RAPF - BACSU - GREMLIN Contacts

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RAPF - Response regulator aspartate phosphatase F

UniProt:	P71002	Sequences: MTGVISSSSIGEKINEWYMYIRRFSIPDAEYLRREIKQELDQMEEDQDLHLYYSLMEFRHNLMLEYLEPLEKMRIEEQPRLSDLLLEIDKKQARLTGLLEYYFNFFRGMYELDQREYLSAIKFFKKAESKLIFVKDRIEKAEFFFKMSESYYYMKQTYFSMDYARQAYEIYKEHEAYNIRLLQCHSLFATNFLDLKQYEDAISHFQKAYSMAEAEKQPQLMGRTLYNIGLCKNSQSQYEDAIPYFKRAIAVFEESNILPSLPQAYFLITQIHYKLGKIDKAHEYHSKGMAYSQKAGDVIYLSEFEFLKSLYLSGPDEEAIQGFFDFLESKMLYADLEDFAIDVAKYYHERKNFQKASAYFLKVEQVRQLIQGGVSLYEIEV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	381 (322)
Sequences:	1172 (1060)
Seq/√Len:	59.1

ECOLI - LPSRP HEMY NLPI
BACSU - RAPF RAPC RAPH RAPA RAPB RAPJ RAPI RAPK RAPD RAPG RAPE YVCD YPIA
HALSA - Q9HMM8
SULSO - Q97V36

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
237_Q	240_D	5.468	1.00
197_Q	200_D	4.717	1.00
277_K	280_K	4.408	1.00
148_S	164_A	4.386	1.00
229_G	245_F	4.194	1.00
144_F	163_Y	3.966	1.00
156_Q	159_F	3.736	1.00
161_M	188_F	3.562	1.00
268_I	272_H	3.157	1.00
108_G	124_F	3.118	1.00
272_H	277_K	2.941	1.00
189_A	205_F	2.913	1.00
193_L	205_F	2.836	1.00
245_F	267_L	2.634	1.00
320_I	323_F	2.532	1.00
352_N	355_K	2.519	1.00
269_T	285_H	2.489	1.00
116_E	119_S	2.456	1.00
355_K	358_A	2.391	1.00
185_H	204_H	2.297	1.00
272_H	280_K	2.248	1.00
104_N	123_F	2.216	1.00
246_K	268_I	2.155	1.00
205_F	227_N	2.133	1.00
164_A	187_L	2.080	1.00
202_I	228_I	2.067	1.00
189_A	204_H	2.066	1.00
165_R	188_F	2.039	1.00
145_F	187_L	2.008	1.00
348_H	361_L	1.994	1.00
229_G	268_I	1.989	1.00
28_D	31_Y	1.952	1.00
229_G	241_A	1.936	1.00
358_A	362_K	1.921	1.00
225_L	244_Y	1.899	1.00
328_E	362_K	1.885	1.00
232_K	240_D	1.884	1.00
121_I	151_Y	1.852	1.00
25_S	28_D	1.843	1.00
121_I	147_M	1.842	1.00
268_I	284_Y	1.811	0.99
161_M	192_F	1.811	0.99
148_S	189_A	1.792	0.99
104_N	126_K	1.788	0.99
242_I	272_H	1.751	0.99
29_A	36_I	1.751	0.99
343_V	347_Y	1.736	0.99
47_Q	50_H	1.734	0.99
107_R	111_E	1.731	0.99
33_R	37_K	1.671	0.99
182_L	208_A	1.669	0.99
240_D	243_P	1.663	0.99
188_F	192_F	1.642	0.99
108_G	127_A	1.617	0.99
147_M	151_Y	1.564	0.98
280_K	283_E	1.564	0.98
168_Y	185_H	1.563	0.98
29_A	32_L	1.537	0.98
209_Y	225_L	1.527	0.98
166_Q	169_E	1.524	0.98
202_I	235_Q	1.509	0.98
202_I	231_C	1.498	0.98
242_I	275_L	1.477	0.98
221_M	225_L	1.476	0.98
27_P	38_Q	1.468	0.98
265_Y	284_Y	1.465	0.98
189_A	201_A	1.449	0.97
27_P	31_Y	1.447	0.97
242_I	271_I	1.433	0.97
34_R	38_Q	1.399	0.97
345_K	360_F	1.394	0.97
