RAPJ - BACSU - GREMLIN Contacts

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RAPJ - Response regulator aspartate phosphatase J

UniProt:	O34327	Sequences: MRAKIPSEEVAVKLNEWYKLIRAFEADQAEALKQEIEYDLEDMEENQDLLLYFSLMEFRHRIMLDKLMPVKDSDTKPPFSDMLNEIESNQQKLTGLLEYYFYYFRGMYEFKQKNFILAIDHYKHAEEKLEYVEDEIEKAEFLFKVAEVYYHIKQTYFSMNYASQALDIYTKYELYGRRRVQCEFIIAGNLTDVYHHEKALTHLCSALEHARQLEEAYMIAAAYYNVGHCKYSLGDYKEAEGYFKTAAAIFEEHNFQQAVQAVFSLTHIYCKEGKYDKAVEAYDRGIKSAAEWEDDMYLTKFRLIHELYLGSGDLNVLTECFDLLESRQLLADAEDLLHDTAERFNQLEHYESAAFFYRRLMNIKKKLAEQRFQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	373 (305)
Sequences:	1780 (1582)
Seq/√Len:	90.6

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

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
195_H	198_K	4.936	1.00
187_A	203_L	4.436	1.00
235_D	238_E	4.392	1.00
274_K	277_K	4.068	1.00
227_G	243_F	3.995	1.00
349_H	352_S	3.982	1.00
142_L	161_Y	3.702	1.00
114_N	117_L	3.603	1.00
154_Q	157_F	3.600	1.00
106_G	122_Y	3.532	1.00
146_A	162_A	3.487	1.00
266_T	282_Y	3.268	1.00
230_K	238_E	2.994	1.00
223_Y	242_Y	2.654	1.00
149_Y	157_F	2.616	1.00
244_K	265_L	2.392	1.00
227_G	242_Y	2.357	1.00
243_F	264_S	2.336	1.00
200_L	226_V	2.286	1.00
340_T	344_F	2.239	1.00
240_E	269_Y	2.186	1.00
159_M	189_N	2.176	1.00
223_Y	245_T	2.150	1.00
183_E	202_H	2.109	1.00
145_V	149_Y	2.104	1.00
341_A	357_Y	2.101	1.00
159_M	186_I	2.087	1.00
105_R	109_E	2.072	1.00
240_E	265_L	2.071	1.00
317_L	320_C	2.064	1.00
240_E	268_I	2.062	1.00
277_K	280_E	2.024	1.00
198_K	201_T	1.971	1.00
162_A	185_I	1.911	1.00
262_V	281_A	1.903	1.00
119_I	149_Y	1.899	1.00
190_L	198_K	1.876	1.00
186_I	190_L	1.847	1.00
226_V	242_Y	1.813	1.00
220_A	246_A	1.813	1.00
240_E	272_E	1.765	1.00
143_F	185_I	1.738	1.00
122_Y	144_K	1.734	1.00
142_L	164_Q	1.716	1.00
164_Q	167_D	1.708	1.00
247_A	262_V	1.704	1.00
352_S	355_F	1.684	1.00
227_G	239_A	1.678	1.00
109_E	117_L	1.676	1.00
200_L	233_L	1.643	1.00
184_F	225_N	1.588	1.00
238_E	241_G	1.576	1.00
204_C	226_V	1.568	1.00
265_L	281_A	1.562	1.00
344_F	349_H	1.535	1.00
226_V	230_K	1.511	1.00
145_V	161_Y	1.506	1.00
191_T	203_L	1.502	1.00
223_Y	246_A	1.499	1.00
207_L	226_V	1.476	1.00
102_Y	124_H	1.449	0.99
187_A	206_A	1.444	0.99
180_V	206_A	1.439	0.99
227_G	246_A	1.432	0.99
210_A	219_I	1.413	0.99
269_Y	274_K	1.413	0.99
76_K	80_S	1.405	0.99
242_Y	246_A	1.398	0.99
