequences: MITHNFNTLDLLTSPVWIVSPFEEQLIYANSAAKLLMQDLTFSQLRTGPYSVSSQKELPKYLSDLQNQHDIIEILTVQRKEEETALSCRLVLRKLTETEPVIIFEGIEAPATLGLKASRSANYQRKKQGFYARFFLTNSAPMLLIDPSRDGQIVDANLAALNFYGYNHETMCQKHTWEINMLGRRVMPIMHEISHLPGGHKPLNFVHKLADGSTRHVQTYAGPIEIYGDKLMLCIVHDITEQKRLEEQLEHAAHHDAMTGLLNRRQFYHITEPGQMQHLAIAQDYSLLLIDTDRFKHINDLYGHSKGDEVLCALARTLESCARKGDLVFRWGGEEFVLLLPRTPLDTALSLAETIRVSVAKVSISGLPRFTVSIGVAHHEGNESIDELFKRVDDALYRAKNDGRNRVLAA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13355
Length:	410 (316)
Sequences:	1484 (1331)
Seq/√Len:	74.9

ECOLI - YDAM YEGE YEDQ DOSC GMR DOSP YEAJ YLIF YDEH YEAP YEAI YCDT YFIN
BACSU - YTRP YKOW

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
323_R	326_D	5.992	1.00
288_L	374_I	3.941	1.00
251_H	255_H	3.861	1.00
294_R	404_R	3.757	1.00
242_Q	246_E	3.565	1.00
322_A	328_V	3.535	1.00
267_F	337_V	3.298	1.00
117_A	121_A	3.289	1.00
140_A	237_H	3.205	1.00
288_L	352_A	3.014	1.00
384_S	387_E	3.003	1.00
286_S	378_H	2.947	1.00
393_D	397_Y	2.714	1.00
304_H	397_Y	2.666	1.00
113_L	117_A	2.513	1.00
356_R	407_V	2.448	1.00
267_F	339_L	2.417	1.00
243_K	246_E	2.401	1.00
143_L	234_C	2.375	1.00
382_N	391_R	2.314	1.00
399_A	406_R	2.312	1.00
128_Q	132_A	2.310	1.00
114_G	117_A	2.279	1.00
271_T	385_I	2.275	1.00
274_G	277_Q	2.273	1.00
280_A	323_R	2.083	1.00
300_D	304_H	2.062	1.00
99_E	103_I	2.045	1.00
261_L	315_A	2.022	1.00
289_L	396_L	2.009	1.00
270_I	327_L	1.998	1.00
300_D	397_Y	1.993	1.00
333_G	397_Y	1.986	1.00
166_Y	210_A	1.971	1.00
262_L	266_Q	1.968	1.00
110_P	113_L	1.895	1.00
309_E	312_C	1.875	1.00
296_K	300_D	1.861	1.00
141_P	236_V	1.835	1.00
170_T	210_A	1.835	1.00
146_D	150_D	1.830	1.00
359_V	372_V	1.816	1.00
226_I	229_D	1.792	1.00
340_L	351_L	1.788	1.00
117_A	120_S	1.781	1.00
348_A	352_A	1.779	1.00
135_F	155_D	1.766	1.00
103_I	106_G	1.765	1.00
352_A	376_V	1.757	1.00
379_H	382_N	1.743	1.00
300_D	393_D	1.738	1.00
270_I	273_P	1.731	1.00
204_N	243_K	1.717	1.00
185_R	206_V	1.716	1.00
296_K	304_H	1.705	1.00
304_H	393_D	1.681	1.00
166_Y	170_T	1.680	1.00
239_I	243_K	1.662	1.00
292_T	372_V	1.652	1.00
120_S	124_Q	1.638	1.00
371_T	405_N	1.622	1.00
121_A	125_R	1.606	0.99
103_I	107_I	1.597	0.99
353_E	357_V	1.573	0.99
313_A	317_T	1.565	0.99
107_I	110_P	1.562	0.99
396_L	404_R	1.560	0.99
360_A	405_N	1.507	0.99
266_Q	269_H	1.507	0.99
289_L	337_V	1.505	0.99
344_P	347_T	1.496	0.99
262_L	327_L	1.490	0.99
376_V	407_V	1.489	0.99
286_S	348_A	1.483	0.99
106_G	110_P	1.477	0.99
