RAPD - BACSU - GREMLIN Contacts

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RAPD - Response regulator aspartate phosphatase D

UniProt:	P94583	Sequences: MISKFIEKRMLNMLDEWYSAMSKRKMNHVCTLKEKIDQHLPKIKKNTKLWMRYQLFQARHQLLFENQNGLDSLFDGLYGLEDKMDDELKYYLYFFSGLYEMVKTAPKHAVHHFKKAEQYLAAIHNTFEAADLYYQTAGAYYLMKSPPLSVQYVKKALHIYLHQFGYIKKVITCKLLLAVNYIDQERYEKAEQLFKEIIKKTQQLHDENLLCHAYYNLGFLKATEKKDQEALLYFRKVLKNQEFEMNSPVSYLHCVYESVRALFKTGNITEAKAVLQKGKELSEKVDIQTIYLKLKTLEALYTSAEDPYEQLLEYVLELEKIEAWVDLEVLLEDITEYYKKKDDFEKAAFFIMRG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	354 (298)
Sequences:	2009 (1786)
Seq/√Len:	103.5

ECOLI - LPSRP HEMY NLPI
BACSU - RAPD RAPF RAPA RAPC RAPH RAPK RAPJ RAPG RAPB RAPI RAPE YVCD YPIA YRRB GUTR
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
267_N	270_E	5.256	1.00
226_K	229_E	5.047	1.00
186_R	189_K	4.312	1.00
178_A	194_F	4.034	1.00
145_S	148_L	3.957	1.00
137_A	153_V	3.942	1.00
218_G	234_F	3.815	1.00
105_A	108_H	3.768	1.00
97_G	113_F	3.498	1.00
191_E	217_L	3.354	1.00
133_Y	152_Y	3.152	1.00
150_V	177_L	3.018	1.00
259_V	275_L	2.884	1.00
231_L	258_S	2.726	1.00
270_E	273_A	2.613	1.00
57_Q	61_Q	2.595	1.00
178_A	193_L	2.574	1.00
214_Y	236_K	2.537	1.00
113_F	135_Q	2.516	1.00
234_F	257_E	2.468	1.00
93_Y	112_H	2.394	1.00
258_S	262_L	2.171	1.00
110_V	140_Y	2.160	1.00
262_L	270_E	2.154	1.00
214_Y	233_Y	2.119	1.00
258_S	274_V	2.111	1.00
182_I	194_F	2.106	1.00
255_V	274_V	2.067	1.00
195_K	217_L	2.063	1.00
231_L	261_A	2.030	1.00
153_V	176_L	2.020	1.00
136_T	140_Y	2.010	1.00
100_E	108_H	2.006	1.00
221_K	229_E	1.998	1.00
217_L	221_K	1.992	1.00
100_E	105_A	1.988	1.00
229_E	232_L	1.936	1.00
97_G	116_A	1.911	1.00
66_N	69_G	1.910	1.00
177_L	181_Y	1.898	1.00
140_Y	148_L	1.895	1.00
218_G	233_Y	1.861	1.00
191_E	224_E	1.850	1.00
134_Y	176_L	1.836	1.00
101_M	113_F	1.827	1.00
174_K	193_L	1.827	1.00
262_L	267_N	1.808	1.00
97_G	112_H	1.773	1.00
180_N	184_Q	1.756	1.00
148_L	151_Q	1.744	1.00
211_C	237_V	1.725	1.00
174_K	196_E	1.708	1.00
93_Y	115_K	1.696	1.00
181_Y	189_K	1.690	1.00
58_A	70_L	1.655	1.00
96_S	100_E	1.654	1.00
307_P	310_Q	1.611	1.00
228_Q	265_T	1.557	1.00
191_E	220_L	1.545	1.00
307_P	311_L	1.526	1.00
221_K	226_K	1.526	1.00
257_E	260_R	1.525	1.00
191_E	195_K	1.507	1.00
189_K	192_Q	1.494	1.00
133_Y	155_K	1.493	1.00
