YEJB - ECOLI - GREMLIN Contacts

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YEJB - Inner membrane ABC transporter permease protein YejB

UniProt:	P0AFU0	Sequences: MGAYLIRRLLLVIPTLWAIITINFFIVQIAPGGPVDQAIAAIEFGNAGVLPGAGGEGVRASHAQTGVGNISDSNYRGGRGLDPEVIAEITHRYGFDKPIHERYFKMLWDYIRFDFGDSLFRSASVLTLIKDSLPVSITLGLWSTLIIYLVSIPLGIRKAVYNGSRFDVWSSAFIIIGYAIPAFLFAILLIVFFAGGSYFDLFPLRGLVSANFDSLPWYQKITDYLWHITLPVLATVIGGFAALTMLTKNSFLDEVRKQYVVTARAKGVSEKNILWKHVFRNAMLLVIAGFPATFISMFFTGSLLIEVMFSLNGLGLLGYEATVSRDYPVMFGTLYIFTLIGLLLNIVSDISYTLVDPRIDFEGR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12038
Length:	364 (278)
Sequences:	9514 (6020)
Seq/√Len:	361.1

ECOLI - YEJB DPPB DDPB NIKB YEJE GSIC OPPB SAPB DPPC SAPC DDPC GSID NIKC OPPC
BACSU - APPB OPPB DPPB DPPC APPC OPPC
HALSA - Q9HMX0 Q9HMI2 Q9HMW3 Q9HMW2 Q9HMI1 Q9HMX1
SULSO - Q97YQ0 Q97VF8 Q97UH1 Q97UG4 Q97VK6 Q97YP1 Q97YP9 Q97YP2 Q97VK7 Q97UG3 Q97UH2 Q97VF6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
97_K	101_E	3.609	1.00
91_H	96_D	3.390	1.00
97_K	105_K	3.300	1.00
104_F	108_W	3.152	1.00
83_P	87_A	2.941	1.00
108_W	112_R	2.940	1.00
251_F	278_V	2.644	1.00
264_R	270_E	2.618	1.00
272_N	276_K	2.519	1.00
100_H	104_F	2.494	1.00
202_F	226_W	2.368	1.00
316_L	320_E	2.357	1.00
260_V	278_V	2.321	1.00
128_L	317_L	2.320	1.00
142_W	232_V	2.298	1.00
135_V	311_L	2.246	1.00
287_I	355_V	2.215	1.00
123_A	127_T	2.202	1.00
146_I	236_V	2.159	1.00
124_S	127_T	2.150	1.00
194_A	204_L	2.137	1.00
222_T	226_W	2.128	1.00
88_E	92_R	2.091	1.00
202_F	229_T	2.077	1.00
101_E	105_K	2.020	1.00
87_A	91_H	2.010	1.00
87_A	90_T	1.973	1.00
109_D	114_D	1.948	1.00
86_I	90_T	1.944	1.00
262_T	266_K	1.933	1.00
291_P	348_S	1.928	1.00
85_V	88_E	1.903	1.00
121_R	128_L	1.879	1.00
271_K	275_W	1.874	1.00
161_Y	164_S	1.859	1.00
209_S	223_D	1.853	1.00
255_V	278_V	1.810	1.00
165_R	169_W	1.775	1.00
254_E	259_Y	1.775	1.00
269_S	272_N	1.769	1.00
154_L	170_S	1.765	1.00
254_E	257_K	1.764	1.00
321_A	329_V	1.745	1.00
160_V	274_L	1.740	1.00
351_S	354_L	1.721	1.00
288_A	352_Y	1.704	1.00
157_R	161_Y	1.700	1.00
105_K	108_W	1.673	1.00
149_L	153_P	1.672	1.00
166_F	170_S	1.655	1.00
266_K	277_H	1.654	1.00
157_R	166_F	1.635	1.00
125_V	332_G	1.595	1.00
223_D	227_H	1.588	1.00
110_Y	115_F	1.574	1.00
138_T	224_Y	1.573	1.00
82_D	85_V	1.542	1.00
207_L	311_L	1.525	1.00
232_V	236_V	1.522	1.00
192_F	198_Y	1.474	1.00
188_L	192_F	1.441	1.00
192_F	199_F	1.436	1.00
148_Y	290_F	1.431	1.00
150_V	153_P	1.424	1.00
161_Y	166_F	1.422	1.00
159_A	251_F	1.416	1.00
189_L	234_A	1.404	1.00
135_V	207_L	1.402	1.00
103_Y	107_L	1.400	1.00
260_V	273_I	1.387	1.00
167_D	248_K	1.377	1.00
128_L	329_V	1.377	1.00
98_P	101_E	1.376	1.00
89_I	92_R	1.376	1.00
105_K	109_D	1.376	1.00
229_T	233_L	1.362	1.00
101_E	104_F	1.362	1.00
156_I	251_F	1.349	1.00
284_L	352_Y	1.345	1.00
236_V	240_F	1.334	1.00
126_L	130_K	1.334	1.00
184_L	188_L	1.332	1.00
254_E	260_V	1.325	1.00
225_L	229_T	1.321	1.00
259_Y	281_N	1.315	1.00
191_V	198_Y	1.314	1.00
318_G	333_T	1.312	1.00