250_F	258_A	1.390	0.99
244_K	277_K	1.383	0.99
110_F	122_Y	1.379	0.99
187_A	202_H	1.370	0.99
188_G	203_L	1.368	0.99
300_K	304_I	1.366	0.99
37_E	40_L	1.359	0.99
354_A	358_R	1.352	0.99
163_S	186_I	1.347	0.99
82_M	85_E	1.334	0.99
223_Y	262_V	1.330	0.99
237_K	272_E	1.310	0.99
240_E	244_K	1.303	0.99
38_Y	42_D	1.283	0.99
102_Y	121_H	1.282	0.99
99_Y	125_A	1.280	0.99
103_Y	144_K	1.265	0.99
150_Y	162_A	1.259	0.98
200_L	204_C	1.259	0.98
36_I	43_M	1.258	0.98
190_L	195_H	1.255	0.98
309_L	313_D	1.254	0.98
344_F	352_S	1.252	0.98
126_E	142_L	1.249	0.98
341_A	360_L	1.236	0.98
325_E	359_R	1.236	0.98
200_L	230_K	1.232	0.98
183_E	205_S	1.222	0.98
34_Q	37_E	1.219	0.98
308_Y	313_D	1.218	0.98
224_Y	227_G	1.201	0.98
223_Y	227_G	1.196	0.98
119_I	152_I	1.188	0.98
353_A	361_M	1.187	0.98
264_S	267_H	1.184	0.98
34_Q	38_Y	1.175	0.98
200_L	229_C	1.169	0.98
139_A	165_A	1.134	0.97
247_A	261_A	1.123	0.97
355_F	359_R	1.122	0.97
301_F	308_Y	1.107	0.97
106_G	125_A	1.105	0.97
47_Q	53_F	1.103	0.97
341_A	353_A	1.101	0.96
149_Y	154_Q	1.091	0.96
49_L	53_F	1.086	0.96
142_L	223_Y	1.083	0.96
159_M	190_L	1.081	0.96
158_S	189_N	1.080	0.96
65_D	70_V	1.076	0.96
49_L	52_Y	1.071	0.96
296_M	303_L	1.070	0.96
41_E	44_E	1.065	0.96
188_G	225_N	1.061	0.96
304_I	308_Y	1.055	0.96
281_A	284_R	1.050	0.95
147_E	162_A	1.048	0.95
146_A	187_A	1.041	0.95
350_Y	353_A	1.037	0.95
337_L	359_R	1.035	0.95
57_E	61_R	1.032	0.95
266_T	281_A	1.029	0.95
309_L	312_G	1.029	0.95
35_E	41_E	1.019	0.95
183_E	262_V	1.018	0.95
305_H	309_L	1.010	0.94
316_V	319_E	1.010	0.94
50_L	53_F	1.010	0.94
216_A	219_I	1.008	0.94
322_D	325_E	1.007	0.94
61_R	67_L	1.001	0.94
336_L	340_T	0.994	0.94
37_E	41_E	0.993	0.94
43_M	53_F	0.992	0.94
107_M	122_Y	0.991	0.94
47_Q	50_L	0.989	0.94
149_Y	161_Y	0.988	0.94
156_Y	193_V	0.979	0.93
268_I	272_E	0.977	0.93
226_V	265_L	0.972	0.93
236_Y	240_E	0.969	0.93
50_L	56_M	0.968	0.93
342_E	357_Y	0.967	0.93
194_Y	348_E	0.966	0.93
205_S	208_E	0.966	0.93
144_K	147_E	0.966	0.93
316_V	320_C	0.965	0.93
265_L	269_Y	0.964	0.93
236_Y	268_I	0.959	0.93
60_H	63_M	0.958	0.93
244_K	269_Y	0.955	0.92
262_V	284_R	0.954	0.92
186_I	202_H	0.952	0.92
138_K	142_L	0.950	0.92
63_M	69_P	0.947	0.92
270_C	282_Y	0.944	0.92
339_D	342_E	0.943	0.92
250_F	261_A	0.936	0.92
210_A	218_M	0.936	0.92
184_F	188_G	0.934	0.92
142_L	165_A	0.933	0.92
116_I	152_I	0.929	0.91
