RAPA - BACSU - GREMLIN Contacts

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RAPA - Response regulator aspartate phosphatase A

UniProt:	Q00828	Sequences: MRMKQTIPSSYVGLKINEWYTHIRQFHVAEAERVKLEVEREIEDMEEDQDLLLYYSLMEFRHRVMLDYIKPFGEDTSQLEFSELLEDIEGNQYKLTGLLEYYFNFFRGMYEFKQKMFVSAMMYYKRAEKNLALVSDDIEKAEFAFKMAEIFYNLKQTYVSMSYAVQALETYQMYETYTVRRIQCEFVIAGNYDDMQYPERALPHLELALDLAKKEGNPRLISSALYNLGNCYEKMGELQKAAEYFGKSVSICKSEKFDNLPHSIYSLTQVLYKQKNDAEAQKKYREGLEIARQYSDELFVELFQFLHALYGKNIDTESVSHTFQFLEEHMLYPYIEELAHDAAQFYIENGQPEKALSFYEKMVHAQKQIQRGDCLYEI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	378 (319)
Sequences:	1386 (1261)
Seq/√Len:	70.6

ECOLI - LPSRP HEMY NLPI
BACSU - RAPA RAPB RAPH RAPC RAPF RAPJ RAPI RAPK RAPG RAPE RAPD YVCD YPIA
HALSA - Q9HMM8
SULSO - Q97V36 Q97VC4 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
237_E	240_K	5.342	1.00
229_G	245_F	4.980	1.00
276_N	279_E	4.947	1.00
108_G	124_Y	4.879	1.00
189_A	205_L	4.821	1.00
197_Y	200_R	4.432	1.00
116_M	119_S	3.493	1.00
302_L	306_L	3.487	1.00
351_Q	354_K	3.399	1.00
225_L	244_Y	3.245	1.00
193_D	205_L	2.927	1.00
104_N	126_R	2.897	1.00
144_A	163_Y	2.787	1.00
347_I	360_E	2.713	1.00
188_I	192_Y	2.665	1.00
148_A	164_A	2.560	1.00
268_T	284_Y	2.490	1.00
202_L	231_C	2.462	1.00
202_L	228_L	2.448	1.00
267_L	271_L	2.392	1.00
264_I	283_K	2.370	1.00
245_F	266_S	2.363	1.00
107_R	111_E	2.340	1.00
225_L	247_K	2.234	1.00
242_A	274_Q	2.194	1.00
242_A	270_V	2.174	1.00
279_E	282_K	2.159	1.00
232_Y	240_K	2.137	1.00
339_A	358_F	2.125	1.00
104_N	123_Y	2.111	1.00
343_A	359_Y	2.086	1.00
242_A	271_L	2.067	1.00
246_G	267_L	2.028	1.00
185_E	204_H	2.016	1.00
342_A	346_Y	2.010	1.00
147_M	151_F	1.988	1.00
229_G	244_Y	1.968	1.00
267_L	283_K	1.948	1.00
226_Y	266_S	1.943	1.00
242_A	267_L	1.931	1.00
202_L	235_M	1.912	1.00
242_A	246_G	1.880	1.00
319_V	322_T	1.877	1.00
303_F	310_Y	1.855	1.00
202_L	232_Y	1.827	1.00
354_K	357_S	1.816	1.00
39_E	42_I	1.791	1.00
209_L	221_I	1.765	1.00
200_R	203_P	1.754	1.00
166_Q	169_E	1.746	1.00
315_D	318_S	1.745	1.00
111_E	119_S	1.722	1.00
238_L	270_V	1.719	1.00
272_Y	284_Y	1.693	1.00
339_A	361_K	1.691	1.00
161_M	188_I	1.687	1.00
36_L	40_R	1.685	1.00
226_Y	229_G	1.675	1.00
119_S	122_M	1.672	1.00
205_L	227_N	1.666	1.00
186_F	227_N	1.665	1.00
327_E	361_K	1.653	0.99
338_L	342_A	1.584	0.99
132_A	140_K	1.562	0.99
240_K	243_E	1.561	0.99
249_V	264_I	1.539	0.99
109_M	124_Y	1.511	0.99
182_I	208_A	1.506	0.99
157_T	160_S	1.501	0.99
