ALSB - ECOLI - GREMLIN Contacts

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ALSB - D-allose-binding periplasmic protein

UniProt:	P39265	Sequences: MNKYLKYFSGTLVGLMLSTSAFAAAEYAVVLKTLSNPFWVDMKKGIEDEAKTLGVSVDIFASPSEGDFQSQLQLFEDLSNKNYKGIAFAPLSSVNLVMPVARAWKKGIYLVNLDEKIDMDNLKKAGGNVEAFVTTDNVAVGAKGASFIIDKLGAEGGEVAIIEGKAGNASGEARRNGATEAFKKASQIKLVASQPADWDRIKALDVATNVLQRNPNIKAIYCANDTMAMGVAQAVANAGKTGKVLVVGTDGIPEARKMVEAGQMTATVAQNPADIGATGLKLMVDAEKSGKVIPLDKAPEFKLVDSILVTQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12458
Length:	311 (282)
Sequences:	38359 (28602)
Seq/√Len:	1703.2

ECOLI - ALSB XYLF GALS YTFQ RBSB IDNR LACI CRA GALR CYTR MALI PURR ASCG GNTR RBSR LSRB YCJW ARAF YPHF TORT DGAL EBGR TRER XYLR
BACSU - RBSR CCPA KDGR DEGA NTDR RBSB MSMR YKVZ GANR ARAR YVDE EXUR 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
138_V	180_E	3.473	1.00
154_A	218_K	3.356	1.00
85_G	283_M	2.787	1.00
154_A	245_L	2.697	1.00
144_G	247_V	2.694	1.00
175_R	179_T	2.673	1.00
251_G	269_A	2.629	1.00
131_A	286_A	2.527	1.00
142_A	184_K	2.356	1.00
204_L	237_N	2.311	1.00
49_E	52_T	2.287	1.00
208_T	238_A	2.249	1.00
149_I	185_A	2.202	1.00
146_S	181_A	2.196	1.00
142_A	181_A	2.158	1.00
49_E	281_K	2.154	1.00
142_A	180_E	2.144	1.00
208_T	234_A	2.143	1.00
139_A	143_K	2.094	1.00
278_T	281_K	2.083	1.00
50_A	280_L	2.029	1.00
49_E	277_A	1.994	1.00
140_V	249_T	1.992	1.00
138_V	176_N	1.986	1.00
141_G	145_A	1.981	1.00
148_I	219_A	1.975	1.00
45_G	276_G	1.927	1.00
203_A	230_G	1.920	1.00
190_L	193_S	1.906	1.00
146_S	150_D	1.858	1.00
145_A	178_A	1.851	1.00
269_A	302_K	1.809	1.00
141_G	221_Y	1.808	1.00
28_A	83_Y	1.808	1.00
212_Q	238_A	1.791	1.00
160_A	217_I	1.790	1.00
235_V	244_V	1.788	1.00
48_D	273_A	1.757	1.00
222_C	231_V	1.750	1.00
142_A	146_S	1.746	1.00
161_I	223_A	1.746	1.00
204_L	234_A	1.741	1.00
207_A	231_V	1.710	1.00
271_N	274_D	1.701	1.00
113_L	279_G	1.694	1.00
146_S	185_A	1.685	1.00
49_E	53_L	1.668	1.00
278_T	297_K	1.636	1.00
143_K	301_F	1.633	1.00
234_A	238_A	1.625	1.00
45_G	273_A	1.615	1.00
240_K	243_K	1.609	1.00
264_M	307_I	1.603	1.00
139_A	142_A	1.603	1.00
176_N	180_E	1.596	1.00
158_E	216_N	1.591	1.00
147_F	150_D	1.559	1.00
260_E	263_Q	1.558	1.00
147_F	305_D	1.536	1.00
149_I	181_A	1.534	1.00
53_L	284_V	1.530	1.00
247_V	266_A	1.505	1.00
234_A	237_N	1.504	1.00
187_Q	192_A	1.503	1.00
158_E	189_K	1.491	1.00
274_D	278_T	1.487	1.00
173_A	176_N	1.480	1.00
179_T	183_K	1.462	1.00
204_L	233_Q	1.458	1.00
158_E	218_K	1.438	1.00
136_D	139_A	1.429	1.00
236_A	263_Q	1.415	1.00
49_E	280_L	1.405	1.00
274_D	277_A	1.400	1.00
235_V	240_K	1.389	1.00
251_G	306_S	1.385	1.00
25_A	84_K	1.382	1.00
197_D	202_K	1.372	1.00
204_L	208_T	1.365	1.00
236_A	260_E	1.363	1.00
140_V	301_F	1.362	1.00
141_G	177_G	1.356	1.00