290_I	372_V	1.467	0.99
141_P	163_F	1.447	0.99
318_L	328_V	1.441	0.99
143_L	153_I	1.439	0.99
294_R	334_E	1.432	0.99
298_I	310_V	1.430	0.99
333_G	393_D	1.429	0.99
293_D	373_S	1.427	0.99
356_R	360_A	1.412	0.99
305_S	390_K	1.388	0.98
296_K	393_D	1.380	0.98
289_L	334_E	1.374	0.98
310_V	370_F	1.374	0.98
351_L	354_T	1.371	0.98
146_D	152_Q	1.369	0.98
266_Q	270_I	1.366	0.98
296_K	397_Y	1.359	0.98
353_E	356_R	1.348	0.98
332_G	397_Y	1.322	0.98
343_T	347_T	1.315	0.98
274_G	341_P	1.291	0.98
288_L	340_L	1.290	0.98
159_A	162_N	1.288	0.98
114_G	121_A	1.280	0.97
96_T	100_P	1.279	0.97
291_D	296_K	1.268	0.97
292_T	334_E	1.259	0.97
304_H	333_G	1.259	0.97
356_R	405_N	1.248	0.97
209_L	213_S	1.241	0.97
110_P	114_G	1.227	0.97
299_N	307_G	1.227	0.97
313_A	316_R	1.212	0.96
399_A	403_G	1.211	0.96
352_A	374_I	1.209	0.96
300_D	333_G	1.206	0.96
348_A	376_V	1.197	0.96
132_A	136_L	1.189	0.96
226_I	230_K	1.187	0.96
266_Q	327_L	1.174	0.96
291_D	397_Y	1.167	0.96
334_E	396_L	1.163	0.95
92_L	95_L	1.163	0.95
138_N	142_M	1.148	0.95
153_I	157_N	1.146	0.95
121_A	124_Q	1.144	0.95
243_K	247_E	1.140	0.95
241_E	244_R	1.128	0.95
246_E	250_E	1.125	0.95
99_E	106_G	1.125	0.95
174_K	178_E	1.118	0.94
113_L	121_A	1.117	0.94
326_D	351_L	1.114	0.94
218_Q	237_H	1.112	0.94
295_F	311_L	1.112	0.94
261_L	328_V	1.111	0.94
314_L	359_V	1.097	0.94
141_P	157_N	1.095	0.94
269_H	327_L	1.091	0.94
128_Q	131_Y	1.080	0.93
99_E	107_I	1.077	0.93
92_L	96_T	1.076	0.93
291_D	400_K	1.076	0.93
334_E	371_T	1.072	0.93
340_L	348_A	1.065	0.93
291_D	299_N	1.060	0.93
381_G	391_R	1.054	0.92
157_N	238_D	1.051	0.92
291_D	393_D	1.046	0.92
290_I	374_I	1.046	0.92
335_E	397_Y	1.040	0.92
379_H	388_L	1.036	0.92
291_D	304_H	1.032	0.92
100_P	107_I	1.023	0.91
315_A	328_V	1.023	0.91
335_E	393_D	1.017	0.91
245_L	249_L	1.015	0.91
156_A	161_L	1.010	0.91
304_H	307_G	1.010	0.91
277_Q	280_A	1.009	0.91
310_V	364_I	1.002	0.90
353_E	407_V	0.994	0.90
377_A	382_N	0.993	0.90
291_D	300_D	0.986	0.90
302_Y	394_D	0.986	0.90
402_D	406_R	0.985	0.90
356_R	371_T	0.984	0.90
299_N	333_G	0.977	0.89
395_A	399_A	0.973	0.89
164_Y	171_M	0.972	0.89
399_A	408_L	0.971	0.89
302_Y	367_L	0.968	0.89
285_Y	354_T	0.967	0.89
134_F	144_L	0.967	0.89
167_N	170_T	0.957	0.88
350_S	354_T	0.952	0.88
402_D	408_L	0.948	0.88
206_V	216_H	0.945	0.88
307_G	332_G	0.937	0.87
181_M	185_R	0.937	0.87
286_S	343_T	0.936	0.87
254_H	266_Q	0.924	0.86
255_H	334_E	0.921	0.86
96_T	99_E	0.916	0.86
331_W	334_E	0.904	0.85
292_T	311_L	0.903	0.85
