ARAF - ECOLI - GREMLIN Contacts

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ARAF - L-arabinose-binding periplasmic protein

UniProt:	P02924	Sequences: MHKFTKALAAIGLAAVMSQSAMAENLKLGFLVKQPEEPWFQTEWKFADKAGKDLGFEVIKIAVPDGEKTLNAIDSLAASGAKGFVICTPDPKLGSAIVAKARGYDMKVIAVDDQFVNAKGKPMDTVPLVMMAATKIGERQGQELYKEMQKRGWDVKESAVMAITANELDTARRRTTGSMDALKAAGFPEKQIYQVPTKSNDIPGAFDAANSMLVQHPEVKHWLIVGMNDSTVLGGVRATEGQGFKAADIIGIGINGVDAVSELSKAQATGFYGSLLPSPDVHGYKSSEMLYNWVAKDVEPPKFTEVTDVVLITRDNFKEELEKKGLGGK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10057
Length:	329 (288)
Sequences:	38618 (29324)
Seq/√Len:	1727.9

ECOLI - ARAF LSRB XYLF ALSB YTFQ GALR GALS PURR DGAL LACI CYTR ASCG RBSB CRA IDNR MALI RBSR GNTR YCJW TORT YPHF EBGR TRER XYLR
BACSU - CCPA DEGA KDGR MSMR NTDR RBSR ARAR RBSB EXUR YKVZ YVDE GANR CCPB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
134_T	180_D	3.563	1.00
149_Q	220_K	3.238	1.00
83_G	290_L	2.839	1.00
140_Q	252_I	2.716	1.00
175_T	179_M	2.653	1.00
127_P	293_W	2.640	1.00
256_G	276_L	2.625	1.00
149_Q	250_I	2.508	1.00
138_E	184_A	2.400	1.00
50_A	53_D	2.324	1.00
206_F	241_G	2.318	1.00
210_N	242_Q	2.257	1.00
138_E	180_D	2.224	1.00
50_A	288_E	2.218	1.00
142_Q	181_A	2.175	1.00
138_E	181_A	2.165	1.00
285_K	288_E	2.130	1.00
145_Y	185_A	2.119	1.00
135_K	139_R	2.107	1.00
210_N	238_A	2.102	1.00
136_I	254_I	2.067	1.00
51_G	287_S	2.059	1.00
137_G	141_G	2.034	1.00
134_T	176_T	2.032	1.00
144_L	223_L	2.002	1.00
46_F	283_G	1.995	1.00
50_A	284_Y	1.973	1.00
142_Q	146_K	1.950	1.00
205_A	234_G	1.950	1.00
147_E	317_F	1.872	1.00
214_V	242_Q	1.839	1.00
239_T	249_I	1.828	1.00
137_G	225_V	1.827	1.00
49_K	280_D	1.815	1.00
29_G	81_A	1.797	1.00
276_L	310_V	1.789	1.00
141_G	178_S	1.773	1.00
138_E	142_Q	1.767	1.00
160_V	219_V	1.760	1.00
161_M	227_M	1.746	1.00
206_F	238_A	1.741	1.00
142_Q	185_A	1.731	1.00
226_G	235_G	1.731	1.00
278_S	281_V	1.705	1.00
209_A	235_G	1.704	1.00
111_V	286_S	1.684	1.00
244_F	248_D	1.676	1.00
46_F	280_D	1.657	1.00
176_T	180_D	1.645	1.00
292_N	298_V	1.643	1.00
50_A	54_L	1.642	1.00
135_K	138_E	1.634	1.00
143_E	147_E	1.628	1.00
139_R	309_V	1.615	1.00
245_K	248_D	1.591	1.00
238_A	242_Q	1.575	1.00
266_A	315_D	1.558	1.00
145_Y	181_A	1.556	1.00
54_L	291_Y	1.544	1.00
143_E	146_K	1.529	1.00