28_D	35_E	1.382	0.97
124_F	146_K	1.366	0.96
57_E	61_N	1.324	0.96
64_L	69_P	1.317	0.96
150_S	154_M	1.315	0.96
342_D	345_K	1.314	0.96
145_F	184_C	1.313	0.95
225_L	247_R	1.313	0.95
113_D	117_Y	1.303	0.95
24_F	27_P	1.302	0.95
26_I	37_K	1.300	0.95
31_Y	34_R	1.290	0.95
332_L	335_D	1.284	0.95
209_Y	221_M	1.284	0.95
190_T	205_F	1.278	0.95
360_F	364_E	1.254	0.94
102_Y	106_F	1.253	0.94
61_N	65_E	1.252	0.94
233_N	238_Y	1.250	0.94
303_E	335_D	1.250	0.94
358_A	361_L	1.249	0.94
28_D	32_L	1.246	0.94
144_F	166_Q	1.241	0.94
147_M	154_M	1.238	0.94
32_L	35_E	1.236	0.94
225_L	248_A	1.232	0.94
49_L	53_Y	1.231	0.94
108_G	123_F	1.224	0.93
344_A	360_F	1.223	0.93
144_F	265_Y	1.220	0.93
307_L	311_Y	1.219	0.93
50_H	54_S	1.210	0.93
52_Y	56_M	1.209	0.93
120_A	281_A	1.198	0.93
311_Y	316_D	1.189	0.92
267_L	270_Q	1.189	0.92
271_I	275_L	1.189	0.92
299_I	303_E	1.184	0.92
249_I	264_A	1.181	0.92
147_M	163_Y	1.173	0.92
124_F	128_E	1.172	0.92
28_D	38_Q	1.170	0.92
242_I	268_I	1.165	0.92
356_A	363_V	1.155	0.91
127_A	143_F	1.154	0.91
309_S	314_G	1.154	0.91
308_K	312_L	1.152	0.91
349_E	365_Q	1.144	0.91
238_Y	271_I	1.141	0.91
31_Y	48_D	1.128	0.90
82_S	85_L	1.123	0.90
226_Y	264_A	1.123	0.90
200_D	203_S	1.117	0.90
25_S	38_Q	1.112	0.90
36_I	39_E	1.109	0.89
37_K	40_L	1.106	0.89
246_K	280_K	1.101	0.89
361_L	365_Q	1.097	0.89
111_E	123_F	1.094	0.89
55_L	58_F	1.090	0.89
30_E	34_R	1.090	0.89
34_R	41_D	1.089	0.89
202_I	232_K	1.082	0.88
28_D	41_D	1.069	0.88
26_I	30_E	1.066	0.88
191_N	195_L	1.051	0.87
112_L	124_F	1.046	0.87
207_K	210_S	1.043	0.86
186_S	227_N	1.042	0.86
31_Y	35_E	1.041	0.86
40_L	47_Q	1.040	0.86
26_I	36_I	1.038	0.86
25_S	31_Y	1.037	0.86
27_P	34_R	1.033	0.86
249_I	268_I	1.033	0.86
132_I	140_K	1.031	0.86
30_E	43_M	1.029	0.86
167_A	170_I	1.024	0.85
50_H	53_Y	1.021	0.85
178_N	181_L	1.010	0.85
36_I	40_L	1.009	0.85
55_L	59_R	1.009	0.85
161_M	191_N	1.008	0.84
344_A	356_A	1.006	0.84
290_A	293_Q	1.002	0.84
353_F	356_A	1.002	0.84
146_K	149_E	1.000	0.84
269_T	288_G	0.998	0.84
48_D	51_L	0.997	0.84
329_S	348_H	0.997	0.84
46_D	49_L	0.995	0.84
356_A	359_Y	0.995	0.84
127_A	227_N	0.985	0.83
208_A	356_A	0.985	0.83
306_F	317_E	0.982	0.83
297_D	300_Y	0.975	0.82
61_N	66_Y	0.975	0.82
208_A	224_T	0.971	0.82
24_F	28_D	0.969	0.82
269_T	284_Y	0.968	0.82
266_F	285_H	0.966	0.82
127_A	131_L	0.960	0.81
336_L	356_A	0.944	0.80
54_S	61_N	0.944	0.80
29_A	43_M	0.940	0.80
346_Y	350_R	0.939	0.80
119_S	122_K	0.938	0.80
105_F	109_M	0.938	0.80
52_Y	59_R	0.937	0.80