294_R	362_V	0.902	0.85
299_N	308_D	0.896	0.85
244_R	248_Q	0.894	0.85
356_R	374_I	0.892	0.84
134_F	159_A	0.889	0.84
100_P	103_I	0.879	0.84
267_F	271_T	0.879	0.84
390_K	394_D	0.876	0.83
218_Q	242_Q	0.875	0.83
93_R	100_P	0.875	0.83
295_F	399_A	0.875	0.83
253_A	304_H	0.872	0.83
296_K	299_N	0.872	0.83
107_I	114_G	0.870	0.83
202_P	218_Q	0.870	0.83
249_L	252_A	0.864	0.83
124_Q	128_Q	0.861	0.82
256_D	330_R	0.859	0.82
306_K	364_I	0.858	0.82
294_R	359_V	0.854	0.82
304_H	335_E	0.848	0.81
337_V	389_F	0.845	0.81
352_A	403_G	0.844	0.81
316_R	319_E	0.843	0.81
209_L	215_R	0.840	0.81
157_N	240_T	0.832	0.80
143_L	160_A	0.829	0.80
293_D	403_G	0.829	0.80
298_I	362_V	0.829	0.80
294_R	396_L	0.827	0.80
359_V	362_V	0.824	0.79
116_K	119_R	0.823	0.79
274_G	280_A	0.820	0.79
219_T	236_V	0.814	0.79
329_F	337_V	0.814	0.79
144_L	157_N	0.809	0.78
280_A	326_D	0.804	0.78
146_D	149_R	0.803	0.78
277_Q	341_P	0.802	0.78
349_L	353_E	0.801	0.78
310_V	334_E	0.801	0.78
99_E	102_I	0.799	0.77
180_N	189_I	0.795	0.77
258_M	304_H	0.790	0.77
377_A	395_A	0.789	0.76
321_C	354_T	0.789	0.76
124_Q	127_K	0.787	0.76
175_H	178_E	0.784	0.76
398_R	408_L	0.781	0.76
204_N	218_Q	0.780	0.76
364_I	367_L	0.775	0.75
107_I	111_A	0.773	0.75
206_V	214_T	0.772	0.75
176_T	181_M	0.772	0.75
343_T	378_H	0.770	0.75
181_M	184_R	0.768	0.75
255_H	262_L	0.766	0.74
363_S	368_P	0.763	0.74
317_T	334_E	0.763	0.74
289_L	389_F	0.762	0.74
153_I	171_M	0.758	0.74
96_T	106_G	0.754	0.73
160_A	164_Y	0.751	0.73
107_I	113_L	0.747	0.72
307_G	333_G	0.737	0.71
291_D	307_G	0.736	0.71
164_Y	215_R	0.735	0.71
106_G	114_G	0.733	0.71
134_F	216_H	0.733	0.71
300_D	335_E	0.731	0.71
333_G	400_K	0.730	0.71
127_K	130_F	0.730	0.71
252_A	255_H	0.725	0.70
377_A	391_R	0.725	0.70
326_D	354_T	0.722	0.70
300_D	332_G	0.721	0.70
141_P	238_D	0.720	0.70
288_L	338_L	0.720	0.70
216_H	239_I	0.719	0.70
285_Y	379_H	0.718	0.69
271_T	339_L	0.718	0.69
181_M	206_V	0.718	0.69
299_N	304_H	0.712	0.69
165_G	212_G	0.712	0.69
373_S	403_G	0.711	0.69
195_H	200_H	0.710	0.69
225_E	231_L	0.709	0.68
250_E	254_H	0.709	0.68
156_A	171_M	0.709	0.68
262_L	329_F	0.707	0.68
267_F	329_F	0.706	0.68
354_T	396_L	0.705	0.68
95_L	99_E	0.705	0.68
180_N	185_R	0.704	0.68
346_D	384_S	0.702	0.68
283_Q	342_R	0.699	0.67
296_K	335_E	0.699	0.67
309_E	313_A	0.698	0.67
331_W	337_V	0.697	0.67
100_P	110_P	0.697	0.67
110_P	117_A	0.695	0.67
155_D	158_L	0.690	0.66
335_E	400_K	0.689	0.66
255_H	261_L	0.685	0.66
264_R	308_D	0.684	0.66