252_I	273_G	1.524	1.00
240_E	264_S	1.517	1.00
199_S	204_G	1.495	1.00
173_R	176_T	1.493	1.00
281_V	285_K	1.489	1.00
179_M	183_K	1.484	1.00
238_A	241_G	1.480	1.00
26_L	82_K	1.478	1.00
206_F	237_R	1.455	1.00
132_A	135_K	1.450	1.00
189_E	192_I	1.445	1.00
50_A	287_S	1.434	1.00
137_G	177_G	1.419	1.00
281_V	284_Y	1.416	1.00
136_I	309_V	1.403	1.00
29_G	76_L	1.398	1.00
256_G	314_R	1.387	1.00
143_E	313_T	1.386	1.00
141_G	145_Y	1.386	1.00
210_N	241_G	1.375	1.00
99_A	103_G	1.372	1.00
160_V	212_M	1.369	1.00
239_T	244_F	1.368	1.00
181_A	184_A	1.366	1.00
141_G	177_G	1.365	1.00
74_D	100_K	1.358	1.00
141_G	181_A	1.339	1.00
177_G	181_A	1.337	1.00
209_A	224_I	1.328	1.00
134_T	138_E	1.325	1.00
206_F	210_N	1.324	1.00
288_E	292_N	1.319	1.00
149_Q	223_L	1.318	1.00
61_I	76_L	1.312	1.00
85_V	286_S	1.307	1.00
209_A	239_T	1.305	1.00
51_G	58_V	1.302	1.00
196_P	211_S	1.291	1.00
26_L	56_F	1.287	1.00
28_L	51_G	1.281	1.00
190_K	193_Y	1.277	1.00
139_R	142_Q	1.265	1.00
27_K	57_E	1.264	1.00
61_I	72_A	1.259	1.00
210_N	214_V	1.250	1.00
47_A	287_S	1.241	1.00
48_D	52_K	1.213	1.00
30_F	47_A	1.206	1.00
236_V	251_G	1.206	1.00
280_D	284_Y	1.204	1.00
216_H	219_V	1.203	1.00
178_S	182_L	1.174	1.00
234_G	238_A	1.174	1.00
161_M	175_T	1.174	1.00
54_L	288_E	1.171	1.00
203_P	207_D	1.168	1.00
15_A	18_S	1.167	1.00
211_S	215_Q	1.155	1.00
134_T	177_G	1.149	1.00
47_A	85_V	1.143	1.00
178_S	225_V	1.140	1.00
30_F	58_V	1.136	1.00
27_K	59_I	1.133	1.00
229_D	274_S	1.131	1.00
142_Q	184_A	1.131	1.00
134_T	173_R	1.130	1.00
162_A	235_G	1.127	1.00
143_E	317_F	1.123	1.00
224_I	235_G	1.115	1.00
250_I	317_F	1.114	1.00
180_D	184_A	1.111	1.00
201_D	204_G	1.110	1.00
6_K	9_A	1.098	1.00
208_A	211_S	1.080	1.00
229_D	253_G	1.078	1.00
285_K	289_M	1.076	1.00
181_A	185_A	1.067	1.00
172_R	176_T	1.067	1.00
159_A	182_L	1.066	1.00
140_Q	225_V	1.055	1.00
182_L	187_F	1.055	1.00
283_G	287_S	1.055	1.00
68_K	71_N	1.054	1.00
202_I	237_R	1.049	1.00
176_T	179_M	1.046	1.00
44_W	48_D	1.046	1.00
204_G	207_D	1.043	1.00
14_A	17_M	1.037	1.00
147_E	313_T	1.037	1.00
145_Y	187_F	1.035	1.00
207_D	211_S	1.033	1.00
226_G	231_T	1.030	1.00
147_E	250_I	1.028	1.00
52_K	68_K	1.023	1.00
290_L	294_V	1.012	1.00
284_Y	288_E	1.008	1.00
291_Y	296_K	1.007	1.00
16_V	19_Q	1.003	1.00
