RAPE - BACSU - GREMLIN Contacts

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RAPE - Response regulator aspartate phosphatase E

UniProt:	P45943	Sequences: MISITSAEVGMKINEWHRHIQKFNVTDAEMLKAEIERDIEVMEEDQDLLIYYQLMAFRHKIMLEYTLPSDENRMELSEYLNKIEGHKKKLDNMRAYYYNFFRGMYEFRNGEYTRAITYYKKAERKIPTISDKIEKAEFYFKLSEVYYHMKMTHISMHYAELSYNIYKKHELYSVRRIQCHFVIAGNYDDLENHEKALPHLQEALKGAELLKSKNTHIYATAFFNLGNCYHKMDNLNKAARYIEQALVQYRKINSDVLPQAYHDLALIYFKQGKKEQAMDCFRKGIRSAVDFKDELFMNLFEALDVLYIRNGDTPKLLNIFSRLENGKGYPYLEELALLGGNLFDYNGKIEDSIICFKKMVYAQKQISKGECMYEI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	375 (296)
Sequences:	2272 (1965)
Seq/√Len:	114.2

ECOLI - LPSRP HEMY NLPI YBEQ
BACSU - RAPE RAPB RAPH RAPA RAPG RAPK RAPJ RAPF RAPC RAPI YVCD RAPD YPIA YRRB
HALSA - Q9HMM8
SULSO - Q97V36 Q97WM3 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
192_N	195_K	4.725	1.00
273_K	276_Q	4.573	1.00
348_K	351_D	4.426	1.00
234_N	237_K	4.329	1.00
111_E	114_R	3.919	1.00
184_A	200_L	3.725	1.00
151_M	154_I	3.598	1.00
226_G	242_I	3.594	1.00
143_S	159_A	3.509	1.00
103_G	119_Y	3.207	1.00
312_D	315_K	3.081	1.00
102_R	106_E	2.807	1.00
339_G	343_F	2.737	1.00
268_Y	276_Q	2.478	1.00
139_Y	158_Y	2.447	1.00
304_D	320_F	2.404	1.00
239_A	264_L	2.370	1.00
116_I	146_Y	2.357	1.00
343_F	351_D	2.289	1.00
264_L	268_Y	2.189	1.00
351_D	354_I	2.178	1.00
276_Q	279_D	2.175	1.00
142_L	146_Y	2.163	1.00
184_A	203_A	2.143	1.00
225_L	229_Y	2.111	1.00
239_A	271_Q	2.096	1.00
119_Y	141_K	2.083	1.00
197_L	225_L	2.079	1.00
317_L	343_F	2.044	1.00
222_F	241_Y	2.035	1.00
265_A	281_F	2.025	1.00
243_E	264_L	2.017	1.00
120_K	142_L	1.951	1.00
160_E	183_I	1.895	1.00
269_F	281_F	1.892	1.00
183_I	187_Y	1.869	1.00
229_Y	237_K	1.831	1.00
303_L	307_Y	1.817	1.00
99_N	118_Y	1.804	1.00
281_F	302_A	1.780	1.00
187_Y	195_K	1.769	1.00
142_L	158_Y	1.757	1.00
106_E	111_E	1.755	1.00
187_Y	192_N	1.729	1.00
340_G	356_F	1.701	1.00
239_A	268_Y	1.691	1.00
336_A	355_C	1.659	1.00
146_Y	154_I	1.657	1.00
267_I	271_Q	1.640	1.00
180_H	199_H	1.616	1.00
197_L	228_C	1.609	1.00
317_L	339_G	1.606	1.00
265_A	284_G	1.595	1.00
229_Y	234_N	1.574	1.00
225_L	241_Y	1.559	1.00
278_M	282_R	1.528	1.00
239_A	243_E	1.527	1.00
343_F	355_C	1.523	1.00
261_Y	280_C	1.517	1.00
343_F	348_K	1.508	1.00
268_Y	273_K	1.495	1.00
195_K	198_P	1.475	1.00