231_L	265_T	1.474	1.00
90_Y	116_A	1.461	1.00
221_K	262_L	1.448	1.00
231_L	262_L	1.442	1.00
259_V	274_V	1.442	1.00
130_A	156_A	1.433	1.00
138_G	176_L	1.424	1.00
150_V	180_N	1.408	1.00
58_A	74_F	1.403	1.00
235_R	270_E	1.400	1.00
33_K	37_D	1.398	1.00
198_I	210_L	1.389	1.00
235_R	258_S	1.389	1.00
116_A	119_Y	1.388	1.00
191_E	221_K	1.366	1.00
252_L	259_V	1.326	0.99
136_T	152_Y	1.315	0.99
34_E	38_Q	1.315	0.99
231_L	235_R	1.313	0.99
171_I	197_I	1.300	0.99
262_L	274_V	1.298	0.99
58_A	77_L	1.288	0.99
336_E	339_K	1.288	0.99
255_V	277_K	1.274	0.99
114_K	148_L	1.267	0.99
137_A	152_Y	1.263	0.99
218_G	230_A	1.263	0.99
113_F	117_E	1.255	0.99
154_K	177_L	1.251	0.99
334_I	338_Y	1.242	0.99
261_A	265_T	1.241	0.99
110_V	136_T	1.233	0.99
132_L	135_Q	1.233	0.99
137_A	156_A	1.232	0.99
202_Q	210_L	1.225	0.99
114_K	136_T	1.225	0.99
197_I	237_V	1.215	0.99
217_L	233_Y	1.210	0.99
110_V	114_K	1.204	0.99
329_V	333_D	1.201	0.99
175_L	197_I	1.197	0.99
97_G	109_A	1.189	0.99
278_G	281_L	1.186	0.99
136_T	177_L	1.185	0.99
218_G	237_V	1.183	0.99
93_Y	116_A	1.181	0.99
94_F	135_Q	1.172	0.98
219_F	234_F	1.169	0.98
259_V	278_G	1.164	0.98
178_A	197_I	1.152	0.98
156_A	159_I	1.152	0.98
134_Y	173_C	1.127	0.98
227_D	261_A	1.122	0.98
215_Y	254_C	1.114	0.98
187_Y	227_D	1.104	0.98
179_V	194_F	1.102	0.98
135_Q	138_G	1.093	0.98
193_L	197_I	1.091	0.98
238_L	251_Y	1.085	0.97
36_I	39_H	1.056	0.97
191_E	231_L	1.050	0.97
140_Y	152_Y	1.048	0.97
315_V	318_L	1.045	0.97
151_Q	155_K	1.042	0.97
61_Q	70_L	1.039	0.97
327_L	331_L	1.038	0.97
177_L	193_L	1.036	0.97
215_Y	257_E	1.024	0.96
98_L	113_F	1.019	0.96
108_H	111_H	1.018	0.96
110_V	139_A	0.997	0.96
107_K	143_M	0.995	0.96
232_L	236_K	0.993	0.96
311_L	314_Y	0.992	0.96
202_Q	205_H	0.987	0.96
272_K	276_Q	0.980	0.95
292_L	299_A	0.977	0.95
181_Y	186_R	0.975	0.95
309_E	313_E	0.970	0.95
33_K	40_L	0.962	0.95
238_L	255_V	0.958	0.95
126_T	129_A	0.954	0.95
238_L	258_S	0.952	0.95
309_E	312_L	0.948	0.94
323_A	326_D	0.943	0.94
100_E	112_H	0.943	0.94
252_L	278_G	0.934	0.94
237_V	240_N	0.927	0.94
218_G	258_S	0.922	0.94
38_Q	41_P	0.911	0.93
260_R	275_L	0.910	0.93
37_D	40_L	0.904	0.93
216_N	219_F	0.898	0.93
55_L	59_R	0.894	0.93
256_Y	260_R	0.893	0.93
201_T	204_L	0.889	0.92
278_G	282_S	0.888	0.92
52_R	56_F	0.886	0.92
110_V	143_M	0.886	0.92
219_F	257_E	0.881	0.92