181_A	184_K	1.352	1.00
145_A	149_I	1.339	1.00
160_A	210_V	1.335	1.00
208_T	237_N	1.325	1.00
145_A	181_A	1.321	1.00
194_Q	209_N	1.319	1.00
145_A	177_G	1.317	1.00
87_A	279_G	1.298	1.00
207_A	235_V	1.296	1.00
138_V	142_A	1.293	1.00
50_A	57_V	1.292	1.00
177_G	181_A	1.280	1.00
281_K	285_D	1.277	1.00
25_A	55_V	1.277	1.00
208_T	212_Q	1.267	1.00
28_A	78_L	1.263	1.00
143_K	146_S	1.260	1.00
76_E	102_R	1.257	1.00
60_F	74_L	1.253	1.00
207_A	220_I	1.250	1.00
27_Y	50_A	1.246	1.00
101_A	105_K	1.244	1.00
60_F	78_L	1.219	1.00
46_I	280_L	1.211	1.00
154_A	219_A	1.206	1.00
189_K	192_A	1.202	1.00
273_A	277_A	1.194	1.00
26_E	56_S	1.182	1.00
178_A	182_F	1.173	1.00
29_V	46_I	1.173	1.00
232_A	246_V	1.171	1.00
230_G	234_A	1.165	1.00
26_E	58_D	1.157	1.00
157_G	218_K	1.145	1.00
47_E	51_K	1.142	1.00
138_V	177_G	1.140	1.00
161_I	175_R	1.140	1.00
138_V	173_A	1.134	1.00
209_N	213_R	1.131	1.00
199_D	202_K	1.127	1.00
53_L	281_K	1.126	1.00
201_I	205_D	1.121	1.00
13_V	16_M	1.119	1.00
158_E	191_V	1.113	1.00
206_V	209_N	1.108	1.00
29_V	57_V	1.093	1.00
46_I	87_A	1.091	1.00
214_N	217_I	1.090	1.00
180_E	184_K	1.088	1.00
285_D	291_K	1.087	1.00
159_V	182_F	1.083	1.00
15_L	18_S	1.081	1.00
285_D	290_G	1.078	1.00
146_S	184_K	1.078	1.00
144_G	221_Y	1.074	1.00
178_A	221_Y	1.069	1.00
162_I	231_V	1.068	1.00
278_T	282_L	1.068	1.00
200_R	233_Q	1.066	1.00
220_I	231_V	1.063	1.00
276_G	280_L	1.060	1.00
225_D	267_T	1.054	1.00
172_E	176_N	1.053	1.00
282_L	297_K	1.050	1.00
158_E	215_P	1.049	1.00
176_N	179_T	1.040	1.00
147_F	266_A	1.035	1.00
222_C	227_M	1.032	1.00
51_K	70_S	1.031	1.00
225_D	248_G	1.031	1.00
205_D	209_N	1.029	1.00
277_A	281_K	1.017	1.00
55_V	284_V	1.015	1.00
202_K	205_D	1.010	1.00
181_A	185_A	1.007	1.00
43_K	47_E	1.004	1.00
203_A	207_A	1.001	1.00
70_S	73_Q	0.992	1.00
150_D	185_A	0.981	1.00
72_L	76_E	0.981	1.00
283_M	287_E	0.980	1.00
13_V	19_T	0.977	1.00
169_A	173_A	0.976	1.00
76_E	80_N	0.976	1.00
179_T	190_L	0.973	1.00
159_V	219_A	0.971	1.00
97_V	101_A	0.970	1.00
222_C	228_A	0.965	1.00
16_M	19_T	0.964	1.00
166_A	195_P	0.964	1.00
12_L	17_L	0.963	1.00
139_A	300_E	0.962	1.00
144_G	268_V	0.960	1.00
278_T	299_P	0.958	1.00
145_A	182_F	0.956	1.00
52_T	277_A	0.954	1.00
67_D	70_S	0.942	1.00
131_A	282_L	0.941	1.00
302_K	305_D	0.936	1.00
44_K	48_D	0.936	1.00
207_A	211_L	0.934	1.00
149_I	157_G	0.926	1.00
164_G	198_W	0.925	1.00
87_A	283_M	0.914	1.00
188_I	192_A	0.913	1.00
225_D	251_G	0.913	1.00
194_Q	206_V	0.905	1.00
271_N	302_K	0.897	1.00
38_F	272_P	0.886	1.00
240_K	244_V	0.886	1.00
220_I	244_V	0.880	1.00
48_D	277_A	0.878	1.00
46_I	276_G	0.876	1.00
14_G	17_L	0.873	1.00
132_F	296_D	0.873	1.00
137_N	174_R	0.872	1.00
205_D	208_T	0.870	1.00
27_Y	87_A	0.867	1.00
269_A	304_V	0.865	1.00
136_D	298_A	0.864	1.00
160_A	220_I	0.862	1.00