205_A	209_A	1.001	1.00
53_D	284_Y	0.998	1.00
70_L	74_D	0.998	1.00
56_F	291_Y	0.996	1.00
135_K	308_D	0.993	1.00
45_K	49_K	0.988	1.00
74_D	78_A	0.983	1.00
146_K	185_A	0.980	1.00
95_S	99_A	0.976	1.00
140_Q	275_L	0.975	1.00
285_K	307_T	0.971	1.00
14_A	20_S	0.969	1.00
65_D	68_K	0.969	1.00
143_E	273_G	0.966	1.00
226_G	232_V	0.960	1.00
164_T	200_N	0.957	1.00
141_G	182_L	0.952	1.00
39_W	279_P	0.947	1.00
169_D	173_R	0.942	1.00
28_L	85_V	0.935	1.00
209_A	213_L	0.935	1.00
17_M	20_S	0.931	1.00
127_P	289_M	0.928	1.00
85_V	290_L	0.927	1.00
151_R	220_K	0.924	1.00
261_S	265_K	0.923	1.00
159_A	223_L	0.915	1.00
310_V	313_T	0.913	1.00
166_N	197_T	0.911	1.00
13_L	18_S	0.910	1.00
229_D	256_G	0.901	1.00
49_K	284_Y	0.898	1.00
213_L	238_A	0.896	1.00
131_M	278_S	0.894	1.00
47_A	283_G	0.893	1.00
278_S	310_V	0.891	1.00
145_Y	150_K	0.888	1.00
207_D	210_N	0.884	1.00
49_K	53_D	0.880	1.00
204_G	208_A	0.878	1.00
131_M	277_P	0.876	1.00
239_T	251_G	0.874	1.00
133_A	174_R	0.870	1.00
244_F	249_I	0.869	1.00
27_K	79_S	0.869	1.00
83_G	294_V	0.868	1.00
167_E	172_R	0.868	1.00
160_V	224_I	0.868	1.00
236_V	263_L	0.864	1.00
30_F	44_W	0.864	1.00
224_I	249_I	0.862	1.00
151_R	190_K	0.860	1.00
256_G	260_V	0.859	1.00
180_D	183_K	0.853	1.00
276_L	312_I	0.853	1.00
278_S	307_T	0.851	1.00
150_K	187_F	0.845	1.00
150_K	220_K	0.836	1.00
232_V	253_G	0.836	1.00
44_W	60_K	0.834	1.00
43_E	111_V	0.830	1.00
198_K	231_T	0.827	1.00
31_L	72_A	0.826	1.00
289_M	292_N	0.826	1.00
71_N	74_D	0.825	1.00
253_G	274_S	0.823	1.00
163_I	175_T	0.820	1.00
196_P	208_A	0.820	1.00
47_A	58_V	0.818	1.00
100_K	103_G	0.817	1.00
59_I	81_A	0.816	1.00
25_N	82_K	0.814	1.00
129_V	289_M	0.814	1.00
131_M	309_V	0.809	1.00
68_K	72_A	0.805	1.00
287_S	291_Y	0.803	1.00
255_N	277_P	0.802	1.00
12_G	78_A	0.798	1.00
161_M	225_V	0.793	1.00
179_M	189_E	0.789	1.00
42_T	280_D	0.789	1.00
13_L	16_V	0.786	1.00
209_A	238_A	0.784	1.00
135_K	309_V	0.784	1.00
83_G	109_I	0.777	1.00
46_F	284_Y	0.776	1.00
101_A	108_V	0.775	1.00
45_K	48_D	0.773	1.00
213_L	242_Q	0.771	1.00
33_K	40_F	0.770	1.00
229_D	232_V	0.770	1.00
144_L	252_I	0.770	1.00
143_E	311_L	0.769	1.00
256_G	312_I	0.769	1.00
173_R	177_G	0.768	1.00
209_A	212_M	0.765	1.00
237_R	240_E	0.764	1.00
138_E	177_G	0.760	1.00
59_I	79_S	0.760	1.00
