RAPH - BACSU - GREMLIN Contacts

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RAPH - Response regulator aspartate phosphatase H

UniProt:	Q59HN8	Sequences: MSQAIPSSRVGVKINEWYKMIRQFSVPDAEILKAEVEQDIQQMEEDQDLLIYYSLMCFRHQLMLDYLEPGKTYGNRPTVTELLETIETPQKKLTGLLKYYSLFFRGMYEFDQKEYVEAIGYYREAEKELPFVSDDIEKAEFHFKVAEAYYHMKQTHVSMYHILQALDIYQNHPLYSIRTIQSLFVIAGNYDDFKHYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYDRSGDDQMAVEHFQKAAKVSREKVPDLLPKVLFGLSWTLCKAGQTQKAFQFIEEGLDHITARSHKFYKELFLFLQAVYKETVDERKIHDLLSYFEKKNLHAYIEACARSAAAVFESSCHFEQAAAFYRKVLKAQEDILKGECLYAY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	376 (312)
Sequences:	1651 (1465)
Seq/√Len:	83.0

ECOLI - LPSRP HEMY NLPI
BACSU - RAPH RAPA RAPB RAPF RAPJ RAPI RAPK RAPC RAPG RAPE RAPD YVCD YPIA
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
146_A	162_I	5.065	1.00
274_Q	277_K	4.694	1.00
235_D	238_M	4.192	1.00
227_A	243_F	3.774	1.00
195_H	198_K	3.747	1.00
114_E	117_E	3.698	1.00
142_H	161_H	3.487	1.00
187_A	203_L	3.445	1.00
349_H	352_Q	3.353	1.00
106_G	122_Y	3.231	1.00
154_Q	157_V	3.126	1.00
244_Q	265_L	2.936	1.00
105_R	109_E	2.737	1.00
243_F	264_G	2.627	1.00
200_L	226_I	2.539	1.00
159_M	186_I	2.497	1.00
266_S	282_I	2.496	1.00
149_Y	157_V	2.466	1.00
162_I	185_V	2.443	1.00
238_M	241_E	2.380	1.00
240_V	268_T	2.259	1.00
240_V	265_L	2.203	1.00
198_K	201_P	2.183	1.00
223_L	245_K	2.173	1.00
345_E	358_R	2.082	1.00
277_K	280_Q	2.065	1.00
262_L	281_F	2.054	1.00
200_L	233_S	2.027	1.00
102_L	124_E	1.999	1.00
102_L	121_Y	1.989	1.00
308_Y	313_D	1.988	1.00
230_Y	238_M	1.981	1.00
265_L	281_F	1.906	1.00
340_A	344_F	1.891	1.00
142_H	164_Q	1.877	1.00
226_I	242_H	1.859	1.00
125_A	141_F	1.847	1.00
106_G	121_Y	1.838	1.00
180_I	206_A	1.820	1.00
350_F	353_A	1.812	1.00
240_V	272_A	1.799	1.00
309_K	312_V	1.785	1.00
145_V	149_Y	1.763	1.00
341_A	357_Y	1.761	1.00
187_A	206_A	1.733	1.00
184_F	225_N	1.730	1.00
269_L	274_Q	1.715	1.00
240_V	269_L	1.714	1.00
223_L	242_H	1.706	1.00
200_L	230_Y	1.702	1.00
122_Y	144_K	1.686	1.00
187_A	202_H	1.653	1.00
352_Q	355_A	1.640	1.00
143_F	185_V	1.628	1.00
270_C	282_I	1.585	1.00
110_F	122_Y	1.539	1.00
203_L	225_N	1.531	1.00
191_D	203_L	1.524	0.99
183_L	202_H	1.517	0.99
34_A	37_E	1.517	0.99
211_M	219_I	1.504	0.99
333_I	337_A	1.501	0.99
106_G	125_A	1.498	0.99
240_V	244_Q	1.483	0.99
265_L	269_L	1.480	0.99
275_T	279_F	1.469	0.99
156_H	193_F	1.462	0.99
119_I	149_Y	1.454	0.99