32_L	41_D	0.936	0.80
24_F	30_E	0.929	0.79
126_K	129_S	0.927	0.79
29_A	33_R	0.918	0.78
222_G	248_A	0.918	0.78
228_I	244_Y	0.917	0.78
355_K	359_Y	0.914	0.78
167_A	184_C	0.912	0.78
348_H	357_S	0.911	0.78
104_N	127_A	0.906	0.78
35_E	39_E	0.903	0.77
341_I	364_E	0.902	0.77
145_F	266_F	0.902	0.77
323_F	332_L	0.894	0.77
24_F	197_Q	0.891	0.76
226_Y	267_L	0.889	0.76
264_A	296_G	0.886	0.76
305_E	312_L	0.885	0.76
207_K	211_M	0.883	0.76
357_S	360_F	0.881	0.75
25_S	33_R	0.878	0.75
340_A	359_Y	0.875	0.75
247_R	251_V	0.875	0.75
52_Y	55_L	0.874	0.75
104_N	185_H	0.865	0.74
106_F	109_M	0.862	0.74
116_E	168_Y	0.861	0.74
304_F	316_D	0.858	0.74
311_Y	314_G	0.856	0.73
40_L	43_M	0.853	0.73
205_F	220_L	0.853	0.73
112_L	150_S	0.851	0.73
205_F	276_G	0.851	0.73
273_Y	285_H	0.849	0.73
144_F	225_L	0.848	0.73
26_I	44_E	0.848	0.73
262_P	269_T	0.848	0.73
111_E	119_S	0.848	0.73
233_N	267_L	0.844	0.72
298_V	301_L	0.841	0.72
351_K	361_L	0.839	0.72
31_Y	38_Q	0.839	0.72
120_A	149_E	0.834	0.71
248_A	259_P	0.831	0.71
152_Y	164_A	0.829	0.71
33_R	40_L	0.828	0.71
38_Q	41_D	0.827	0.71
168_Y	181_L	0.827	0.71
359_Y	363_V	0.823	0.70
101_Y	106_F	0.821	0.70
159_F	272_H	0.813	0.69
79_P	82_S	0.809	0.69
32_L	39_E	0.808	0.69
312_L	315_P	0.807	0.69
62_L	65_E	0.807	0.69
239_E	275_L	0.803	0.69
39_E	43_M	0.796	0.68
108_G	112_L	0.795	0.68
206_Q	228_I	0.795	0.68
148_S	151_Y	0.794	0.68
242_I	246_K	0.794	0.68
211_M	336_L	0.792	0.67
25_S	42_Q	0.791	0.67
38_Q	42_Q	0.790	0.67
101_Y	127_A	0.788	0.67
26_I	29_A	0.787	0.67
215_E	218_P	0.787	0.67
93_A	213_E	0.782	0.66
348_H	360_F	0.779	0.66
102_Y	131_L	0.779	0.66
28_D	39_E	0.776	0.66
81_L	84_L	0.773	0.66
52_Y	58_F	0.772	0.65
337_E	340_A	0.769	0.65
317_E	327_L	0.768	0.65
54_S	57_E	0.766	0.65
174_H	215_E	0.765	0.65
128_E	144_F	0.765	0.65
193_L	230_L	0.762	0.64
46_D	50_H	0.761	0.64
224_T	351_K	0.760	0.64
223_R	226_Y	0.759	0.64
24_F	31_Y	0.758	0.64
165_R	192_F	0.757	0.64
174_H	236_S	0.755	0.64
213_E	221_M	0.755	0.64
265_Y	287_K	0.754	0.64
248_A	251_V	0.747	0.63
28_D	34_R	0.745	0.63
229_G	244_Y	0.745	0.63
39_E	44_E	0.745	0.63
25_S	30_E	0.744	0.63
34_R	37_K	0.741	0.62
109_M	124_F	0.737	0.62
31_Y	42_Q	0.737	0.62
278_I	282_H	0.737	0.62
48_D	53_Y	0.736	0.62
245_F	263_Q	0.734	0.62
50_H	55_L	0.731	0.61
152_Y	191_N	0.728	0.61
265_Y	288_G	0.726	0.61
79_P	86_L	0.724	0.60
230_L	233_N	0.724	0.60
232_K	237_Q	0.721	0.60
357_S	361_L	0.720	0.60
152_Y	190_T	0.720	0.60
311_Y	315_P	0.720	0.60
151_Y	159_F	0.719	0.60
60_H	64_L	0.719	0.60