110_F	115_F	0.928	0.91
206_A	222_A	0.925	0.91
315_N	319_E	0.923	0.91
224_Y	264_S	0.922	0.91
148_V	152_I	0.922	0.91
58_F	65_D	0.922	0.91
39_D	42_D	0.919	0.91
37_E	43_M	0.917	0.91
102_Y	125_A	0.915	0.91
48_D	51_L	0.913	0.91
191_T	229_C	0.911	0.91
130_E	138_K	0.906	0.90
337_L	356_F	0.897	0.90
357_Y	361_M	0.892	0.90
48_D	55_L	0.891	0.90
181_Q	184_F	0.891	0.90
312_G	316_V	0.891	0.90
49_L	54_S	0.891	0.90
247_A	265_L	0.888	0.89
61_R	70_V	0.888	0.89
161_Y	165_A	0.883	0.89
34_Q	44_E	0.880	0.89
51_L	55_L	0.873	0.89
166_L	183_E	0.869	0.88
57_E	62_I	0.867	0.88
229_C	233_L	0.867	0.88
333_A	337_L	0.866	0.88
122_Y	148_V	0.865	0.88
230_K	235_D	0.865	0.88
146_A	189_N	0.863	0.88
229_C	268_I	0.862	0.88
110_F	148_V	0.860	0.88
39_D	43_M	0.860	0.88
266_T	285_G	0.858	0.88
65_D	68_M	0.858	0.88
44_E	47_Q	0.858	0.88
331_A	335_D	0.853	0.87
203_L	225_N	0.853	0.87
38_Y	41_E	0.844	0.87
231_Y	236_Y	0.841	0.87
308_Y	314_L	0.837	0.86
269_Y	281_A	0.834	0.86
297_Y	300_K	0.833	0.86
302_R	305_H	0.831	0.86
311_S	322_D	0.831	0.86
163_S	208_E	0.830	0.86
146_A	165_A	0.829	0.86
340_T	356_F	0.824	0.86
354_A	357_Y	0.821	0.85
106_G	110_F	0.818	0.85
183_E	206_A	0.815	0.85
159_M	240_E	0.814	0.85
278_A	282_Y	0.810	0.85
66_K	72_D	0.809	0.85
109_E	121_H	0.809	0.85
258_A	261_A	0.802	0.84
62_I	66_K	0.800	0.84
58_F	63_M	0.797	0.84
207_L	223_Y	0.795	0.83
48_D	52_Y	0.788	0.83
309_L	316_V	0.785	0.83
58_F	62_I	0.784	0.83
34_Q	42_D	0.783	0.83
36_I	39_D	0.777	0.82
40_L	43_M	0.777	0.82
119_I	145_V	0.772	0.82
240_E	274_K	0.771	0.82
225_N	228_H	0.769	0.81
35_E	44_E	0.766	0.81
155_T	158_S	0.763	0.81
234_G	271_K	0.763	0.81
142_L	262_V	0.763	0.81
98_E	102_Y	0.761	0.81
228_H	243_F	0.759	0.81
40_L	50_L	0.756	0.80
35_E	43_M	0.755	0.80
185_I	188_G	0.755	0.80
64_L	77_P	0.753	0.80
43_M	47_Q	0.748	0.80
307_L	310_G	0.748	0.80
111_K	115_F	0.745	0.79
317_L	324_L	0.741	0.79
283_D	287_K	0.741	0.79
303_L	307_L	0.741	0.79
269_Y	277_K	0.739	0.79
216_A	249_I	0.739	0.79
345_N	358_R	0.738	0.79
39_D	44_E	0.737	0.79
140_E	144_K	0.736	0.79
119_I	148_V	0.735	0.78
103_Y	122_Y	0.733	0.78
124_H	127_E	0.729	0.78
265_L	284_R	0.728	0.78
280_E	284_R	0.728	0.78
225_N	231_Y	0.728	0.78
79_F	82_M	0.724	0.77
99_Y	129_L	0.723	0.77
38_Y	61_R	0.717	0.77
234_G	312_G	0.714	0.76
245_T	249_I	0.712	0.76
39_D	49_L	0.711	0.76
35_E	38_Y	0.709	0.76
299_T	306_E	0.709	0.76