268_T	272_A	1.446	0.99
228_N	243_F	1.438	0.99
226_I	230_Y	1.428	0.99
47_Q	50_L	1.428	0.99
220_A	246_A	1.420	0.99
82_L	85_T	1.409	0.99
164_Q	167_D	1.409	0.99
190_Y	198_K	1.406	0.99
266_S	285_G	1.404	0.99
243_F	268_T	1.402	0.99
99_Y	125_A	1.399	0.99
145_V	161_H	1.394	0.99
236_D	268_T	1.394	0.99
186_I	202_H	1.385	0.99
186_I	190_Y	1.385	0.99
119_I	148_A	1.374	0.99
119_I	145_V	1.374	0.99
165_A	168_I	1.369	0.99
38_Q	41_Q	1.336	0.99
31_I	35_E	1.324	0.99
79_V	82_L	1.324	0.99
103_F	144_K	1.312	0.98
219_I	223_L	1.305	0.98
230_Y	235_D	1.302	0.98
269_L	277_K	1.297	0.98
33_K	37_E	1.296	0.98
325_E	359_K	1.293	0.98
226_I	265_L	1.280	0.98
227_A	242_H	1.272	0.98
107_M	144_K	1.268	0.98
40_I	47_Q	1.265	0.98
40_I	44_E	1.263	0.98
166_L	183_L	1.258	0.98
301_F	304_L	1.254	0.98
237_Q	272_A	1.248	0.98
109_E	114_E	1.238	0.98
38_Q	42_Q	1.224	0.98
182_S	185_V	1.223	0.98
336_C	340_A	1.220	0.98
183_L	205_A	1.216	0.97
355_A	358_R	1.185	0.97
344_F	352_Q	1.168	0.97
52_Y	56_M	1.160	0.97
109_E	117_E	1.153	0.97
301_F	317_I	1.149	0.96
159_M	189_N	1.142	0.96
224_L	264_G	1.140	0.96
264_G	267_W	1.134	0.96
163_L	186_I	1.132	0.96
235_D	274_Q	1.131	0.96
247_A	262_L	1.129	0.96
301_F	313_D	1.128	0.96
262_L	284_E	1.124	0.96
163_L	198_K	1.124	0.96
107_M	122_Y	1.122	0.96
110_F	148_A	1.117	0.96
144_K	147_E	1.112	0.96
179_T	183_L	1.104	0.96
157_V	160_Y	1.100	0.95
36_V	39_D	1.096	0.95
117_E	120_G	1.096	0.95
150_Y	162_I	1.092	0.95
188_G	225_N	1.090	0.95
200_L	229_S	1.089	0.95
146_A	158_S	1.086	0.95
204_E	226_I	1.083	0.95
244_Q	277_K	1.080	0.95
241_E	245_K	1.079	0.95
190_Y	195_H	1.070	0.95
31_I	34_A	1.067	0.95
266_S	281_F	1.065	0.95
149_Y	154_Q	1.065	0.95
143_F	182_S	1.060	0.94
246_A	285_G	1.051	0.94
300_L	304_L	1.050	0.94
310_E	313_D	1.048	0.94
142_H	223_L	1.045	0.94
262_L	285_G	1.043	0.94
55_L	68_E	1.043	0.94
303_F	307_V	1.031	0.94
118_A	122_Y	1.024	0.93
247_A	265_L	1.024	0.93
35_E	40_I	1.021	0.93
197_D	233_S	1.019	0.93
50_L	54_S	1.003	0.93
37_E	40_I	1.000	0.92
33_K	43_M	0.996	0.92
32_L	43_M	0.991	0.92
301_F	308_Y	0.989	0.92
35_E	41_Q	0.989	0.92
341_A	353_A	0.988	0.92
227_A	239_A	0.979	0.92
313_D	316_K	0.979	0.92
161_H	165_A	0.975	0.92
78_T	82_L	0.962	0.91
273_G	351_E	0.961	0.91
140_E	144_K	0.960	0.91
224_L	227_A	0.957	0.91
298_K	302_L	0.956	0.91
31_I	36_V	0.955	0.91
304_L	308_Y	0.949	0.90
113_K	117_E	0.943	0.90
216_D	219_I	0.938	0.90
228_N	264_G	0.934	0.90