271_L	276_N	1.490	0.99
310_Y	315_D	1.484	0.99
35_K	39_E	1.479	0.99
271_L	279_E	1.466	0.99
35_K	42_I	1.458	0.99
124_Y	146_K	1.452	0.99
268_T	287_G	1.445	0.99
359_Y	363_V	1.424	0.98
270_V	274_Q	1.424	0.98
190_G	205_L	1.419	0.98
101_Y	127_A	1.397	0.98
229_G	241_A	1.394	0.98
33_R	36_L	1.380	0.98
108_G	280_A	1.370	0.98
222_S	248_S	1.356	0.98
59_E	63_R	1.343	0.98
108_G	127_A	1.343	0.98
248_S	263_S	1.314	0.97
49_Q	52_L	1.303	0.97
170_T	174_Y	1.290	0.97
40_R	46_E	1.283	0.97
302_L	334_Y	1.282	0.97
156_Q	159_V	1.276	0.97
57_L	62_H	1.257	0.97
126_R	129_K	1.256	0.97
145_F	187_V	1.236	0.96
335_I	339_A	1.234	0.96
266_S	269_Q	1.212	0.96
313_N	318_S	1.201	0.96
302_L	305_F	1.200	0.96
303_F	306_L	1.198	0.95
230_N	245_F	1.193	0.95
189_A	208_A	1.166	0.95
206_E	228_L	1.148	0.94
140_K	144_A	1.135	0.94
346_Y	354_K	1.135	0.94
189_A	201_A	1.123	0.94
314_I	318_S	1.122	0.94
48_D	51_L	1.120	0.94
207_L	210_D	1.118	0.93
357_S	361_K	1.114	0.93
192_Y	200_R	1.107	0.93
246_G	283_K	1.100	0.93
233_E	238_L	1.098	0.93
131_L	143_F	1.095	0.93
186_F	224_A	1.091	0.93
54_Y	61_R	1.091	0.93
96_T	150_I	1.084	0.92
228_L	232_Y	1.077	0.92
81_F	84_L	1.075	0.92
54_Y	57_L	1.069	0.92
292_R	297_E	1.068	0.92
34_V	39_E	1.068	0.92
236_G	273_K	1.061	0.92
122_M	216_G	1.060	0.92
192_Y	204_H	1.056	0.91
301_E	350_G	1.056	0.91
182_I	212_A	1.053	0.91
239_Q	274_Q	1.052	0.91
47_E	50_D	1.028	0.90
343_A	347_I	1.027	0.90
158_Y	162_S	1.021	0.90
326_L	338_L	1.021	0.90
158_Y	192_Y	1.018	0.90
40_R	43_E	1.018	0.90
72_F	78_Q	1.013	0.90
51_L	55_Y	1.013	0.90
129_K	132_A	1.010	0.89
113_K	117_F	1.009	0.89
33_R	44_D	1.007	0.89
33_R	41_E	1.004	0.89
300_V	304_Q	1.004	0.89
54_Y	60_F	1.003	0.89
190_G	227_N	0.996	0.89
108_G	123_Y	0.994	0.89
229_G	263_S	0.992	0.89
121_M	154_L	0.991	0.89
42_I	45_M	0.984	0.88
249_V	267_L	0.984	0.88
146_K	149_E	0.983	0.88
38_V	41_E	0.976	0.88
33_R	42_I	0.975	0.88
33_R	45_M	0.965	0.87
105_F	124_Y	0.962	0.87
168_L	185_E	0.951	0.86
172_Q	188_I	0.944	0.86
248_S	251_I	0.941	0.86
205_L	228_L	0.937	0.86
112_F	117_F	0.934	0.85
84_L	87_D	0.931	0.85
46_E	49_Q	0.931	0.85
116_M	123_Y	0.930	0.85
111_E	123_Y	0.929	0.85
145_F	148_A	0.927	0.85
246_G	279_E	0.926	0.85
181_R	184_C	0.925	0.85
189_A	204_H	0.920	0.85
37_E	40_R	0.914	0.84
36_L	39_E	0.911	0.84
199_E	235_M	0.910	0.84
228_L	244_Y	0.910	0.84
242_A	287_G	0.904	0.83
41_E	45_M	0.901	0.83
209_L	225_L	0.900	0.83
265_Y	269_Q	0.898	0.83
233_E	270_V	0.891	0.83
209_L	228_L	0.888	0.82
304_Q	307_H	0.886	0.82