179_V	216_N	0.880	0.92
94_F	113_F	0.878	0.92
155_K	158_H	0.877	0.92
175_L	216_N	0.877	0.92
140_Y	145_S	0.875	0.92
256_Y	278_G	0.875	0.92
196_E	200_K	0.869	0.91
263_F	275_L	0.864	0.91
96_S	112_H	0.860	0.91
146_P	150_V	0.859	0.91
117_E	133_Y	0.852	0.91
173_C	194_F	0.850	0.91
152_Y	156_A	0.847	0.90
295_K	302_T	0.844	0.90
295_K	298_E	0.844	0.90
222_A	227_D	0.837	0.90
150_V	154_K	0.836	0.90
241_Q	254_C	0.835	0.90
198_I	214_Y	0.815	0.89
291_Y	295_K	0.815	0.89
256_Y	275_L	0.812	0.88
60_H	64_F	0.809	0.88
194_F	217_L	0.808	0.88
153_V	173_C	0.806	0.88
32_L	37_D	0.806	0.88
193_L	196_E	0.804	0.88
188_E	224_E	0.801	0.88
32_L	43_I	0.794	0.87
157_L	174_K	0.794	0.87
310_Q	313_E	0.793	0.87
293_K	298_E	0.793	0.87
241_Q	250_S	0.789	0.87
194_F	216_N	0.781	0.86
268_I	272_K	0.777	0.86
38_Q	43_I	0.775	0.86
307_P	314_Y	0.774	0.86
198_I	217_L	0.773	0.86
207_E	210_L	0.771	0.86
201_T	213_A	0.763	0.85
39_H	43_I	0.761	0.85
118_Q	121_A	0.761	0.85
308_Y	311_L	0.755	0.85
116_A	132_L	0.754	0.84
90_Y	139_A	0.754	0.84
328_E	331_L	0.753	0.84
227_D	264_K	0.753	0.84
325_V	328_E	0.752	0.84
184_Q	265_T	0.750	0.84
55_L	58_A	0.745	0.84
171_I	201_T	0.743	0.84
134_Y	172_T	0.741	0.83
222_A	234_F	0.741	0.83
285_V	288_Q	0.741	0.83
133_Y	255_V	0.738	0.83
106_P	139_A	0.738	0.83
290_I	293_K	0.738	0.83
32_L	35_K	0.737	0.83
45_K	49_L	0.736	0.83
272_K	298_E	0.735	0.83
32_L	39_H	0.734	0.83
238_L	254_C	0.734	0.83
138_G	153_V	0.731	0.83
315_V	319_E	0.726	0.82
297_L	301_Y	0.724	0.82
55_L	70_L	0.721	0.82
35_K	45_K	0.720	0.82
333_D	336_E	0.719	0.82
196_E	199_K	0.716	0.81
38_Q	42_K	0.714	0.81
35_K	39_H	0.714	0.81
237_V	254_C	0.714	0.81
68_N	284_K	0.712	0.81
74_F	78_Y	0.712	0.81
178_A	190_A	0.712	0.81
157_L	177_L	0.711	0.81
231_L	267_N	0.711	0.81
46_N	50_W	0.711	0.81
202_Q	236_K	0.710	0.81
112_H	116_A	0.709	0.81
278_G	288_Q	0.708	0.81
129_A	133_Y	0.706	0.80
61_Q	65_E	0.705	0.80
180_N	261_A	0.705	0.80
74_F	96_S	0.704	0.80
325_V	333_D	0.703	0.80
93_Y	119_Y	0.703	0.80
197_I	200_K	0.701	0.80
332_E	335_T	0.701	0.80
202_Q	214_Y	0.700	0.80
235_R	262_L	0.699	0.80
55_L	65_E	0.698	0.80
324_W	331_L	0.698	0.80
153_V	177_L	0.698	0.80
228_Q	272_K	0.696	0.79
33_K	36_I	0.695	0.79
298_E	304_A	0.692	0.79
73_L	76_G	0.692	0.79
117_E	132_L	0.692	0.79
248_P	251_Y	0.686	0.78
170_V	173_C	0.685	0.78
306_D	310_Q	0.684	0.78
