RAPB - BACSU - GREMLIN Contacts

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RAPB - Response regulator aspartate phosphatase B

UniProt:	P70962	Sequences: MAAYEIPSSQVGVKINKWYKHILAFQVADAVKLKEEIDLDIEQMEEDQLLLLYYQLISYRHQIMLDYVKPDLHEESQLQYRELIKTLESNQDSISGLSEYYFHLFRGMYEFEQNNYISAISFYRKAEKMLAFVEDEIERAEFHFKVAEVFYIMKQTHFSMNHAVQALETYKAHDFYRVRRIQCHFVISGNYIDYRNYEKALEHLDDAYRLALLEGQPRLIGSALYNIGNCYDDKGELDQAAEYFEKALPVFEDYQLEQLPKALFSLTRVLFKKQDSEAAIRYYEKGIAIAQKRNDFFSLAKYKFLQALYVESVNLNMIQEVFDYMEEKGLYVYIEEFALDAASYFSHREQYKEAVYFYEKAVSMREMIQRNDCLYEV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	377 (317)
Sequences:	1767 (1624)
Seq/√Len:	91.2

ECOLI - LPSRP HEMY NLPI YBEQ
BACSU - RAPB RAPA RAPH RAPF RAPJ RAPC RAPG RAPI RAPK RAPE RAPD YVCD YPIA YRRB
HALSA - Q9HMM8
SULSO - Q97V36 Q97VC4 Q97WM3 Q97ZS3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
236_E	239_Q	4.651	1.00
275_D	278_A	4.459	1.00
147_A	163_A	4.393	1.00
196_N	199_K	4.177	1.00
228_G	244_F	4.059	1.00
188_S	204_L	3.485	1.00
107_G	123_Y	3.443	1.00
350_Q	353_E	3.398	1.00
143_H	162_H	2.979	1.00
155_Q	158_F	2.945	1.00
244_F	265_S	2.855	1.00
115_N	118_S	2.835	1.00
163_A	186_V	2.530	1.00
341_A	345_F	2.457	1.00
245_E	266_L	2.455	1.00
160_M	187_I	2.445	1.00
267_T	283_Y	2.423	1.00
201_L	227_I	2.389	1.00
103_H	122_F	2.339	1.00
106_R	110_E	2.339	1.00
231_Y	239_Q	2.325	1.00
110_E	115_N	2.307	1.00
224_L	243_Y	2.302	1.00
239_Q	242_E	2.238	1.00
224_L	246_K	2.230	1.00
309_Y	314_N	2.209	1.00
185_F	226_N	2.191	1.00
184_H	203_H	2.173	1.00
278_A	281_R	2.147	1.00
346_S	359_E	2.135	1.00
201_L	231_Y	2.081	1.00
144_F	186_V	2.062	1.00
199_K	202_E	2.014	1.00
301_K	305_L	1.997	1.00
143_H	165_Q	1.981	1.00
270_L	278_A	1.958	1.00
241_A	269_V	1.940	1.00
241_A	270_L	1.939	1.00
302_Y	309_Y	1.937	1.00
187_I	191_Y	1.905	1.00
150_F	158_F	1.903	1.00
227_I	231_Y	1.887	1.00
263_L	282_Y	1.875	1.00
241_A	266_L	1.874	1.00
146_V	150_F	1.856	1.00
266_L	270_L	1.850	1.00
123_Y	145_K	1.845	1.00
201_L	230_C	1.834	1.00
241_A	273_K	1.831	1.00
100_Y	126_A	1.790	1.00
228_G	243_Y	1.787	1.00
310_V	313_V	1.776	1.00
160_M	190_N	1.775	1.00
188_S	207_A	1.768	1.00
192_I	204_L	1.751	1.00
181_I	207_A	1.719	1.00
353_E	356_Y	1.704	1.00
184_H	206_D	1.691	1.00
205_D	227_I	1.666	1.00
342_A	358_Y	1.636	1.00
110_E	118_S	1.631	1.00
267_T	286_G	1.609	1.00
107_G	126_A	1.593	1.00
238_D	273_K	1.590	1.00
167_L	184_H	1.572	1.00
270_L	275_D	1.564	1.00
107_G	122_F	1.545	1.00
227_I	243_Y	1.528	1.00