162_A	226_G	0.755	1.00
46_F	50_A	0.742	1.00
29_G	84_F	0.739	1.00
24_E	82_K	0.738	1.00
273_G	311_L	0.736	1.00
73_I	84_F	0.733	1.00
48_D	58_V	0.729	1.00
7_A	10_A	0.728	1.00
211_S	214_V	0.726	1.00
132_A	308_D	0.721	1.00
228_N	255_N	0.715	1.00
99_A	102_R	0.711	1.00
110_A	115_F	0.710	1.00
193_Y	196_P	0.710	1.00
215_Q	218_E	0.709	1.00
85_V	111_V	0.706	1.00
97_I	100_K	0.706	1.00
48_D	62_A	0.706	1.00
130_M	306_V	0.705	1.00
182_L	189_E	0.701	1.00
218_E	244_F	0.698	1.00
37_E	230_S	0.697	1.00
12_G	16_V	0.696	1.00
225_V	252_I	0.692	1.00
28_L	287_S	0.687	1.00
313_T	317_F	0.686	1.00
12_G	74_D	0.685	1.00
303_F	306_V	0.685	1.00
77_A	104_Y	0.683	1.00
139_R	275_L	0.681	1.00
112_D	170_T	0.680	1.00
67_E	71_N	0.680	1.00
171_A	200_N	0.678	1.00
109_I	293_W	0.677	1.00
70_L	97_I	0.673	1.00
233_L	263_L	0.672	1.00
102_R	126_V	0.672	1.00
198_K	204_G	0.671	1.00
260_V	265_K	0.670	1.00
200_N	227_M	0.668	1.00
151_R	218_E	0.666	1.00
25_N	57_E	0.665	1.00
11_I	14_A	0.665	1.00
209_A	234_G	0.663	1.00
11_I	17_M	0.661	1.00
161_M	178_S	0.661	1.00
215_Q	219_V	0.660	1.00
112_D	133_A	0.658	1.00
77_A	106_M	0.657	1.00
192_I	195_V	0.656	1.00
237_R	266_A	0.655	1.00
145_Y	182_L	0.652	1.00
273_G	317_F	0.644	1.00
228_N	231_T	0.643	1.00
237_R	264_S	0.642	1.00
220_K	223_L	0.641	1.00
266_A	314_R	0.638	1.00
190_K	194_Q	0.637	1.00
189_E	194_Q	0.635	1.00
236_V	240_E	0.634	1.00
66_G	70_L	0.633	1.00
237_R	241_G	0.632	1.00
28_L	83_G	0.629	1.00
220_K	250_I	0.628	1.00
205_A	208_A	0.627	1.00
83_G	286_S	0.625	1.00
46_F	279_P	0.624	1.00
10_A	13_L	0.620	1.00
174_R	277_P	0.620	1.00
262_E	265_K	0.618	1.00
102_R	108_V	0.617	1.00
110_A	128_L	0.616	1.00
239_T	242_Q	0.613	1.00
202_I	234_G	0.612	1.00
28_L	56_F	0.611	1.00
109_I	129_V	0.609	1.00
159_A	220_K	0.608	1.00
102_R	119_K	0.608	1.00
225_V	254_I	0.608	1.00
144_L	225_V	0.606	1.00
51_G	56_F	0.606	1.00
96_A	99_A	0.605	1.00
40_F	87_C	0.604	1.00
229_D	257_V	0.603	1.00
280_D	283_G	0.602	1.00
133_A	173_R	0.600	1.00
18_S	22_M	0.599	1.00
43_E	279_P	0.599	1.00
84_F	106_M	0.599	1.00
39_W	43_E	0.598	1.00
42_T	279_P	0.597	1.00
28_L	294_V	0.595	1.00
164_T	171_A	0.591	1.00
56_F	82_K	0.590	1.00
219_V	244_F	0.588	1.00
148_M	220_K	0.587	1.00
254_I	277_P	0.586	1.00
45_K	280_D	0.585	1.00
133_A	170_T	0.584	1.00