140_F	182_V	1.457	1.00
304_D	323_L	1.451	1.00
278_M	307_Y	1.442	1.00
106_E	114_R	1.437	1.00
161_L	164_N	1.431	1.00
321_S	339_G	1.430	1.00
317_L	321_S	1.430	1.00
315_K	318_N	1.429	1.00
143_S	158_Y	1.425	1.00
114_R	117_T	1.416	1.00
181_F	224_N	1.387	1.00
202_E	205_K	1.382	1.00
197_L	229_Y	1.382	1.00
264_L	280_C	1.372	1.00
201_Q	225_L	1.372	1.00
116_I	142_L	1.362	1.00
261_Y	283_K	1.360	1.00
237_K	240_R	1.355	1.00
104_M	119_Y	1.354	1.00
197_L	201_Q	1.354	1.00
344_D	357_K	1.337	1.00
242_I	263_D	1.308	1.00
184_A	199_H	1.306	1.00
184_A	196_A	1.298	1.00
103_G	122_A	1.298	1.00
162_S	165_I	1.293	0.99
239_A	267_I	1.291	0.99
307_Y	315_K	1.286	0.99
197_L	232_M	1.284	0.99
122_A	125_K	1.280	0.99
146_Y	151_M	1.257	0.99
340_G	359_M	1.243	0.99
138_F	142_L	1.232	0.99
159_A	182_V	1.219	0.99
158_Y	162_S	1.218	0.99
143_S	162_S	1.218	0.99
185_G	200_L	1.212	0.99
103_G	107_F	1.188	0.99
180_H	261_Y	1.179	0.99
268_Y	280_C	1.171	0.99
278_M	303_L	1.169	0.99
246_L	257_L	1.162	0.99
47_D	50_I	1.160	0.99
99_N	121_K	1.156	0.99
183_I	199_H	1.155	0.99
160_E	195_K	1.148	0.99
236_N	271_Q	1.146	0.99
162_S	179_C	1.141	0.99
313_T	346_N	1.136	0.99
319_I	323_L	1.128	0.99
222_F	245_A	1.117	0.98
123_E	139_Y	1.117	0.98
79_Y	82_K	1.110	0.98
200_L	224_N	1.108	0.98
106_E	118_Y	1.107	0.98
156_M	186_N	1.100	0.98
219_A	245_A	1.098	0.98
300_F	319_I	1.093	0.98
241_Y	245_A	1.093	0.98
196_A	228_C	1.090	0.98
143_S	155_S	1.086	0.98
49_L	53_Q	1.068	0.98
119_Y	122_A	1.063	0.98
79_Y	83_I	1.061	0.98
226_G	238_A	1.060	0.98
156_M	187_Y	1.056	0.98
99_N	122_A	1.053	0.98
344_D	356_F	1.047	0.98
36_E	39_I	1.042	0.98
221_A	228_C	1.040	0.98
156_M	183_I	1.033	0.97
116_I	149_M	1.032	0.97
226_G	245_A	1.026	0.97
265_A	280_C	1.023	0.97
139_Y	161_L	1.017	0.97
244_Q	247_V	1.014	0.97
246_L	261_Y	1.011	0.97
242_I	264_L	1.007	0.97
116_I	120_K	1.003	0.97
304_D	307_Y	1.002	0.97
245_A	260_A	1.001	0.97
159_A	163_Y	0.993	0.97
335_L	339_G	0.990	0.97
45_D	48_L	0.985	0.97
47_D	54_L	0.982	0.97
76_L	79_Y	0.977	0.96
222_F	244_Q	0.976	0.96
336_A	359_M	0.972	0.96
139_Y	162_S	0.972	0.96
224_N	227_N	0.972	0.96
177_I	207_A	0.969	0.96
246_L	260_A	0.968	0.96
50_I	58_R	0.968	0.96
319_I	322_R	0.966	0.96
339_G	355_C	0.963	0.96
262_H	266_L	0.963	0.96
45_D	49_L	0.961	0.96
40_E	43_E	0.958	0.96
163_Y	167_K	0.956	0.96
354_I	358_K	0.956	0.96