248_L	263_L	1.525	1.00
266_L	282_Y	1.519	1.00
241_A	245_E	1.516	1.00
225_Y	265_S	1.499	1.00
221_G	247_A	1.498	1.00
334_I	338_A	1.486	1.00
118_S	121_S	1.480	1.00
201_L	205_D	1.476	1.00
144_F	183_C	1.456	1.00
147_A	166_A	1.442	0.99
204_L	226_N	1.428	0.99
311_E	314_N	1.411	0.99
228_G	240_A	1.410	0.99
191_Y	199_K	1.404	0.99
103_H	125_K	1.402	0.99
201_L	234_K	1.391	0.99
269_V	273_K	1.384	0.99
146_V	162_H	1.378	0.99
338_A	357_F	1.373	0.99
139_R	143_H	1.363	0.99
326_E	360_K	1.358	0.99
32_K	35_E	1.354	0.99
189_G	204_L	1.346	0.99
160_M	191_Y	1.332	0.99
318_I	321_V	1.321	0.99
140_A	170_Y	1.311	0.99
188_S	203_H	1.297	0.99
126_A	142_F	1.296	0.99
48_Q	51_L	1.287	0.99
248_L	262_A	1.278	0.99
80_Y	83_L	1.273	0.99
342_A	361_A	1.271	0.99
265_S	268_R	1.266	0.99
164_V	187_I	1.265	0.99
345_F	353_E	1.259	0.99
248_L	266_L	1.258	0.99
356_Y	360_K	1.254	0.98
237_L	269_V	1.246	0.98
305_L	309_Y	1.242	0.98
158_F	161_N	1.239	0.98
267_T	282_Y	1.235	0.98
281_R	285_K	1.210	0.98
34_K	38_D	1.205	0.98
150_F	155_Q	1.193	0.98
39_L	42_E	1.192	0.98
143_H	166_A	1.190	0.98
224_L	247_A	1.174	0.98
181_I	211_A	1.173	0.98
120_I	150_F	1.171	0.98
235_G	272_K	1.163	0.98
145_K	148_E	1.146	0.97
302_Y	318_I	1.129	0.97
188_S	230_C	1.128	0.97
212_L	220_I	1.125	0.97
280_I	284_E	1.122	0.97
355_V	359_E	1.119	0.97
263_L	285_K	1.119	0.97
352_K	356_Y	1.118	0.97
351_Y	354_A	1.108	0.97
208_Y	220_I	1.104	0.97
30_A	34_K	1.103	0.97
243_Y	247_A	1.097	0.96
207_A	223_A	1.094	0.96
284_E	301_K	1.093	0.96
203_H	207_A	1.075	0.96
110_E	122_F	1.073	0.96
315_L	319_Q	1.071	0.96
280_I	308_L	1.069	0.96
140_A	166_A	1.067	0.96
167_L	180_R	1.062	0.96
126_A	129_M	1.062	0.96
103_H	126_A	1.058	0.96
107_G	149_V	1.054	0.96
232_D	244_F	1.041	0.95
35_E	39_L	1.040	0.95
30_A	33_L	1.035	0.95
271_F	283_Y	1.032	0.95
127_E	143_H	1.030	0.95
338_A	360_K	1.021	0.95
124_R	146_V	1.018	0.95
346_S	358_Y	1.017	0.95
31_V	40_D	1.014	0.95
147_A	162_H	1.005	0.94
101_Y	105_F	1.004	0.94
120_I	146_V	0.993	0.94
39_L	45_E	0.991	0.94
228_G	247_A	0.990	0.94
120_I	149_V	0.988	0.94
302_Y	314_N	0.988	0.94
189_G	226_N	0.984	0.94
140_A	147_A	0.982	0.94
301_K	304_F	0.978	0.93
247_A	262_A	0.975	0.93
229_N	244_F	0.967	0.93
187_I	203_H	0.964	0.93
270_L	282_Y	0.963	0.93
217_P	220_I	0.944	0.92
34_K	41_I	0.943	0.92
245_E	278_A	0.943	0.92
302_Y	306_Q	0.939	0.92
104_L	145_K	0.933	0.92
96_G	99_E	0.933	0.92
127_E	142_F	0.933	0.92
83_L	86_T	0.931	0.92
170_Y	183_C	0.931	0.92
169_T	173_H	0.922	0.91
345_F	350_Q	0.913	0.91