78_T	81_E	0.934	0.90
34_A	38_Q	0.934	0.90
200_L	207_L	0.925	0.89
353_A	357_Y	0.921	0.89
32_L	35_E	0.917	0.89
132_V	135_D	0.914	0.89
176_S	179_T	0.914	0.89
196_Y	236_D	0.913	0.89
237_Q	241_E	0.912	0.89
79_V	83_L	0.911	0.88
207_L	226_I	0.910	0.88
316_K	319_D	0.909	0.88
183_L	262_L	0.907	0.88
224_L	261_V	0.899	0.88
31_I	39_D	0.895	0.88
104_F	185_V	0.891	0.87
355_A	359_K	0.890	0.87
180_I	210_A	0.890	0.87
139_A	165_A	0.888	0.87
314_E	318_H	0.888	0.87
357_Y	361_L	0.888	0.87
84_E	88_T	0.875	0.86
341_A	360_V	0.874	0.86
115_Y	119_I	0.874	0.86
186_I	192_D	0.872	0.86
57_C	61_Q	0.872	0.86
38_Q	44_E	0.870	0.86
69_P	72_T	0.870	0.86
146_A	165_A	0.867	0.86
55_L	59_R	0.867	0.86
160_Y	164_Q	0.863	0.86
98_K	102_L	0.855	0.85
337_A	356_F	0.852	0.85
123_R	149_Y	0.849	0.85
297_Y	300_L	0.848	0.85
58_F	61_Q	0.846	0.84
83_L	86_I	0.845	0.84
335_A	339_S	0.844	0.84
86_I	89_P	0.843	0.84
31_I	37_E	0.842	0.84
34_A	40_I	0.840	0.84
200_L	203_L	0.838	0.84
247_A	261_V	0.835	0.84
48_D	51_I	0.831	0.83
66_Y	70_G	0.829	0.83
35_E	43_M	0.827	0.83
99_Y	141_F	0.824	0.83
207_L	223_L	0.818	0.82
148_A	152_M	0.813	0.82
37_E	41_Q	0.811	0.82
199_A	229_S	0.809	0.82
236_D	240_V	0.808	0.82
250_S	261_V	0.807	0.82
47_Q	56_M	0.806	0.82
346_S	357_Y	0.805	0.81
348_C	351_E	0.802	0.81
84_E	87_E	0.801	0.81
299_E	306_A	0.797	0.81
80_T	83_L	0.795	0.81
166_L	182_S	0.789	0.80
351_E	354_A	0.788	0.80
200_L	204_E	0.787	0.80
210_A	213_I	0.783	0.80
38_Q	45_E	0.777	0.79
37_E	67_L	0.776	0.79
183_L	223_L	0.775	0.79
331_A	339_S	0.775	0.79
185_V	203_L	0.773	0.79
259_P	266_S	0.764	0.78
39_D	43_M	0.763	0.78
85_T	88_T	0.762	0.78
34_A	43_M	0.760	0.78
61_Q	65_D	0.760	0.78
337_A	359_K	0.759	0.77
250_S	258_L	0.756	0.77
281_F	284_E	0.753	0.77
41_Q	44_E	0.753	0.77
170_Q	179_T	0.751	0.77
52_Y	55_L	0.751	0.77
231_D	243_F	0.748	0.76
354_A	358_R	0.748	0.76
210_A	222_S	0.745	0.76
281_F	285_G	0.745	0.76
314_E	317_I	0.744	0.76
290_T	293_S	0.741	0.76
100_Y	104_F	0.738	0.75
121_Y	125_A	0.732	0.75
317_I	320_L	0.730	0.75
109_E	121_Y	0.729	0.75
238_M	242_H	0.728	0.74
113_K	151_H	0.727	0.74
319_D	322_S	0.724	0.74
83_L	321_L	0.722	0.74
88_T	344_F	0.721	0.74
342_A	350_F	0.718	0.73
242_H	265_L	0.718	0.73
124_E	127_K	0.717	0.73
162_I	182_S	0.717	0.73
85_T	89_P	0.716	0.73
63_M	69_P	0.713	0.73
119_I	154_Q	0.712	0.73
220_A	250_S	0.711	0.73
35_E	45_E	0.702	0.72
36_V	40_I	0.702	0.72
164_Q	205_A	0.702	0.72
184_F	222_S	0.701	0.72