299_F	302_L	0.883	0.82
56_S	59_E	0.882	0.82
65_M	71_P	0.882	0.82
53_L	58_M	0.878	0.82
233_E	266_S	0.874	0.81
300_V	303_F	0.874	0.81
52_L	56_S	0.873	0.81
230_N	266_S	0.872	0.81
43_E	46_E	0.866	0.81
185_E	225_L	0.856	0.80
212_A	221_I	0.853	0.80
102_Y	106_F	0.852	0.80
42_I	47_E	0.852	0.80
345_F	349_N	0.849	0.79
111_E	116_M	0.848	0.79
249_V	263_S	0.847	0.79
117_F	229_G	0.847	0.79
283_K	287_G	0.839	0.79
39_E	43_E	0.838	0.79
139_E	143_F	0.834	0.78
324_Q	327_E	0.830	0.78
280_A	284_Y	0.825	0.77
193_D	231_C	0.820	0.77
206_E	244_Y	0.819	0.77
163_Y	166_Q	0.818	0.77
214_K	258_D	0.818	0.77
339_A	342_A	0.814	0.76
352_P	355_A	0.813	0.76
352_P	357_S	0.811	0.76
134_V	137_D	0.810	0.76
345_F	353_E	0.809	0.76
218_P	221_I	0.809	0.76
301_E	305_F	0.808	0.76
42_I	52_L	0.807	0.76
55_Y	62_H	0.800	0.75
217_N	220_L	0.799	0.75
355_A	359_Y	0.797	0.75
338_L	358_F	0.796	0.75
231_C	235_M	0.795	0.75
350_G	357_S	0.793	0.75
189_A	231_C	0.789	0.74
202_L	206_E	0.789	0.74
247_K	251_I	0.787	0.74
247_K	250_S	0.787	0.74
127_A	131_L	0.785	0.74
346_Y	358_F	0.780	0.73
206_E	247_K	0.780	0.73
149_E	171_Y	0.780	0.73
150_I	154_L	0.780	0.73
360_E	363_V	0.779	0.73
264_I	287_G	0.778	0.73
232_Y	237_E	0.777	0.73
236_G	350_G	0.777	0.73
101_Y	131_L	0.776	0.73
185_E	207_L	0.776	0.73
124_Y	128_E	0.773	0.73
271_L	274_Q	0.773	0.73
353_E	363_V	0.772	0.73
34_V	37_E	0.772	0.73
265_Y	268_T	0.765	0.72
129_K	311_G	0.764	0.72
38_V	42_I	0.764	0.72
340_H	363_V	0.762	0.72
213_K	221_I	0.760	0.71
37_E	46_E	0.759	0.71
54_Y	59_E	0.759	0.71
122_M	126_R	0.757	0.71
125_K	129_K	0.757	0.71
111_E	271_L	0.756	0.71
42_I	46_E	0.754	0.71
39_E	46_E	0.749	0.70
226_Y	252_C	0.748	0.70
174_Y	177_Y	0.748	0.70
81_F	85_L	0.748	0.70
34_V	41_E	0.747	0.70
218_P	251_I	0.745	0.70
112_F	245_F	0.744	0.70
33_R	40_R	0.742	0.70
38_V	66_L	0.739	0.69
354_K	358_F	0.737	0.69
218_P	361_K	0.736	0.69
86_E	90_G	0.736	0.69
62_H	68_Y	0.736	0.69
185_E	192_Y	0.736	0.69
301_E	306_L	0.734	0.69
268_T	283_K	0.730	0.68
39_E	44_D	0.730	0.68
301_E	304_Q	0.728	0.68
303_F	325_F	0.728	0.68
188_I	204_H	0.725	0.68
310_Y	322_T	0.724	0.68
213_K	292_R	0.724	0.68
282_K	286_E	0.724	0.68
284_Y	359_Y	0.722	0.68
56_S	63_R	0.722	0.68
220_L	223_S	0.721	0.67
232_Y	242_A	0.718	0.67
33_R	47_E	0.716	0.67
285_R	289_E	0.713	0.67
313_N	354_K	0.713	0.67
287_G	290_I	0.712	0.66
206_E	240_K	0.712	0.66
101_Y	105_F	0.705	0.66
40_R	63_R	0.704	0.66
79_L	84_L	0.704	0.66
108_G	112_F	0.704	0.66
252_C	260_L	0.702	0.65