229_N	265_S	0.913	0.91
82_E	86_T	0.907	0.91
144_F	182_Q	0.899	0.90
147_A	186_V	0.899	0.90
157_H	194_Y	0.898	0.90
232_D	272_K	0.890	0.90
35_E	38_D	0.887	0.90
354_A	361_A	0.887	0.90
340_D	343_S	0.886	0.89
120_I	124_R	0.882	0.89
120_I	153_M	0.882	0.89
35_E	42_E	0.882	0.89
108_M	123_Y	0.880	0.89
141_E	145_K	0.867	0.88
244_F	259_L	0.866	0.88
166_A	183_C	0.863	0.88
198_E	234_K	0.860	0.88
33_L	38_D	0.860	0.88
206_D	209_R	0.859	0.88
109_Y	113_Q	0.856	0.88
169_T	216_Q	0.855	0.88
67_Y	71_D	0.855	0.88
248_L	259_L	0.850	0.87
164_V	168_E	0.850	0.87
124_R	162_H	0.849	0.87
285_K	334_I	0.845	0.87
287_I	291_Q	0.843	0.87
185_F	223_A	0.843	0.87
131_A	139_R	0.842	0.87
33_L	37_I	0.840	0.87
53_Y	57_I	0.840	0.87
55_Q	58_S	0.838	0.87
200_A	279_A	0.838	0.87
208_Y	224_L	0.837	0.87
282_Y	286_G	0.827	0.86
151_Y	163_A	0.826	0.86
181_I	188_S	0.823	0.86
160_M	194_Y	0.822	0.86
77_Q	80_Y	0.820	0.86
123_Y	142_F	0.819	0.85
264_F	286_G	0.819	0.85
207_A	210_L	0.819	0.85
343_S	358_Y	0.816	0.85
165_Q	168_E	0.814	0.85
144_F	148_E	0.810	0.85
119_A	123_Y	0.806	0.85
33_L	39_L	0.804	0.84
32_K	40_D	0.800	0.84
37_I	44_M	0.796	0.84
80_Y	84_I	0.795	0.84
106_R	122_F	0.792	0.83
230_C	234_K	0.787	0.83
107_G	111_F	0.786	0.83
305_L	313_V	0.784	0.83
40_D	44_M	0.783	0.83
150_F	153_M	0.781	0.83
37_I	40_D	0.780	0.83
315_L	341_A	0.777	0.82
283_Y	300_A	0.776	0.82
53_Y	56_L	0.775	0.82
325_M	337_F	0.773	0.82
116_Y	120_I	0.773	0.82
143_H	263_L	0.772	0.82
264_F	268_R	0.770	0.82
310_V	314_N	0.765	0.81
31_V	35_E	0.764	0.81
158_F	193_D	0.763	0.81
283_Y	287_I	0.761	0.81
104_L	108_M	0.758	0.81
347_H	360_K	0.757	0.81
355_V	358_Y	0.756	0.81
30_A	37_I	0.754	0.80
224_L	228_G	0.752	0.80
41_I	45_E	0.749	0.80
314_N	317_M	0.747	0.80
182_Q	185_F	0.741	0.79
87_L	90_N	0.739	0.79
191_Y	196_N	0.737	0.79
31_V	34_K	0.737	0.79
111_F	123_Y	0.732	0.78
220_I	224_L	0.732	0.78
33_L	42_E	0.731	0.78
188_S	339_L	0.730	0.78
151_Y	190_N	0.728	0.78
36_E	40_D	0.727	0.78
305_L	310_V	0.725	0.78
346_S	355_V	0.725	0.78
357_F	361_A	0.724	0.78
171_K	213_L	0.720	0.77
225_Y	262_A	0.720	0.77
233_D	236_E	0.718	0.77
337_F	341_A	0.717	0.77
53_Y	60_R	0.716	0.77
201_L	208_Y	0.711	0.76
39_L	43_Q	0.707	0.76
35_E	50_L	0.706	0.76
121_S	125_K	0.706	0.76
84_I	87_L	0.703	0.76
197_Y	237_L	0.701	0.75
57_I	60_R	0.698	0.75
226_N	229_N	0.694	0.75
62_Q	71_D	0.694	0.75
317_M	321_V	0.693	0.75
154_K	159_S	0.692	0.74
357_F	360_K	0.691	0.74
304_F	308_L	0.691	0.74
147_A	159_S	0.691	0.74
41_I	51_L	0.690	0.74