245_A	248_Q	0.953	0.96
304_D	316_L	0.952	0.96
122_A	138_F	0.951	0.96
156_M	190_L	0.946	0.96
63_L	67_L	0.938	0.96
181_F	221_A	0.938	0.96
117_T	121_K	0.930	0.95
81_N	84_E	0.927	0.95
227_N	263_D	0.924	0.95
140_F	162_S	0.920	0.95
46_Q	53_Q	0.919	0.95
333_E	340_G	0.912	0.95
278_M	306_L	0.908	0.95
48_L	55_M	0.905	0.95
181_F	203_A	0.904	0.95
355_C	358_K	0.903	0.95
353_I	357_K	0.900	0.94
227_N	242_I	0.900	0.94
100_F	104_M	0.899	0.94
110_G	150_K	0.896	0.94
176_R	180_H	0.894	0.94
350_E	357_K	0.893	0.94
115_A	119_Y	0.893	0.94
51_Y	57_F	0.892	0.94
308_I	342_L	0.890	0.94
353_I	356_F	0.884	0.94
59_H	62_M	0.881	0.94
258_P	288_A	0.878	0.94
47_D	57_F	0.875	0.94
45_D	53_Q	0.872	0.93
107_F	119_Y	0.872	0.93
262_H	302_A	0.871	0.93
258_P	284_G	0.870	0.93
59_H	63_L	0.863	0.93
36_E	44_E	0.858	0.93
47_D	61_I	0.848	0.92
336_A	358_K	0.848	0.92
54_L	57_F	0.847	0.92
45_D	51_Y	0.846	0.92
46_Q	49_L	0.844	0.92
36_E	40_E	0.841	0.92
166_Y	169_H	0.832	0.92
48_L	51_Y	0.832	0.92
143_S	182_V	0.824	0.91
306_L	310_N	0.821	0.91
73_R	76_L	0.820	0.91
349_I	353_I	0.819	0.91
222_F	248_Q	0.819	0.91
301_E	305_V	0.817	0.91
181_F	185_G	0.816	0.91
200_L	225_L	0.813	0.91
180_H	202_E	0.811	0.91
305_V	309_R	0.811	0.91
188_D	228_C	0.809	0.91
244_Q	248_Q	0.809	0.91
204_L	222_F	0.804	0.90
54_L	58_R	0.803	0.90
226_G	241_Y	0.803	0.90
139_Y	222_F	0.795	0.90
118_Y	122_A	0.794	0.90
96_Y	122_A	0.789	0.90
243_E	276_Q	0.786	0.89
116_I	145_V	0.783	0.89
104_M	141_K	0.782	0.89
123_E	138_F	0.778	0.89
153_H	157_H	0.773	0.89
199_H	203_A	0.772	0.88
300_F	323_L	0.769	0.88
223_F	260_A	0.768	0.88
278_M	285_I	0.761	0.88
235_L	267_I	0.760	0.88
146_Y	307_Y	0.759	0.88
54_L	70_D	0.758	0.88
258_P	265_A	0.758	0.88
280_C	284_G	0.756	0.87
180_H	203_A	0.754	0.87
307_Y	312_D	0.750	0.87
182_V	185_G	0.749	0.87
136_A	162_S	0.743	0.87
65_Y	124_R	0.742	0.86
160_E	187_Y	0.739	0.86
44_E	48_L	0.737	0.86
140_F	178_Q	0.736	0.86
39_I	43_E	0.735	0.86
62_M	65_Y	0.733	0.86
163_Y	176_R	0.730	0.86
51_Y	55_M	0.727	0.85
121_K	124_R	0.725	0.85
230_H	235_L	0.723	0.85
337_L	340_G	0.723	0.85
191_E	231_K	0.715	0.84
103_G	118_Y	0.714	0.84
199_H	202_E	0.712	0.84
207_A	218_Y	0.711	0.84
58_R	61_I	0.710	0.84
204_L	218_Y	0.706	0.84
103_G	115_A	0.703	0.83
300_F	303_L	0.702	0.83
75_E	82_K	0.701	0.83
317_L	320_F	0.700	0.83
139_Y	142_L	0.699	0.83
263_D	266_L	0.696	0.83