33_K	53_Y	0.682	0.78
198_I	213_A	0.682	0.78
327_L	334_I	0.681	0.78
61_Q	64_F	0.680	0.78
72_S	75_D	0.679	0.78
139_A	143_M	0.678	0.78
304_A	310_Q	0.677	0.78
299_A	304_A	0.676	0.77
291_Y	298_E	0.676	0.77
133_Y	156_A	0.675	0.77
60_H	63_L	0.674	0.77
70_L	77_L	0.674	0.77
175_L	213_A	0.673	0.77
126_T	159_I	0.673	0.77
134_Y	138_G	0.673	0.77
234_F	238_L	0.673	0.77
34_E	40_L	0.671	0.77
278_G	294_L	0.669	0.77
58_A	65_E	0.666	0.76
107_K	147_P	0.666	0.76
40_L	44_K	0.666	0.76
45_K	48_K	0.664	0.76
55_L	60_H	0.661	0.76
217_L	258_S	0.661	0.76
320_K	326_D	0.661	0.76
328_E	332_E	0.660	0.76
53_Y	57_Q	0.655	0.75
77_L	80_L	0.652	0.75
255_V	278_G	0.652	0.75
147_P	184_Q	0.651	0.75
323_A	329_V	0.650	0.75
36_I	40_L	0.644	0.74
133_Y	174_K	0.644	0.74
150_V	184_Q	0.641	0.74
54_Q	61_Q	0.641	0.74
94_F	97_G	0.638	0.73
197_I	213_A	0.633	0.73
225_K	268_I	0.631	0.72
113_F	139_A	0.628	0.72
85_D	88_L	0.627	0.72
227_D	268_I	0.627	0.72
335_T	339_K	0.627	0.72
127_F	166_Y	0.627	0.72
148_L	229_E	0.626	0.72
201_T	209_L	0.624	0.72
49_L	52_R	0.617	0.71
46_N	52_R	0.615	0.71
217_L	220_L	0.613	0.70
59_R	95_F	0.613	0.70
114_K	140_Y	0.613	0.70
90_Y	97_G	0.613	0.70
97_G	139_A	0.611	0.70
319_E	328_E	0.610	0.70
327_L	333_D	0.610	0.70
167_I	248_P	0.609	0.70
68_N	103_K	0.608	0.70
40_L	46_N	0.608	0.70
230_A	234_F	0.607	0.70
96_S	109_A	0.607	0.70
226_K	260_R	0.606	0.69
176_L	179_V	0.606	0.69
167_I	170_V	0.602	0.69
269_T	276_Q	0.600	0.69
51_M	60_H	0.600	0.69
35_K	41_P	0.600	0.69
94_F	98_L	0.597	0.68
104_T	142_L	0.596	0.68
312_L	316_L	0.593	0.68
167_I	203_Q	0.593	0.68
311_L	318_L	0.592	0.68
294_L	297_L	0.592	0.68
328_E	339_K	0.590	0.67
259_V	271_A	0.589	0.67
33_K	52_R	0.588	0.67
98_L	135_Q	0.587	0.67
284_K	313_E	0.587	0.67
94_F	116_A	0.584	0.67
233_Y	236_K	0.584	0.67
59_R	62_L	0.584	0.67
269_T	272_K	0.583	0.66
308_Y	312_L	0.582	0.66
229_E	233_Y	0.580	0.66
140_Y	294_L	0.579	0.66
35_K	42_K	0.579	0.66
275_L	292_L	0.579	0.66
153_V	180_N	0.578	0.66
154_K	158_H	0.578	0.66
294_L	298_E	0.577	0.66
189_K	229_E	0.577	0.66
191_E	226_K	0.575	0.65
32_L	41_P	0.575	0.65
41_P	46_N	0.572	0.65
181_Y	193_L	0.571	0.65
293_K	326_D	0.569	0.65
214_Y	255_V	0.569	0.65
221_K	225_K	0.569	0.65
32_L	44_K	0.569	0.65
183_D	278_G	0.567	0.64
70_L	99_Y	0.567	0.64
324_W	335_T	0.567	0.64
140_Y	143_M	0.565	0.64
330_L	333_D	0.565	0.64