338_H	342_E	0.708	0.76
303_L	308_Y	0.706	0.76
298_L	302_R	0.705	0.75
205_S	209_H	0.704	0.75
103_Y	141_F	0.704	0.75
142_L	183_E	0.703	0.75
190_L	269_Y	0.698	0.75
55_L	58_F	0.698	0.75
195_H	282_Y	0.697	0.75
37_E	67_L	0.696	0.75
159_M	163_S	0.696	0.75
199_A	229_C	0.695	0.74
304_I	307_L	0.695	0.74
125_A	141_F	0.695	0.74
35_E	39_D	0.694	0.74
275_Y	279_V	0.694	0.74
105_R	121_H	0.693	0.74
61_R	71_K	0.691	0.74
203_L	226_V	0.690	0.74
103_Y	125_A	0.686	0.73
99_Y	106_G	0.684	0.73
204_C	238_E	0.680	0.73
54_S	67_L	0.680	0.73
60_H	68_M	0.679	0.73
66_K	83_L	0.679	0.73
355_F	358_R	0.677	0.73
115_F	148_V	0.677	0.73
40_L	44_E	0.676	0.72
61_R	69_P	0.675	0.72
52_Y	55_L	0.673	0.72
142_L	145_V	0.672	0.72
231_Y	243_F	0.672	0.72
129_L	141_F	0.669	0.72
61_R	66_K	0.668	0.72
60_H	64_L	0.668	0.72
86_I	119_I	0.667	0.71
56_M	61_R	0.661	0.71
106_G	118_A	0.656	0.70
123_K	166_L	0.655	0.70
150_Y	189_N	0.655	0.70
190_L	201_T	0.655	0.70
187_A	199_A	0.653	0.70
207_L	219_I	0.651	0.70
313_D	317_L	0.651	0.70
334_E	355_F	0.651	0.70
145_V	164_Q	0.650	0.69
143_F	165_A	0.649	0.69
351_E	361_M	0.647	0.69
52_Y	56_M	0.646	0.69
47_Q	51_L	0.644	0.69
42_D	49_L	0.644	0.69
137_E	148_V	0.639	0.68
246_A	261_A	0.639	0.68
297_Y	304_I	0.637	0.68
339_D	343_R	0.632	0.67
165_A	206_A	0.632	0.67
227_G	265_L	0.631	0.67
170_T	179_R	0.631	0.67
150_Y	155_T	0.631	0.67
35_E	42_D	0.630	0.67
183_E	223_Y	0.626	0.67
313_D	316_V	0.625	0.66
312_G	317_L	0.625	0.66
231_Y	285_G	0.624	0.66
90_Q	93_L	0.623	0.66
39_D	51_L	0.622	0.66
188_G	192_D	0.620	0.66
39_D	50_L	0.619	0.66
308_Y	312_G	0.618	0.66
62_I	68_M	0.615	0.65
305_H	311_S	0.615	0.65
51_L	56_M	0.615	0.65
68_M	71_K	0.615	0.65
279_V	286_I	0.615	0.65
329_L	332_D	0.614	0.65
49_L	56_M	0.614	0.65
34_Q	40_L	0.612	0.65
76_K	79_F	0.611	0.65
157_F	160_N	0.611	0.65
48_D	56_M	0.610	0.65
163_S	198_K	0.609	0.64
125_A	128_K	0.609	0.64
228_H	264_S	0.608	0.64
157_F	269_Y	0.607	0.64
343_R	347_L	0.605	0.64
37_E	50_L	0.604	0.64
36_I	41_E	0.602	0.64
168_I	225_N	0.602	0.64
245_T	248_A	0.598	0.63
321_F	359_R	0.598	0.63
78_P	82_M	0.597	0.63
35_E	40_L	0.594	0.63
34_Q	39_D	0.594	0.63
184_F	222_A	0.594	0.63
301_F	313_D	0.593	0.62
210_A	217_Y	0.592	0.62
163_S	190_L	0.592	0.62
43_M	54_S	0.590	0.62
344_F	350_Y	0.589	0.62
43_M	63_M	0.588	0.62
265_L	268_I	0.586	0.61
57_E	70_V	0.586	0.61
182_C	185_I	0.584	0.61
34_Q	43_M	0.583	0.61