299_N	335_E	0.682	0.65
275_Q	385_I	0.681	0.65
245_L	252_A	0.681	0.65
270_I	339_L	0.679	0.65
323_R	354_T	0.678	0.65
382_N	387_E	0.678	0.65
292_T	371_T	0.676	0.65
248_Q	252_A	0.675	0.65
332_G	335_E	0.675	0.65
307_G	397_Y	0.675	0.65
118_S	121_A	0.674	0.65
257_A	265_R	0.673	0.64
321_C	355_I	0.671	0.64
285_Y	388_L	0.669	0.64
291_D	333_G	0.669	0.64
99_E	113_L	0.667	0.64
135_F	160_A	0.665	0.64
113_L	120_S	0.664	0.63
307_G	393_D	0.662	0.63
338_L	355_I	0.661	0.63
383_E	391_R	0.661	0.63
323_R	397_Y	0.659	0.63
278_H	379_H	0.658	0.63
398_R	404_R	0.656	0.62
193_I	221_A	0.655	0.62
100_P	106_G	0.653	0.62
254_H	265_R	0.651	0.62
322_A	355_I	0.651	0.62
296_K	333_G	0.651	0.62
136_L	390_K	0.647	0.61
223_P	230_K	0.646	0.61
242_Q	245_L	0.646	0.61
255_H	266_Q	0.645	0.61
125_R	128_Q	0.643	0.61
106_G	117_A	0.642	0.61
313_A	362_V	0.642	0.61
295_F	403_G	0.642	0.61
248_Q	251_H	0.641	0.61
306_K	309_E	0.641	0.61
300_D	307_G	0.640	0.61
117_A	123_Y	0.639	0.60
259_T	311_L	0.636	0.60
271_T	285_Y	0.633	0.60
292_T	298_I	0.633	0.60
299_N	400_K	0.631	0.60
328_V	338_L	0.631	0.60
103_I	110_P	0.630	0.59
221_A	234_C	0.629	0.59
292_T	314_L	0.628	0.59
191_H	195_H	0.627	0.59
309_E	365_S	0.626	0.59
138_N	165_G	0.625	0.59
347_T	350_S	0.620	0.58
273_P	327_L	0.620	0.58
210_A	215_R	0.619	0.58
300_D	400_K	0.616	0.58
359_V	370_F	0.616	0.58
332_G	393_D	0.616	0.58
257_A	396_L	0.616	0.58
302_Y	396_L	0.612	0.57
274_G	334_E	0.610	0.57
352_A	399_A	0.610	0.57
280_A	342_R	0.609	0.57
207_H	217_V	0.608	0.57
141_P	233_L	0.605	0.56
308_D	330_R	0.603	0.56
205_F	219_T	0.602	0.56
310_V	396_L	0.599	0.56
317_T	358_S	0.598	0.55
275_Q	379_H	0.597	0.55
351_L	355_I	0.594	0.55
352_A	372_V	0.594	0.55
247_E	250_E	0.594	0.55
317_T	362_V	0.593	0.55
135_F	138_N	0.593	0.55
373_S	397_Y	0.593	0.55
338_L	384_S	0.593	0.55
115_L	338_L	0.592	0.55
221_A	232_M	0.591	0.55
295_F	333_G	0.590	0.54
135_F	157_N	0.588	0.54
255_H	396_L	0.587	0.54
288_L	376_V	0.587	0.54
184_R	206_V	0.586	0.54
161_L	164_Y	0.586	0.54
152_Q	175_H	0.586	0.54
285_Y	339_L	0.586	0.54
349_L	407_V	0.585	0.54
144_L	155_D	0.584	0.54
295_F	335_E	0.583	0.54
156_A	160_A	0.583	0.54
176_T	189_I	0.582	0.53
376_V	395_A	0.581	0.53
334_E	404_R	0.581	0.53
204_N	208_K	0.580	0.53
159_A	221_A	0.578	0.53
397_Y	400_K	0.577	0.53
223_P	228_G	0.573	0.52
266_Q	329_F	0.569	0.52
296_K	400_K	0.569	0.52
101_V	105_E	0.569	0.52
99_E	117_A	0.568	0.52
302_Y	334_E	0.568	0.52
310_V	317_T	0.567	0.52
278_H	283_Q	0.566	0.51