313_S	316_D	0.718	0.60
191_N	229_G	0.717	0.60
351_K	354_Q	0.715	0.60
49_L	239_E	0.715	0.60
30_E	37_K	0.714	0.59
30_E	44_E	0.714	0.59
326_F	329_S	0.713	0.59
324_F	327_L	0.712	0.59
230_L	245_F	0.709	0.59
339_F	347_Y	0.709	0.59
34_R	43_M	0.708	0.59
160_S	191_N	0.707	0.59
120_A	128_E	0.707	0.59
305_E	310_L	0.702	0.58
143_F	146_K	0.701	0.58
121_I	154_M	0.700	0.58
50_H	57_E	0.700	0.58
145_F	152_Y	0.699	0.58
51_L	62_L	0.699	0.58
26_I	38_Q	0.697	0.58
159_F	162_D	0.694	0.57
128_E	131_L	0.693	0.57
30_E	39_E	0.693	0.57
343_V	352_N	0.693	0.57
192_F	200_D	0.693	0.57
347_Y	355_K	0.688	0.57
351_K	356_A	0.686	0.56
161_M	195_L	0.686	0.56
303_E	306_F	0.683	0.56
35_E	43_M	0.682	0.56
239_E	325_D	0.681	0.56
26_I	32_L	0.680	0.56
187_L	193_L	0.679	0.56
180_R	183_Q	0.679	0.56
117_Y	150_S	0.677	0.55
127_A	167_A	0.676	0.55
26_I	35_E	0.673	0.55
307_L	334_A	0.673	0.55
350_R	358_A	0.672	0.55
354_Q	358_A	0.672	0.55
270_Q	342_D	0.670	0.55
165_R	200_D	0.670	0.55
105_F	146_K	0.667	0.54
337_E	363_V	0.665	0.54
237_Q	243_P	0.665	0.54
56_M	59_R	0.663	0.54
228_I	232_K	0.661	0.54
346_Y	349_E	0.660	0.53
101_Y	131_L	0.656	0.53
104_N	130_K	0.656	0.53
31_Y	37_K	0.654	0.53
144_F	167_A	0.653	0.53
283_E	287_K	0.653	0.53
328_E	352_N	0.651	0.52
122_K	216_K	0.647	0.52
59_R	64_L	0.646	0.52
217_Q	249_I	0.645	0.52
104_N	201_A	0.644	0.52
149_E	187_L	0.643	0.52
190_T	227_N	0.639	0.51
218_P	251_V	0.637	0.51
189_A	208_A	0.636	0.51
84_L	88_I	0.636	0.51
124_F	307_L	0.636	0.51
217_Q	221_M	0.633	0.50
353_F	361_L	0.633	0.50
38_Q	44_E	0.633	0.50
296_G	299_I	0.631	0.50
108_G	297_D	0.631	0.50
336_L	340_A	0.628	0.50
233_N	271_I	0.627	0.50
27_P	57_E	0.626	0.50
312_L	316_D	0.625	0.50
116_E	236_S	0.619	0.49
62_L	69_P	0.617	0.49
300_Y	303_E	0.615	0.48
236_S	287_K	0.615	0.48
167_A	241_A	0.614	0.48
121_I	124_F	0.613	0.48
262_P	265_Y	0.608	0.48
61_N	64_L	0.607	0.48
304_F	335_D	0.607	0.48
65_E	68_E	0.605	0.47
230_L	234_S	0.603	0.47
321_Q	324_F	0.602	0.47
31_Y	47_Q	0.602	0.47
178_N	214_A	0.601	0.47
111_E	121_I	0.600	0.47
79_P	87_E	0.599	0.47
63_M	67_L	0.599	0.47
34_R	279_D	0.599	0.47
181_L	185_H	0.596	0.46
190_T	230_L	0.595	0.46
249_I	261_L	0.593	0.46
165_R	224_T	0.593	0.46
172_K	290_A	0.591	0.46
251_V	294_K	0.591	0.46
145_F	149_E	0.588	0.45
25_S	34_R	0.587	0.45
35_E	50_H	0.587	0.45
33_R	42_Q	0.583	0.45
288_G	304_F	0.582	0.45
39_E	49_L	0.580	0.45
40_L	50_H	0.579	0.44
306_F	313_S	0.579	0.44
308_K	313_S	0.579	0.44
344_A	363_V	0.577	0.44
158_Y	168_Y	0.576	0.44
188_F	195_L	0.576	0.44