204_E	207_L	0.701	0.72
82_L	90_Q	0.701	0.72
76_R	80_T	0.700	0.72
342_A	357_Y	0.700	0.72
106_G	110_F	0.695	0.71
40_I	43_M	0.694	0.71
345_E	357_Y	0.692	0.71
33_K	44_E	0.692	0.71
343_V	346_S	0.688	0.70
123_R	145_V	0.685	0.70
146_A	189_N	0.685	0.70
119_I	152_M	0.685	0.70
317_I	321_L	0.685	0.70
147_E	151_H	0.684	0.70
223_L	246_A	0.683	0.70
334_E	360_V	0.683	0.70
349_H	355_A	0.681	0.70
31_I	38_Q	0.677	0.69
32_L	38_Q	0.676	0.69
235_D	273_G	0.673	0.69
213_I	216_D	0.668	0.68
62_L	66_Y	0.668	0.68
194_K	234_G	0.667	0.68
146_A	161_H	0.666	0.68
31_I	42_Q	0.661	0.67
34_A	39_D	0.652	0.66
332_Y	339_S	0.652	0.66
142_H	165_A	0.651	0.66
302_L	305_Q	0.647	0.66
234_G	271_K	0.647	0.66
60_H	65_D	0.643	0.65
273_G	293_S	0.643	0.65
139_A	146_A	0.642	0.65
147_E	162_I	0.640	0.65
110_F	151_H	0.638	0.64
42_Q	49_L	0.638	0.64
115_Y	148_A	0.638	0.64
245_K	248_K	0.635	0.64
33_K	36_V	0.634	0.64
229_S	233_S	0.634	0.64
165_A	169_Y	0.634	0.64
55_L	62_L	0.634	0.64
97_L	196_Y	0.634	0.64
350_F	354_A	0.633	0.64
37_E	44_E	0.631	0.64
139_A	169_Y	0.629	0.63
125_A	140_E	0.629	0.63
278_A	282_I	0.628	0.63
35_E	39_D	0.628	0.63
227_A	246_A	0.627	0.63
184_F	188_G	0.627	0.63
315_R	319_D	0.626	0.63
188_G	203_L	0.626	0.63
207_L	219_I	0.625	0.63
189_N	192_D	0.625	0.63
32_L	39_D	0.624	0.63
181_Q	184_F	0.622	0.63
249_V	271_K	0.621	0.62
245_K	249_V	0.621	0.62
52_Y	58_F	0.621	0.62
300_L	332_Y	0.618	0.62
202_H	205_A	0.615	0.62
154_Q	162_I	0.615	0.62
220_A	248_K	0.613	0.61
102_L	125_A	0.612	0.61
246_A	261_V	0.612	0.61
216_D	249_V	0.611	0.61
79_V	86_I	0.610	0.61
34_A	42_Q	0.610	0.61
50_L	53_Y	0.609	0.61
36_V	47_Q	0.609	0.61
206_A	209_L	0.608	0.61
318_H	351_E	0.606	0.61
46_D	49_L	0.606	0.61
225_N	228_N	0.606	0.61
159_M	334_E	0.605	0.60
273_G	352_Q	0.603	0.60
56_M	324_F	0.602	0.60
65_D	69_P	0.598	0.60
59_R	63_M	0.598	0.60
143_F	263_F	0.598	0.60
329_L	332_Y	0.597	0.59
46_D	57_C	0.597	0.59
351_E	355_A	0.597	0.59
203_L	226_I	0.596	0.59
32_L	37_E	0.595	0.59
317_I	339_S	0.594	0.59
146_A	262_L	0.593	0.59
354_A	360_V	0.592	0.59
110_F	115_Y	0.590	0.58
61_Q	64_L	0.589	0.58
71_K	79_V	0.588	0.58
231_D	268_T	0.588	0.58
243_F	261_V	0.587	0.58
52_Y	63_M	0.585	0.58
87_E	90_Q	0.585	0.58
227_A	230_Y	0.584	0.58
100_Y	103_F	0.584	0.58
39_D	42_Q	0.583	0.58
178_R	185_V	0.582	0.57
37_E	48_D	0.581	0.57
146_A	185_V	0.580	0.57
344_F	356_F	0.578	0.57
342_A	346_S	0.578	0.57
105_R	121_Y	0.575	0.57
82_L	88_T	0.574	0.56