167_G	172_E	0.860	1.00
48_D	52_T	0.860	1.00
282_L	285_D	0.859	1.00
43_K	59_I	0.857	1.00
211_L	234_A	0.857	1.00
135_T	271_N	0.854	1.00
228_A	248_G	0.851	1.00
163_E	175_R	0.849	1.00
235_V	246_V	0.847	1.00
42_M	113_L	0.847	1.00
73_Q	76_E	0.844	1.00
202_K	206_V	0.841	1.00
280_L	284_V	0.827	1.00
85_G	287_E	0.825	1.00
135_T	270_Q	0.825	1.00
26_E	81_K	0.824	1.00
180_E	183_K	0.824	1.00
58_D	83_Y	0.822	1.00
187_Q	193_S	0.812	1.00
133_V	282_L	0.809	1.00
134_T	298_A	0.808	1.00
29_V	43_K	0.808	1.00
248_G	267_T	0.805	1.00
271_N	299_P	0.803	1.00
196_A	227_M	0.799	1.00
134_T	296_D	0.795	1.00
148_I	247_V	0.794	1.00
65_E	70_S	0.791	1.00
135_T	301_F	0.787	1.00
58_D	81_K	0.787	1.00
211_L	238_A	0.787	1.00
147_F	303_L	0.787	1.00
102_R	105_K	0.783	1.00
11_T	80_N	0.783	1.00
161_I	221_Y	0.780	1.00
46_I	57_V	0.779	1.00
139_A	301_F	0.776	1.00
116_K	296_D	0.774	1.00
10_G	16_M	0.774	1.00
250_D	270_Q	0.770	1.00
44_K	47_E	0.768	1.00
70_S	74_L	0.766	1.00
45_G	277_A	0.765	1.00
207_A	234_A	0.765	1.00
45_G	49_E	0.764	1.00
131_A	295_L	0.761	1.00
24_A	84_K	0.761	1.00
173_A	177_G	0.761	1.00
30_V	74_L	0.755	1.00
216_N	240_K	0.755	1.00
32_K	39_W	0.755	1.00
149_I	188_I	0.754	1.00
41_D	273_A	0.753	1.00
136_D	300_E	0.751	1.00
233_Q	236_A	0.746	1.00
162_I	222_C	0.741	1.00
187_Q	190_L	0.740	1.00
85_G	111_V	0.739	1.00
104_W	130_E	0.738	1.00
28_A	86_I	0.736	1.00
207_A	210_V	0.736	1.00
251_G	304_V	0.736	1.00
218_K	245_L	0.729	1.00
87_A	113_L	0.724	1.00
209_N	212_Q	0.715	1.00
225_D	228_A	0.713	1.00
142_A	177_G	0.710	1.00
47_E	57_V	0.705	1.00
143_K	268_V	0.703	1.00
27_Y	280_L	0.700	1.00
11_T	15_L	0.688	1.00
99_P	102_R	0.687	1.00
198_W	223_A	0.684	1.00
266_A	303_L	0.680	1.00
101_A	104_W	0.679	1.00
251_G	255_A	0.678	1.00
188_I	193_S	0.678	1.00
79_S	106_K	0.676	1.00
112_N	117_I	0.676	1.00
23_A	84_K	0.674	1.00
260_E	264_M	0.674	1.00
224_N	250_D	0.669	1.00
6_K	9_S	0.669	1.00
111_V	286_A	0.669	1.00
232_A	259_V	0.668	1.00
103_A	110_L	0.667	1.00
171_G	198_W	0.664	1.00
114_D	170_S	0.663	1.00
213_R	217_I	0.662	1.00
36_N	226_T	0.660	1.00
203_A	206_V	0.660	1.00
221_Y	247_V	0.660	1.00
11_T	76_E	0.658	1.00
72_L	99_P	0.657	1.00
229_M	254_E	0.656	1.00
161_I	178_A	0.652	1.00
149_I	182_F	0.649	1.00
69_Q	73_Q	0.647	1.00
255_A	267_T	0.646	1.00
213_R	216_N	0.646	1.00
258_M	263_Q	0.645	1.00
233_Q	237_N	0.644	1.00
200_R	254_E	0.644	1.00
104_W	129_V	0.642	1.00
196_A	202_K	0.642	1.00
85_G	279_G	0.641	1.00
79_S	108_I	0.640	1.00
148_I	221_Y	0.635	1.00
264_M	306_S	0.634	1.00
233_Q	264_M	0.633	1.00
159_V	218_K	0.629	1.00
112_N	132_F	0.626	1.00
221_Y	249_T	0.626	1.00
75_F	86_I	0.626	1.00
164_G	171_G	0.625	1.00
68_F	72_L	0.622	1.00
114_D	137_N	0.622	1.00
224_N	227_M	0.622	1.00
235_V	238_A	0.620	1.00
232_A	236_A	0.617	1.00
273_A	276_G	0.614	1.00