329_F	389_F	0.565	0.51
263_N	332_G	0.565	0.51
249_L	254_H	0.564	0.51
387_E	390_K	0.563	0.51
323_R	347_T	0.563	0.51
153_I	234_C	0.562	0.51
196_L	200_H	0.562	0.51
204_N	242_Q	0.562	0.51
205_F	217_V	0.560	0.51
337_V	396_L	0.560	0.51
141_P	209_L	0.560	0.51
306_K	367_L	0.559	0.51
334_E	393_D	0.557	0.50
143_L	377_A	0.556	0.50
323_R	351_L	0.556	0.50
278_H	285_Y	0.556	0.50
114_G	118_S	0.554	0.50
164_Y	207_H	0.554	0.50
174_K	200_H	0.549	0.49
331_W	396_L	0.548	0.49
202_P	220_Y	0.547	0.49
127_K	132_A	0.547	0.49
321_C	328_V	0.545	0.49
239_I	246_E	0.545	0.49
139_S	157_N	0.544	0.49
192_E	197_P	0.543	0.49
363_S	366_G	0.542	0.48
139_S	233_L	0.542	0.48
304_H	332_G	0.540	0.48
143_L	156_A	0.540	0.48
295_F	395_A	0.540	0.48
334_E	356_R	0.539	0.48
302_Y	310_V	0.537	0.48
157_N	160_A	0.537	0.48
371_T	403_G	0.537	0.48
99_E	114_G	0.537	0.48
254_H	262_L	0.536	0.48
310_V	362_V	0.535	0.48
144_L	153_I	0.535	0.48
357_V	360_A	0.535	0.48
389_F	396_L	0.533	0.47
138_N	141_P	0.533	0.47
334_E	397_Y	0.530	0.47
134_F	145_I	0.529	0.47
359_V	401_N	0.528	0.47
377_A	388_L	0.524	0.46
255_H	294_R	0.524	0.46
275_Q	388_L	0.523	0.46
275_Q	381_G	0.522	0.46
280_A	347_T	0.522	0.46
253_A	292_T	0.521	0.46
92_L	99_E	0.521	0.46
93_R	107_I	0.520	0.46
274_G	289_L	0.519	0.46
284_D	343_T	0.518	0.45
133_R	157_N	0.516	0.45
122_N	126_K	0.516	0.45
252_A	265_R	0.515	0.45
203_L	233_L	0.514	0.45
291_D	295_F	0.513	0.45
193_I	196_L	0.513	0.45
175_H	179_I	0.512	0.45
134_F	139_S	0.512	0.45
107_I	124_Q	0.511	0.45
253_A	266_Q	0.510	0.44
160_A	171_M	0.509	0.44
138_N	217_V	0.509	0.44
122_N	357_V	0.509	0.44
295_F	393_D	0.509	0.44
107_I	117_A	0.508	0.44
104_F	108_E	0.508	0.44
331_W	389_F	0.506	0.44
318_L	338_L	0.505	0.44
238_D	243_K	0.504	0.44
308_D	333_G	0.504	0.44
135_F	159_A	0.504	0.44
261_L	334_E	0.503	0.44
318_L	355_I	0.502	0.43
282_A	353_E	0.502	0.43
143_L	221_A	0.502	0.43
134_F	141_P	0.501	0.43
141_P	144_L	0.500	0.43
151_G	157_N	0.500	0.43

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
1w25A	2	0.8927	100	0.501	Contact Map
3ezuA	2	0.7634	100	0.508	Contact Map
4h54A	2	0.639	100	0.535	Contact Map
4j40A	2	0	100	0.539	Contact Map
3pjxA	1	0.4244	100	0.546	Contact Map
3breA	4	0.661	100	0.555	Contact Map
4rnhA	2	0.3732	100	0.559	Contact Map
3ignA	1	0.3927	100	0.562	Contact Map
3i5cA	2	0.4561	100	0.562	Contact Map
3qyyA	1	0.3732	100	0.568	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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