199_H	229_Y	0.696	0.83
51_Y	54_L	0.692	0.82
120_K	146_Y	0.692	0.82
65_Y	69_S	0.688	0.82
302_A	305_V	0.685	0.82
197_L	234_N	0.685	0.82
188_D	200_L	0.684	0.82
107_F	112_Y	0.681	0.81
317_L	346_N	0.681	0.81
116_I	299_L	0.680	0.81
38_D	43_E	0.676	0.81
242_I	267_I	0.676	0.81
67_L	70_D	0.674	0.81
194_E	232_M	0.674	0.81
102_R	118_Y	0.672	0.81
238_A	242_I	0.671	0.80
51_Y	58_R	0.667	0.80
152_T	186_N	0.665	0.80
305_V	338_L	0.664	0.80
236_N	239_A	0.661	0.79
113_T	149_M	0.661	0.79
107_F	145_V	0.659	0.79
163_Y	180_H	0.657	0.79
223_F	226_G	0.652	0.78
83_I	87_K	0.650	0.78
313_T	316_L	0.649	0.78
149_M	272_G	0.647	0.78
319_I	329_Y	0.647	0.78
264_L	339_G	0.644	0.78
284_G	287_S	0.644	0.78
195_K	199_H	0.644	0.78
101_F	104_M	0.643	0.78
333_E	359_M	0.642	0.77
344_D	347_G	0.640	0.77
340_G	344_D	0.638	0.77
93_M	99_N	0.638	0.77
84_E	87_K	0.638	0.77
263_D	302_A	0.636	0.77
340_G	343_F	0.635	0.77
75_E	78_E	0.632	0.76
181_F	223_F	0.629	0.76
100_F	141_K	0.627	0.76
80_L	84_E	0.625	0.76
241_Y	244_Q	0.623	0.75
162_S	167_K	0.619	0.75
115_A	122_A	0.619	0.75
302_A	307_Y	0.619	0.75
203_A	221_A	0.619	0.75
65_Y	68_P	0.619	0.75
297_M	304_D	0.618	0.75
321_S	325_N	0.618	0.75
44_E	47_D	0.616	0.74
278_M	310_N	0.614	0.74
53_Q	56_A	0.612	0.74
274_K	278_M	0.612	0.74
133_I	139_Y	0.612	0.74
203_A	265_A	0.610	0.74
308_I	345_Y	0.609	0.74
320_F	339_G	0.609	0.74
310_N	318_N	0.609	0.74
277_A	281_F	0.608	0.74
55_M	58_R	0.606	0.73
282_R	286_R	0.600	0.73
343_F	346_N	0.599	0.72
296_F	299_L	0.598	0.72
332_L	336_A	0.597	0.72
320_F	335_L	0.597	0.72
57_F	66_T	0.596	0.72
103_G	226_G	0.595	0.72
137_E	141_K	0.594	0.72
158_Y	161_L	0.594	0.72
356_F	360_V	0.593	0.72
203_A	206_G	0.591	0.71
167_K	176_R	0.591	0.71
304_D	338_L	0.590	0.71
184_A	302_A	0.590	0.71
120_K	124_R	0.590	0.71
234_N	243_E	0.590	0.71
337_L	341_N	0.587	0.71
157_H	164_N	0.586	0.71
310_N	315_K	0.585	0.71
36_E	265_A	0.585	0.71
37_R	44_E	0.584	0.71
96_Y	101_F	0.583	0.70
269_F	302_A	0.581	0.70
226_G	304_D	0.581	0.70
283_K	286_R	0.580	0.70
263_D	267_I	0.579	0.70
140_F	179_C	0.578	0.70
307_Y	319_I	0.577	0.70
55_M	61_I	0.577	0.70
187_Y	199_H	0.574	0.69
60_K	66_T	0.574	0.69
343_F	356_F	0.568	0.68
331_Y	334_E	0.568	0.68
123_E	142_L	0.567	0.68
193_H	228_C	0.567	0.68
119_Y	227_N	0.566	0.68
147_Y	186_N	0.565	0.68
147_Y	159_A	0.564	0.68