353_E	357_F	0.690	0.74
81_R	84_I	0.685	0.74
226_N	265_S	0.682	0.73
63_I	66_D	0.681	0.73
98_S	102_F	0.677	0.73
108_M	145_K	0.675	0.73
309_Y	318_I	0.673	0.72
286_G	290_A	0.672	0.72
37_I	50_L	0.672	0.72
264_F	267_T	0.671	0.72
48_Q	54_Y	0.670	0.72
122_F	126_A	0.669	0.72
38_D	42_E	0.669	0.72
127_E	146_V	0.669	0.72
107_G	147_A	0.668	0.72
302_Y	321_V	0.667	0.72
31_V	41_I	0.667	0.72
239_Q	243_Y	0.666	0.72
50_L	82_E	0.663	0.71
342_A	354_A	0.662	0.71
61_H	196_N	0.661	0.71
35_E	43_Q	0.659	0.71
268_R	283_Y	0.659	0.71
320_E	324_Y	0.657	0.71
75_E	81_R	0.656	0.70
30_A	43_Q	0.651	0.70
276_S	280_I	0.651	0.70
127_E	139_R	0.650	0.70
104_L	126_A	0.650	0.70
228_G	231_Y	0.646	0.69
260_P	267_T	0.644	0.69
191_Y	203_H	0.642	0.69
242_E	277_E	0.641	0.69
62_Q	65_L	0.639	0.68
246_K	249_P	0.637	0.68
107_G	279_A	0.636	0.68
167_L	183_C	0.635	0.68
34_K	37_I	0.634	0.68
185_F	204_L	0.632	0.68
111_F	149_V	0.631	0.67
205_D	243_Y	0.631	0.67
160_M	316_N	0.629	0.67
260_P	290_A	0.626	0.67
99_E	129_M	0.623	0.66
50_L	53_Y	0.622	0.66
267_T	301_K	0.622	0.66
182_Q	286_G	0.621	0.66
31_V	39_L	0.619	0.66
317_M	320_E	0.618	0.66
163_A	187_I	0.618	0.66
321_V	324_Y	0.617	0.66
171_K	206_D	0.617	0.66
31_V	45_E	0.616	0.66
306_Q	314_N	0.615	0.65
333_Y	336_E	0.612	0.65
274_Q	294_N	0.611	0.65
172_A	175_F	0.611	0.65
278_A	282_Y	0.611	0.65
165_Q	182_Q	0.610	0.65
75_E	78_L	0.609	0.65
256_L	262_A	0.609	0.65
237_L	273_K	0.608	0.65
351_Y	356_Y	0.607	0.64
148_E	186_V	0.604	0.64
268_R	272_K	0.602	0.64
112_E	115_N	0.601	0.64
185_F	207_A	0.600	0.64
123_Y	261_K	0.600	0.64
83_L	90_N	0.599	0.63
34_K	42_E	0.598	0.63
30_A	36_E	0.596	0.63
31_V	36_E	0.595	0.63
264_F	283_Y	0.595	0.63
208_Y	223_A	0.595	0.63
171_K	180_R	0.594	0.63
128_K	131_A	0.593	0.63
32_K	37_I	0.593	0.63
126_A	140_A	0.593	0.63
164_V	191_Y	0.592	0.63
30_A	41_I	0.592	0.63
79_Q	83_L	0.592	0.63
77_Q	125_K	0.591	0.62
35_E	40_D	0.589	0.62
107_G	200_A	0.588	0.62
347_H	351_Y	0.588	0.62
344_Y	351_Y	0.587	0.62
232_D	237_L	0.587	0.62
211_A	214_E	0.587	0.62
30_A	44_M	0.585	0.62
166_A	207_A	0.584	0.62
119_A	149_V	0.583	0.61
131_A	356_Y	0.583	0.61
197_Y	201_L	0.580	0.61
55_Q	62_Q	0.579	0.61
180_R	347_H	0.578	0.61
91_Q	98_S	0.577	0.61
38_D	43_Q	0.577	0.61
31_V	50_L	0.577	0.61
144_F	166_A	0.575	0.60
61_H	65_L	0.574	0.60
268_R	271_F	0.573	0.60
33_L	40_D	0.571	0.60
192_I	230_C	0.571	0.60
121_S	215_G	0.571	0.60
180_R	184_H	0.570	0.60
60_R	64_M	0.568	0.59
36_E	44_M	0.566	0.59
299_L	303_K	0.564	0.59
263_L	286_G	0.563	0.59