177_L	217_L	0.564	0.64
171_I	190_A	0.563	0.64
40_L	50_W	0.562	0.64
42_K	49_L	0.561	0.64
33_K	43_I	0.561	0.64
236_K	239_K	0.559	0.63
150_V	181_Y	0.557	0.63
214_Y	237_V	0.556	0.63
47_T	51_M	0.554	0.63
263_F	272_K	0.553	0.62
215_Y	219_F	0.553	0.62
37_D	43_I	0.552	0.62
156_A	173_C	0.550	0.62
172_T	175_L	0.547	0.62
58_A	61_Q	0.546	0.61
229_E	270_E	0.546	0.61
33_K	49_L	0.546	0.61
188_E	192_Q	0.543	0.61
35_K	40_L	0.540	0.61
298_E	303_S	0.539	0.60
40_L	43_I	0.538	0.60
133_Y	214_Y	0.538	0.60
191_E	194_F	0.538	0.60
326_D	330_L	0.537	0.60
47_T	50_W	0.537	0.60
137_A	176_L	0.536	0.60
32_L	36_I	0.536	0.60
46_N	49_L	0.535	0.60
62_L	70_L	0.535	0.60
319_E	331_L	0.535	0.60
35_K	43_I	0.535	0.60
133_Y	137_A	0.533	0.60
328_E	334_I	0.533	0.60
251_Y	255_V	0.533	0.60
32_L	40_L	0.532	0.59
214_Y	232_L	0.532	0.59
283_E	300_L	0.530	0.59
79_G	82_D	0.529	0.59
90_Y	94_F	0.528	0.59
73_L	81_E	0.527	0.59
65_E	70_L	0.527	0.59
239_K	269_T	0.527	0.59
134_Y	153_V	0.526	0.59
277_K	280_E	0.525	0.58
275_L	279_K	0.525	0.58
43_I	52_R	0.525	0.58
54_Q	73_L	0.524	0.58
326_D	333_D	0.523	0.58
39_H	44_K	0.523	0.58
37_D	42_K	0.522	0.58
283_E	288_Q	0.520	0.58
49_L	228_Q	0.520	0.58
220_L	261_A	0.519	0.58
333_D	338_Y	0.518	0.57
138_G	279_K	0.518	0.57
170_V	174_K	0.517	0.57
332_E	336_E	0.516	0.57
323_A	328_E	0.515	0.57
77_L	81_E	0.515	0.57
154_K	195_K	0.515	0.57
36_I	42_K	0.514	0.57
328_E	336_E	0.513	0.57
175_L	215_Y	0.513	0.57
111_H	144_K	0.511	0.56
34_E	44_K	0.511	0.56
140_Y	147_P	0.510	0.56
109_A	113_F	0.509	0.56
141_Y	180_N	0.508	0.56
331_L	334_I	0.507	0.56
276_Q	288_Q	0.507	0.56
32_L	38_Q	0.505	0.56
134_Y	156_A	0.505	0.56
122_A	210_L	0.504	0.55
60_H	65_E	0.503	0.55
334_I	339_K	0.503	0.55
316_L	326_D	0.502	0.55
297_L	320_K	0.502	0.55
79_G	225_K	0.500	0.55
89_K	119_Y	0.500	0.55

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	0.9576	100	0.248	Contact Map
3ulqA	1	0.9802	100	0.248	Contact Map
4gyoA	2	0.9774	100	0.251	Contact Map
3q15A	2	0.9774	100	0.256	Contact Map
4gpkA	3	0.9576	100	0.288	Contact Map
1w3bA	2	0.8588	100	0.367	Contact Map
3sf4A	1	0.8616	100	0.381	Contact Map
4ui9C	2	0.8757	100	0.39	Contact Map
4ui9J	2	0.8701	100	0.391	Contact Map
3ro2A	1	0.8616	100	0.395	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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