52_Y	58_R	0.564	0.68
64_E	68_P	0.563	0.68
71_E	76_L	0.562	0.68
223_F	263_D	0.562	0.68
196_A	200_L	0.561	0.67
258_P	262_H	0.561	0.67
318_N	321_S	0.560	0.67
156_M	160_E	0.560	0.67
177_I	203_A	0.559	0.67
141_K	144_E	0.558	0.67
268_Y	272_G	0.558	0.67
142_L	145_V	0.557	0.67
229_Y	268_Y	0.556	0.67
349_I	352_S	0.556	0.67
289_V	292_K	0.556	0.67
222_F	261_Y	0.555	0.67
61_I	69_S	0.554	0.67
57_F	61_I	0.554	0.67
79_Y	86_H	0.553	0.66
122_A	323_L	0.553	0.66
60_K	65_Y	0.551	0.66
39_I	47_D	0.550	0.66
314_P	317_L	0.549	0.66
296_F	300_F	0.548	0.66
207_A	217_I	0.548	0.66
180_H	222_F	0.547	0.66
74_M	86_H	0.547	0.66
167_K	202_E	0.545	0.65
66_T	69_S	0.544	0.65
282_R	315_K	0.543	0.65
356_F	359_M	0.540	0.65
316_L	319_I	0.540	0.65
133_I	145_V	0.540	0.65
154_I	157_H	0.539	0.64
86_H	89_K	0.539	0.64
57_F	68_P	0.536	0.64
59_H	68_P	0.533	0.64
334_E	341_N	0.530	0.63
64_E	80_L	0.529	0.63
95_A	102_R	0.529	0.63
107_F	141_K	0.528	0.63
55_M	68_P	0.525	0.62
223_F	259_Q	0.524	0.62
141_K	149_M	0.523	0.62
106_E	229_Y	0.523	0.62
43_E	56_A	0.522	0.62
238_A	267_I	0.521	0.62
302_A	311_G	0.521	0.62
324_E	358_K	0.521	0.62
115_A	145_V	0.520	0.62
121_K	125_K	0.520	0.62
179_C	183_I	0.518	0.61
63_L	68_P	0.518	0.61
218_Y	257_L	0.518	0.61
70_D	78_E	0.515	0.61
159_A	179_C	0.515	0.61
53_Q	290_D	0.515	0.61
78_E	81_N	0.514	0.61
52_Y	57_F	0.514	0.61
98_Y	105_Y	0.513	0.61
37_R	43_E	0.513	0.61
324_E	339_G	0.513	0.61
201_Q	237_K	0.512	0.60
60_K	63_L	0.512	0.60
245_A	284_G	0.509	0.60
185_G	224_N	0.508	0.60
77_S	86_H	0.508	0.60
100_F	138_F	0.507	0.60
48_L	64_E	0.505	0.59
106_E	117_T	0.504	0.59
183_I	303_L	0.504	0.59
58_R	63_L	0.504	0.59
83_I	88_K	0.503	0.59
262_H	299_L	0.503	0.59
53_Q	58_R	0.503	0.59
261_Y	300_F	0.502	0.59
92_N	99_N	0.502	0.59
59_H	65_Y	0.501	0.59
136_A	143_S	0.500	0.59
71_E	74_M	0.500	0.59

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	0.976	100	0.268	Contact Map
4i1aA	2	0.9547	100	0.277	Contact Map
3q15A	2	0.9653	100	0.28	Contact Map
4gyoA	2	0.952	100	0.287	Contact Map
4gpkA	3	0.9093	100	0.345	Contact Map
1w3bA	2	0.8187	100	0.352	Contact Map
4l9pA	1	0.744	100	0.362	Contact Map
3dssA	1	0.7013	100	0.366	Contact Map
3q7aA	1	0.736	100	0.373	Contact Map
4ui9C	2	0.856	100	0.376	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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