37_E	41_E	0.699	0.65
301_E	308_A	0.699	0.65
274_Q	283_K	0.699	0.65
38_V	43_E	0.698	0.65
226_Y	263_S	0.694	0.64
313_N	316_T	0.690	0.64
36_L	42_I	0.686	0.64
34_V	45_M	0.685	0.63
225_L	243_E	0.685	0.63
40_R	44_D	0.683	0.63
145_F	184_C	0.679	0.63
307_H	323_F	0.678	0.63
69_I	73_G	0.675	0.62
303_F	319_V	0.674	0.62
192_Y	203_P	0.672	0.62
208_A	287_G	0.671	0.62
62_H	66_L	0.671	0.62
358_F	361_K	0.668	0.61
173_M	176_T	0.668	0.61
35_K	41_E	0.665	0.61
40_R	51_L	0.665	0.61
112_F	150_I	0.665	0.61
37_E	43_E	0.665	0.61
356_L	359_Y	0.665	0.61
71_P	85_L	0.664	0.61
33_R	50_D	0.663	0.61
336_E	343_A	0.662	0.61
61_R	67_D	0.662	0.61
41_E	47_E	0.661	0.61
342_A	354_K	0.660	0.61
302_L	310_Y	0.660	0.61
206_E	283_K	0.657	0.60
346_Y	351_Q	0.656	0.60
53_L	59_E	0.654	0.60
261_P	291_A	0.654	0.60
37_E	42_I	0.653	0.60
61_R	284_Y	0.652	0.60
47_E	56_S	0.652	0.60
356_L	360_E	0.652	0.60
222_S	252_C	0.652	0.60
326_L	329_H	0.650	0.59
39_E	51_L	0.649	0.59
124_Y	127_A	0.648	0.59
299_F	304_Q	0.648	0.59
53_L	60_F	0.645	0.59
340_H	344_Q	0.644	0.59
186_F	208_A	0.642	0.58
108_G	296_D	0.642	0.58
350_G	353_E	0.641	0.58
225_L	248_S	0.640	0.58
225_L	264_I	0.640	0.58
43_E	50_D	0.639	0.58
299_F	303_F	0.639	0.58
168_L	191_N	0.638	0.58
33_R	38_V	0.638	0.58
100_E	130_N	0.636	0.58
186_F	205_L	0.636	0.58
105_F	143_F	0.632	0.57
353_E	357_S	0.631	0.57
252_C	263_S	0.630	0.57
99_L	102_Y	0.621	0.56
261_P	268_T	0.618	0.56
241_A	304_Q	0.618	0.56
112_F	124_Y	0.617	0.55
183_Q	186_F	0.617	0.55
177_Y	181_R	0.616	0.55
202_L	242_A	0.616	0.55
67_D	70_K	0.615	0.55
318_S	321_H	0.612	0.55
208_A	222_S	0.610	0.55
105_F	152_Y	0.610	0.55
164_A	303_F	0.609	0.55
289_E	292_R	0.609	0.55
141_A	145_F	0.606	0.54
169_E	172_Q	0.606	0.54
164_A	321_H	0.606	0.54
41_E	50_D	0.605	0.54
266_S	270_V	0.605	0.54
50_D	53_L	0.604	0.54
351_Q	358_F	0.602	0.54
141_A	167_A	0.601	0.54
60_F	63_R	0.601	0.54
208_A	224_A	0.599	0.53
33_R	39_E	0.597	0.53
54_Y	58_M	0.595	0.53
80_E	83_E	0.591	0.52
51_L	57_L	0.590	0.52
160_S	191_N	0.589	0.52
333_P	337_E	0.589	0.52
60_F	268_T	0.587	0.52
34_V	40_R	0.587	0.52
54_Y	103_F	0.586	0.52
125_K	204_H	0.585	0.52
258_D	281_Q	0.584	0.51
181_R	185_E	0.583	0.51
311_G	314_I	0.581	0.51
320_S	324_Q	0.580	0.51
316_T	320_S	0.580	0.51
201_A	231_C	0.579	0.51
55_Y	61_R	0.577	0.51
170_T	232_Y	0.576	0.50
41_E	59_E	0.575	0.50
214_K	232_Y	0.574	0.50
37_E	65_M	0.573	0.50
344_Q	348_E	0.572	0.50
38_V	48_D	0.571	0.50
336_E	340_H	0.571	0.50
145_F	149_E	0.570	0.50
42_I	292_R	0.569	0.50