304_I	324_L	0.582	0.61
335_D	349_H	0.580	0.61
204_C	208_E	0.578	0.60
320_C	323_L	0.578	0.60
345_N	349_H	0.577	0.60
44_E	53_F	0.577	0.60
39_D	48_D	0.575	0.60
94_T	97_L	0.575	0.60
202_H	205_S	0.574	0.60
36_I	50_L	0.573	0.60
350_Y	359_R	0.567	0.59
143_F	184_F	0.565	0.59
59_R	63_M	0.564	0.59
139_A	169_Y	0.562	0.58
296_M	299_T	0.561	0.58
103_Y	148_V	0.559	0.58
273_G	280_E	0.558	0.58
340_T	343_R	0.555	0.57
96_L	145_V	0.555	0.57
89_N	92_K	0.555	0.57
203_L	282_Y	0.554	0.57
36_I	54_S	0.554	0.57
38_Y	43_M	0.554	0.57
262_V	285_G	0.554	0.57
104_F	126_E	0.554	0.57
57_E	69_P	0.553	0.57
335_D	339_D	0.551	0.57
36_I	40_L	0.548	0.56
324_L	336_L	0.548	0.56
190_L	202_H	0.547	0.56
348_E	351_E	0.547	0.56
141_F	144_K	0.547	0.56
315_N	318_T	0.546	0.56
156_Y	189_N	0.546	0.56
38_Y	47_Q	0.544	0.56
53_F	57_E	0.543	0.56
277_K	281_A	0.539	0.55
61_R	79_F	0.538	0.55
106_G	121_H	0.538	0.55
64_L	69_P	0.534	0.55
116_I	360_L	0.534	0.55
169_Y	210_A	0.530	0.54
49_L	67_L	0.529	0.54
55_L	63_M	0.529	0.54
182_C	290_A	0.529	0.54
37_E	53_F	0.527	0.54
305_H	308_Y	0.526	0.53
350_Y	354_A	0.526	0.53
37_E	42_D	0.526	0.53
297_Y	301_F	0.525	0.53
42_D	84_N	0.524	0.53
283_D	298_L	0.524	0.53
317_L	322_D	0.524	0.53
107_M	144_K	0.523	0.53
147_E	185_I	0.522	0.53
197_E	233_L	0.522	0.53
328_Q	333_A	0.520	0.53
320_C	327_R	0.520	0.53
63_M	66_K	0.519	0.52
186_I	290_A	0.519	0.52
100_Y	112_Q	0.519	0.52
206_A	241_G	0.518	0.52
323_L	327_R	0.517	0.52
335_D	341_A	0.516	0.52
234_G	273_G	0.514	0.52
263_F	267_H	0.513	0.52
52_Y	70_V	0.512	0.51
165_A	182_C	0.511	0.51
53_F	64_L	0.510	0.51
165_A	242_Y	0.509	0.51
314_L	320_C	0.509	0.51
36_I	51_L	0.508	0.51
51_L	57_E	0.508	0.51
219_I	222_A	0.506	0.51
55_L	59_R	0.506	0.51
180_V	209_H	0.505	0.51
224_Y	261_A	0.503	0.50
62_I	70_V	0.502	0.50
60_H	71_K	0.502	0.50
104_F	107_M	0.501	0.50
36_I	48_D	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
4gyoA	2	0.9651	100	0.22	Contact Map
3q15A	2	0.9705	100	0.238	Contact Map
3ulqA	1	0.9866	100	0.245	Contact Map
4i1aA	2	0.9598	100	0.249	Contact Map
4gpkA	3	0.9196	100	0.303	Contact Map
3q7aA	1	0.7399	100	0.382	Contact Map
1w3bA	2	0.8204	100	0.385	Contact Map
4l9pA	1	0.7507	100	0.389	Contact Map
3dssA	1	0.7131	100	0.401	Contact Map
4n5cA	1	0.9357	100	0.409	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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