188_F	204_H	0.574	0.44
345_K	349_E	0.573	0.44
190_T	224_T	0.572	0.44
279_D	356_A	0.571	0.44
80_R	283_E	0.571	0.44
212_A	221_M	0.570	0.44
53_Y	59_R	0.570	0.44
338_D	342_D	0.569	0.43
340_A	343_V	0.568	0.43
110_Y	157_T	0.568	0.43
354_Q	365_Q	0.566	0.43
352_N	358_A	0.565	0.43
157_T	192_F	0.565	0.43
306_F	310_L	0.565	0.43
117_Y	226_Y	0.565	0.43
347_Y	352_N	0.563	0.43
79_P	201_A	0.562	0.43
205_F	228_I	0.560	0.42
205_F	342_D	0.559	0.42
48_D	52_Y	0.559	0.42
27_P	41_D	0.559	0.42
106_F	339_F	0.558	0.42
348_H	353_F	0.558	0.42
64_L	68_E	0.558	0.42
62_L	66_Y	0.556	0.42
34_R	40_L	0.550	0.41
171_Y	180_R	0.550	0.41
245_F	271_I	0.549	0.41
320_I	327_L	0.548	0.41
284_Y	288_G	0.548	0.41
47_Q	57_E	0.547	0.41
209_Y	227_N	0.546	0.41
61_N	68_E	0.544	0.41
60_H	63_M	0.543	0.41
30_E	35_E	0.542	0.40
208_A	288_G	0.542	0.40
317_E	355_K	0.541	0.40
327_L	339_F	0.541	0.40
183_Q	186_S	0.539	0.40
299_I	326_F	0.539	0.40
104_N	116_E	0.538	0.40
349_E	353_F	0.537	0.40
99_L	103_F	0.537	0.40
27_P	30_E	0.536	0.40
29_A	239_E	0.536	0.40
195_L	199_E	0.536	0.40
26_I	47_Q	0.531	0.39
195_L	352_N	0.530	0.39
309_S	312_L	0.529	0.39
212_A	220_L	0.528	0.39
108_G	157_T	0.527	0.39
148_S	191_N	0.526	0.39
239_E	243_P	0.526	0.39
321_Q	328_E	0.526	0.39
124_F	149_E	0.525	0.39
247_R	268_I	0.525	0.39
229_G	267_L	0.523	0.38
307_L	313_S	0.523	0.38
194_D	226_Y	0.523	0.38
278_I	329_S	0.523	0.38
25_S	41_D	0.522	0.38
307_L	310_L	0.521	0.38
129_S	329_S	0.520	0.38
216_K	219_Q	0.519	0.38
302_S	350_R	0.518	0.38
188_F	229_G	0.518	0.38
145_F	186_S	0.512	0.37
353_F	357_S	0.511	0.37
89_D	96_T	0.511	0.37
308_K	311_Y	0.511	0.37
33_R	36_I	0.510	0.37
88_I	340_A	0.509	0.37
24_F	42_Q	0.509	0.37
25_S	40_L	0.509	0.37
223_R	227_N	0.508	0.37
184_C	187_L	0.508	0.37
168_Y	204_H	0.507	0.37
266_F	327_L	0.507	0.37
342_D	351_K	0.506	0.37
268_I	288_G	0.504	0.36
315_P	318_E	0.504	0.36
31_Y	279_D	0.503	0.36
102_Y	110_Y	0.503	0.36
208_A	341_I	0.502	0.36
35_E	44_E	0.500	0.36

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
3ulqA	1	0.9869	100	0.262	Contact Map
4gyoA	2	0.9449	100	0.271	Contact Map
3q15A	2	0.958	100	0.278	Contact Map
4i1aA	2	0.9396	100	0.283	Contact Map
4gpkA	3	0.9055	100	0.338	Contact Map
1w3bA	2	0.8268	100	0.434	Contact Map
4l9pA	1	0.748	100	0.438	Contact Map
3q7aA	1	0.7375	100	0.439	Contact Map
3sf4A	1	0.8241	100	0.447	Contact Map
4ui9O	1	0.9685	100	0.448	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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