41_D	272_P	0.614	1.00
112_N	130_E	0.612	1.00
182_F	190_L	0.610	1.00
55_V	84_K	0.609	1.00
143_K	147_F	0.608	1.00
225_D	252_I	0.605	1.00
50_A	55_V	0.603	1.00
207_A	230_G	0.599	1.00
111_V	283_M	0.598	1.00
137_N	170_S	0.597	1.00
147_F	247_V	0.595	1.00
86_I	108_I	0.594	1.00
289_S	292_V	0.593	1.00
154_A	157_G	0.592	1.00
39_W	89_A	0.589	1.00
119_M	128_N	0.589	1.00
104_W	110_L	0.589	1.00
42_M	272_P	0.586	1.00
55_V	287_E	0.583	1.00
194_Q	213_R	0.583	1.00
200_R	230_G	0.582	1.00
17_L	21_A	0.580	1.00
137_N	173_A	0.580	1.00
111_V	133_V	0.578	1.00
201_I	204_L	0.577	1.00
73_Q	77_D	0.576	1.00
116_K	132_F	0.576	1.00
222_C	248_G	0.572	1.00
27_Y	85_G	0.572	1.00
38_F	42_M	0.572	1.00
60_F	77_D	0.571	1.00
98_M	101_A	0.571	1.00
159_V	178_A	0.570	1.00
110_L	130_E	0.566	1.00
45_G	272_P	0.566	1.00
27_Y	55_V	0.566	1.00
198_W	227_M	0.565	1.00
236_A	241_T	0.563	1.00
206_V	210_V	0.561	1.00
174_R	270_Q	0.561	1.00
131_A	294_P	0.560	1.00
27_Y	287_E	0.559	1.00
257_K	260_E	0.558	1.00
144_G	219_A	0.557	1.00
158_E	217_I	0.557	1.00
145_A	185_A	0.556	1.00
134_T	137_N	0.556	1.00
44_K	273_A	0.555	1.00
114_D	275_I	0.555	1.00
109_Y	287_E	0.554	1.00
24_A	56_S	0.553	1.00
77_D	80_N	0.553	1.00
249_T	270_Q	0.550	1.00
78_L	83_Y	0.546	1.00
168_N	171_G	0.546	1.00
142_A	145_A	0.545	1.00
111_V	282_L	0.545	1.00
111_V	279_G	0.545	1.00
74_L	77_D	0.545	1.00
18_S	21_A	0.541	1.00
47_E	63_P	0.540	1.00
282_L	286_A	0.539	1.00
229_M	252_I	0.537	1.00
102_R	106_K	0.536	1.00
171_G	223_A	0.535	1.00
233_Q	260_E	0.533	1.00
10_G	14_G	0.531	1.00
189_K	193_S	0.531	1.00
158_E	214_N	0.531	1.00
50_A	284_V	0.530	1.00
194_Q	210_V	0.529	1.00
98_M	102_R	0.529	1.00
69_Q	72_L	0.528	1.00
268_V	301_F	0.527	1.00
219_A	245_L	0.525	1.00
14_G	18_S	0.521	1.00
211_L	235_V	0.520	1.00
285_D	289_S	0.520	1.00
204_L	230_G	0.519	1.00
204_L	207_A	0.519	1.00
15_L	19_T	0.518	1.00
232_A	265_T	0.514	1.00
231_V	235_V	0.514	1.00
255_A	264_M	0.514	1.00
225_D	255_A	0.513	1.00
72_L	102_R	0.512	1.00
285_D	295_L	0.510	1.00
26_E	84_K	0.509	1.00
298_A	301_F	0.508	1.00
182_F	188_I	0.506	1.00
275_I	299_P	0.506	1.00
79_S	82_N	0.504	1.00
135_T	140_V	0.503	1.00
37_P	226_T	0.503	1.00
178_A	190_L	0.503	1.00
207_A	222_C	0.502	1.00
278_T	285_D	0.501	1.00
162_I	206_V	0.500	1.00
200_R	226_T	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
2hsgA	1	0.926	100	0.126	Contact Map
3huuA	2	0.8424	100	0.135	Contact Map
1qpzA	2	0.9389	100	0.136	Contact Map
3dbiA	2	0.8714	100	0.14	Contact Map
2iksA	2	0.8746	100	0.14	Contact Map
4o5aA	2	0.8521	100	0.141	Contact Map
2o20A	2	0.8714	100	0.143	Contact Map
3bilA	2	0.8167	100	0.144	Contact Map
3e3mA	2	0.8457	100	0.149	Contact Map
3kjxA	2	0.9389	100	0.151	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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