280_I	301_K	0.563	0.59
354_A	357_F	0.562	0.59
34_K	43_Q	0.561	0.58
229_N	232_D	0.561	0.58
211_A	216_Q	0.560	0.58
351_Y	355_V	0.560	0.58
63_I	68_V	0.559	0.58
284_E	288_A	0.559	0.58
198_E	202_E	0.559	0.58
159_S	190_N	0.558	0.58
345_F	358_Y	0.557	0.58
200_A	230_C	0.557	0.58
87_L	277_E	0.555	0.58
56_L	81_R	0.554	0.58
330_L	337_F	0.554	0.58
315_L	321_V	0.554	0.58
216_Q	273_K	0.553	0.57
212_L	246_K	0.551	0.57
319_Q	351_Y	0.551	0.57
66_D	71_D	0.549	0.57
245_E	270_L	0.547	0.57
95_S	98_S	0.545	0.56
142_F	145_K	0.545	0.56
207_A	247_A	0.544	0.56
345_F	357_F	0.543	0.56
52_L	58_S	0.543	0.56
304_F	307_A	0.543	0.56
57_I	62_Q	0.542	0.56
149_V	153_M	0.541	0.56
356_Y	361_A	0.541	0.56
302_Y	308_L	0.540	0.56
313_V	317_M	0.540	0.56
291_Q	296_F	0.537	0.55
204_L	233_D	0.537	0.55
227_I	266_L	0.537	0.55
316_N	319_Q	0.537	0.55
141_E	144_F	0.537	0.55
342_A	346_S	0.535	0.55
212_L	327_E	0.535	0.55
186_V	267_T	0.533	0.55
224_L	263_L	0.533	0.55
180_R	204_L	0.533	0.55
233_D	289_I	0.533	0.55
147_A	187_I	0.532	0.55
83_L	240_A	0.532	0.55
248_L	255_Q	0.531	0.54
162_H	166_A	0.530	0.54
190_N	194_Y	0.529	0.54
49_L	56_L	0.528	0.54
163_A	183_C	0.527	0.54
225_Y	228_G	0.526	0.54
164_V	199_K	0.526	0.54
349_E	356_Y	0.525	0.54
151_Y	186_V	0.525	0.54
228_G	265_S	0.525	0.54
343_S	347_H	0.524	0.53
100_Y	130_L	0.523	0.53
99_E	103_H	0.523	0.53
36_E	41_I	0.520	0.53
232_D	240_A	0.520	0.53
203_H	210_L	0.518	0.53
58_S	62_Q	0.517	0.52
256_L	319_Q	0.516	0.52
57_I	87_L	0.516	0.52
59_Y	64_M	0.516	0.52
184_H	210_L	0.515	0.52
126_A	138_E	0.515	0.52
146_V	266_L	0.514	0.52
87_L	242_E	0.513	0.52
240_A	244_F	0.513	0.52
48_Q	53_Y	0.511	0.52
123_Y	127_E	0.510	0.51
122_F	125_K	0.509	0.51
314_N	325_M	0.508	0.51
219_L	223_A	0.508	0.51
161_N	165_Q	0.506	0.51
100_Y	141_E	0.505	0.51
341_A	357_F	0.505	0.51
120_I	123_Y	0.503	0.51
33_L	44_M	0.503	0.51
125_K	128_K	0.503	0.51
211_A	223_A	0.503	0.51
34_K	44_M	0.502	0.50
121_S	161_N	0.500	0.50

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
4i1aA	2	0.939	100	0.222	Contact Map
3q15A	2	0.9682	100	0.223	Contact Map
3ulqA	1	0.9735	100	0.232	Contact Map
4gyoA	2	0.9443	100	0.236	Contact Map
4gpkA	3	0.9125	100	0.283	Contact Map
1w3bA	2	0.8435	100	0.359	Contact Map
4ui9C	2	0.8674	100	0.384	Contact Map
3dssA	1	0.7268	100	0.385	Contact Map
4l9pA	1	0.7401	100	0.385	Contact Map
3sf4A	1	0.8382	100	0.387	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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