212_A	224_A	0.569	0.50
306_L	310_Y	0.567	0.49
33_R	43_E	0.567	0.49
347_I	359_Y	0.566	0.49
162_S	286_E	0.566	0.49
96_T	100_E	0.566	0.49
345_F	362_M	0.565	0.49
53_L	71_P	0.564	0.49
208_A	248_S	0.564	0.49
286_E	290_I	0.561	0.49
121_M	151_F	0.561	0.49
324_Q	351_Q	0.561	0.49
47_E	59_E	0.560	0.49
226_Y	231_C	0.559	0.48
55_Y	58_M	0.558	0.48
143_F	146_K	0.558	0.48
86_E	89_E	0.556	0.48
52_L	58_M	0.556	0.48
229_G	267_L	0.554	0.48
325_F	329_H	0.553	0.48
79_L	108_G	0.553	0.48
67_D	81_F	0.553	0.48
83_E	87_D	0.552	0.48
102_Y	105_F	0.552	0.48
262_H	265_Y	0.550	0.47
287_G	303_F	0.550	0.47
121_M	125_K	0.550	0.47
114_Q	346_Y	0.550	0.47
157_T	161_M	0.549	0.47
128_E	241_A	0.549	0.47
111_E	114_Q	0.547	0.47
49_Q	59_E	0.547	0.47
327_E	335_I	0.546	0.47
35_K	45_M	0.546	0.47
155_K	160_S	0.545	0.47
56_S	65_M	0.543	0.46
128_E	143_F	0.540	0.46
105_F	146_K	0.540	0.46
356_L	361_K	0.539	0.46
41_E	44_D	0.538	0.46
57_L	60_F	0.537	0.46
317_E	352_P	0.536	0.46
34_V	52_L	0.536	0.46
48_D	54_Y	0.535	0.46
287_G	297_E	0.534	0.45
103_F	107_R	0.534	0.45
189_A	248_S	0.534	0.45
122_M	199_E	0.532	0.45
245_F	263_S	0.532	0.45
39_E	55_Y	0.532	0.45
245_F	270_V	0.532	0.45
126_R	178_T	0.530	0.45
62_H	72_F	0.528	0.45
110_Y	146_K	0.528	0.45
33_R	37_E	0.526	0.44
333_P	338_L	0.526	0.44
34_V	46_E	0.526	0.44
348_E	362_M	0.524	0.44
45_M	50_D	0.523	0.44
35_K	56_S	0.523	0.44
139_E	208_A	0.520	0.44
109_M	171_Y	0.518	0.43
34_V	42_I	0.517	0.43
128_E	163_Y	0.517	0.43
142_E	146_K	0.516	0.43
191_N	195_M	0.515	0.43
173_M	344_Q	0.515	0.43
90_G	93_Y	0.515	0.43
68_Y	71_P	0.513	0.43
252_C	291_A	0.513	0.43
36_L	43_E	0.512	0.43
357_S	360_E	0.512	0.43
230_N	233_E	0.512	0.43
141_A	182_I	0.511	0.43
110_Y	172_Q	0.509	0.42
233_E	245_F	0.507	0.42
312_K	346_Y	0.507	0.42
92_Q	286_E	0.505	0.42
112_F	146_K	0.504	0.42
278_A	281_Q	0.501	0.41
124_Y	265_Y	0.501	0.41
37_E	45_M	0.501	0.41
217_N	221_I	0.500	0.41
339_A	346_Y	0.500	0.41
147_M	154_L	0.500	0.41

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
4gyoA	2	0.9524	100	0.252	Contact Map
3q15A	2	0.9656	100	0.253	Contact Map
4i1aA	2	0.9471	100	0.255	Contact Map
3ulqA	1	0.9815	100	0.266	Contact Map
4gpkA	3	0.9101	100	0.325	Contact Map
1w3bA	2	0.8122	100	0.418	Contact Map
3q7aA	1	0.7328	100	0.425	Contact Map
4ui9C	2	0.9286	100	0.43	Contact Map
3sf4A	1	0.8386	100	0.432	Contact Map
4l9pA	1	0.7513	100	0.436	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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