336_C	341_A	0.574	0.56
43_M	47_Q	0.572	0.56
39_D	54_S	0.572	0.56
210_A	218_F	0.569	0.56
46_D	53_Y	0.568	0.56
307_V	312_V	0.567	0.56
150_Y	203_L	0.566	0.55
107_M	146_A	0.566	0.55
32_L	40_I	0.565	0.55
52_Y	60_H	0.565	0.55
162_I	280_Q	0.563	0.55
33_K	42_Q	0.562	0.55
32_L	36_V	0.558	0.54
159_M	190_Y	0.558	0.54
321_L	358_R	0.557	0.54
31_I	40_I	0.556	0.54
36_V	45_E	0.555	0.54
38_Q	43_M	0.555	0.54
348_C	353_A	0.555	0.54
247_A	258_L	0.553	0.54
67_L	71_K	0.553	0.54
42_Q	45_E	0.553	0.54
54_S	58_F	0.553	0.54
80_T	84_E	0.551	0.53
125_A	206_A	0.550	0.53
141_F	145_V	0.547	0.53
39_D	50_L	0.547	0.53
207_L	265_L	0.546	0.53
66_Y	69_P	0.545	0.53
49_L	59_R	0.543	0.52
282_I	285_G	0.542	0.52
36_V	43_M	0.539	0.52
162_I	266_S	0.538	0.52
163_L	202_H	0.538	0.52
205_A	209_L	0.535	0.51
48_D	52_Y	0.534	0.51
34_A	44_E	0.534	0.51
118_A	134_D	0.533	0.51
352_Q	356_F	0.533	0.51
104_F	107_M	0.532	0.51
59_R	66_Y	0.530	0.51
223_L	262_L	0.530	0.51
102_L	122_Y	0.529	0.51
59_R	65_D	0.529	0.51
31_I	48_D	0.529	0.51
226_I	246_A	0.528	0.50
188_G	191_D	0.528	0.50
333_I	353_A	0.527	0.50
292_R	295_K	0.526	0.50
156_H	189_N	0.526	0.50
141_F	144_K	0.526	0.50
49_L	55_L	0.525	0.50
290_T	295_K	0.524	0.50
99_Y	106_G	0.524	0.50
258_L	262_L	0.524	0.50
310_E	347_S	0.523	0.50
35_E	38_Q	0.523	0.50
155_T	189_N	0.522	0.50
71_K	77_P	0.522	0.50
348_C	359_K	0.522	0.50
61_Q	70_G	0.521	0.49
78_T	83_L	0.521	0.49
339_S	352_Q	0.521	0.49
148_A	268_T	0.520	0.49
125_A	225_N	0.520	0.49
343_V	350_F	0.517	0.49
62_L	70_G	0.517	0.49
37_E	42_Q	0.516	0.49
266_S	278_A	0.516	0.49
68_E	71_K	0.515	0.49
348_C	361_L	0.514	0.49
84_E	89_P	0.513	0.48
37_E	49_L	0.512	0.48
285_G	289_I	0.509	0.48
48_D	53_Y	0.509	0.48
159_M	193_F	0.508	0.48
197_D	201_P	0.506	0.47
319_D	326_K	0.505	0.47
37_E	43_M	0.505	0.47
62_L	67_L	0.504	0.47
62_L	69_P	0.502	0.47
36_V	61_Q	0.502	0.47
178_R	276_Q	0.500	0.47
305_Q	308_Y	0.500	0.47

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
3q15A	2	0.9707	100	0.228	Contact Map
4gyoA	2	0.9574	100	0.235	Contact Map
3ulqA	1	0.9761	100	0.238	Contact Map
4i1aA	2	0.9521	100	0.239	Contact Map
4gpkA	3	0.9149	100	0.308	Contact Map
1w3bA	2	0.883	100	0.375	Contact Map
4ui9C	2	0.9202	100	0.402	Contact Map
3sf4A	1	0.8431	100	0.416	Contact Map
3q7aA	1	0.7287	100	0.421	Contact Map
4a1sA	1	0.8059	100	0.422	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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