109_I	290_L	0.584	1.00
127_P	302_K	0.583	1.00
297_D	301_P	0.583	1.00
71_N	75_S	0.581	1.00
171_A	227_M	0.579	1.00
196_P	212_M	0.579	1.00
285_K	304_T	0.579	1.00
240_E	245_K	0.579	1.00
114_Q	128_L	0.573	1.00
189_E	193_Y	0.573	1.00
61_I	75_S	0.573	1.00
151_R	217_P	0.572	1.00
138_E	141_G	0.571	1.00
159_A	178_S	0.571	1.00
140_Q	223_L	0.570	1.00
110_A	126_V	0.569	1.00
118_A	126_V	0.568	1.00
203_P	206_F	0.568	1.00
226_G	253_G	0.567	1.00
282_H	307_T	0.565	1.00
100_K	104_Y	0.562	1.00
233_L	257_V	0.561	1.00
261_S	266_A	0.557	1.00
112_D	282_H	0.557	1.00
143_E	252_I	0.557	1.00
27_K	82_K	0.557	1.00
16_V	20_S	0.555	1.00
289_M	293_W	0.554	1.00
260_V	263_L	0.554	1.00
139_R	143_E	0.553	1.00
56_F	294_V	0.553	1.00
200_N	231_T	0.551	1.00
76_L	81_A	0.550	1.00
109_I	289_M	0.550	1.00
208_A	212_M	0.549	1.00
292_N	296_K	0.549	1.00
130_M	133_A	0.547	1.00
206_F	234_G	0.547	1.00
132_A	306_V	0.543	1.00
297_D	300_P	0.543	1.00
263_L	266_A	0.542	1.00
72_A	75_S	0.541	1.00
187_F	190_K	0.539	1.00
212_M	216_H	0.539	1.00
19_Q	22_M	0.539	1.00
131_M	136_I	0.536	1.00
108_V	126_V	0.536	1.00
51_G	291_Y	0.535	1.00
77_A	100_K	0.532	1.00
206_F	209_A	0.531	1.00
26_L	294_V	0.529	1.00
75_S	78_A	0.529	1.00
174_R	255_N	0.528	1.00
289_M	304_T	0.527	1.00
63_V	69_T	0.526	1.00
223_L	250_I	0.525	1.00
202_I	258_D	0.524	1.00
219_V	224_I	0.524	1.00
77_A	80_G	0.521	1.00
38_P	230_S	0.521	1.00
109_I	286_S	0.517	1.00
75_S	79_S	0.516	1.00
81_A	84_F	0.514	1.00
63_V	72_A	0.513	1.00
11_I	16_V	0.513	1.00
232_V	251_G	0.513	1.00
235_G	239_T	0.511	1.00
131_M	254_I	0.509	1.00
194_Q	215_Q	0.507	1.00
196_P	215_Q	0.506	1.00
236_V	272_Y	0.505	1.00
275_L	309_V	0.504	1.00
37_E	40_F	0.502	1.00
229_D	259_A	0.502	1.00
135_K	142_Q	0.500	1.00
107_K	294_V	0.500	1.00

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
3huuA	2	0.7994	100	0.19	Contact Map
2iksA	2	0.8298	100	0.194	Contact Map
2hsgA	1	0.8845	100	0.202	Contact Map
3e3mA	2	0.8116	100	0.203	Contact Map
3brqA	2	0.8298	100	0.204	Contact Map
3dbiA	2	0.8359	100	0.206	Contact Map
1qpzA	2	0.9179	100	0.207	Contact Map
3h5oA	2	0.8146	100	0.212	Contact Map
4o5aA	2	0.8116	100	0.212	Contact Map
2o20A	2	0.8298	100	0.216	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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