350_I	354_L	1.307	1.00
220_K	223_D	1.301	1.00
159_A	255_V	1.294	1.00
123_A	131_D	1.293	1.00
89_I	93_Y	1.285	1.00
115_F	126_L	1.280	1.00
138_T	207_L	1.275	1.00
115_F	332_G	1.274	1.00
147_I	239_G	1.244	1.00
268_V	272_N	1.241	1.00
223_D	226_W	1.241	1.00
193_F	199_F	1.230	1.00
254_E	282_A	1.226	1.00
234_A	238_G	1.221	1.00
258_Q	261_V	1.215	1.00
317_L	329_V	1.210	1.00
159_A	252_L	1.195	1.00
302_S	305_I	1.191	1.00
140_G	298_F	1.174	1.00
217_W	221_I	1.165	1.00
127_T	130_K	1.155	1.00
319_Y	323_V	1.154	1.00
347_V	351_S	1.144	1.00
130_K	134_P	1.143	1.00
117_D	124_S	1.142	1.00
270_E	273_I	1.142	1.00
155_G	159_A	1.131	1.00
247_T	286_V	1.131	1.00
268_V	273_I	1.128	1.00
217_W	220_K	1.125	1.00
144_T	290_F	1.124	1.00
150_V	240_F	1.123	1.00
123_A	128_L	1.118	1.00
189_L	230_L	1.113	1.00
163_G	167_D	1.111	1.00
151_S	247_T	1.101	1.00
135_V	138_T	1.097	1.00
151_S	243_L	1.087	1.00
118_S	326_D	1.084	1.00
158_K	170_S	1.083	1.00
287_I	351_S	1.080	1.00
220_K	224_Y	1.071	1.00
180_I	185_F	1.069	1.00
127_T	131_D	1.065	1.00
78_G	81_L	1.058	1.00
207_L	224_Y	1.048	1.00
186_A	308_M	1.043	1.00
108_W	111_I	1.040	1.00
333_T	337_F	1.039	1.00
177_G	241_A	1.038	1.00
218_Y	222_T	1.036	1.00
222_T	225_L	1.035	1.00
119_L	328_P	1.032	1.00
160_V	270_E	1.031	1.00
110_Y	335_Y	1.027	1.00
182_A	305_I	1.027	1.00
146_I	232_V	1.023	1.00
155_G	247_T	1.019	1.00
88_E	91_H	1.017	1.00
162_N	256_R	1.017	1.00
353_T	359_I	1.016	1.00
132_S	317_L	1.016	1.00
170_S	244_T	1.011	1.00
91_H	97_K	1.010	1.00
259_Y	263_A	1.003	1.00
193_F	201_L	0.999	1.00
77_G	81_L	0.996	1.00
97_K	100_H	0.994	1.00
248_K	252_L	0.980	1.00
120_F	324_S	0.978	1.00
131_D	134_P	0.978	1.00
344_L	348_S	0.968	1.00
94_G	105_K	0.967	1.00
247_T	251_F	0.965	1.00
264_R	273_I	0.961	1.00
186_A	234_A	0.958	1.00
208_V	220_K	0.956	1.00
163_G	168_V	0.947	1.00
154_L	244_T	0.940	1.00
104_F	107_L	0.939	1.00
143_S	236_V	0.933	1.00
174_I	244_T	0.931	1.00
169_W	173_F	0.930	1.00
282_A	285_L	0.930	1.00
141_L	295_I	0.929	1.00
317_L	321_A	0.923	1.00
139_L	232_V	0.921	1.00
254_E	278_V	0.914	1.00
221_I	225_L	0.911	1.00
320_E	324_S	0.909	1.00
94_G	97_K	0.908	1.00
153_P	156_I	0.908	1.00
156_I	275_W	0.902	1.00
296_S	341_G	0.892	1.00
87_A	96_D	0.892	1.00
270_E	274_L	0.886	1.00
263_A	273_I	0.880	1.00
165_R	168_V	0.874	1.00
141_L	145_L	0.872	1.00
193_F	202_F	0.870	1.00
136_S	140_G	0.867	1.00
128_L	131_D	0.866	1.00
106_M	110_Y	0.866	1.00
221_I	224_Y	0.865	1.00
182_A	238_G	0.865	1.00
153_P	157_R	0.864	1.00
173_F	177_G	0.864	1.00
84_E	88_E	0.864	1.00
307_V	316_L	0.862	1.00
330_M	334_L	0.861	1.00
152_I	247_T	0.856	1.00
291_P	344_L	0.851	1.00
148_Y	153_P	0.835	1.00
206_G	227_H	0.834	1.00
208_V	223_D	0.834	1.00
134_P	137_I	0.833	1.00
167_D	252_L	0.831	1.00
83_P	86_I	0.830	1.00
77_G	89_I	0.826	1.00
228_I	232_V	0.823	1.00
107_L	111_I	0.822	1.00
121_R	329_V	0.820	1.00
138_T	142_W	0.818	1.00
117_D	122_S	0.817	1.00
272_N	275_W	0.814	1.00
103_Y	106_M	0.814	1.00
229_T	232_V	0.809	1.00
235_T	302_S	0.806	1.00
155_G	251_F	0.804	1.00
202_F	230_L	0.803	1.00
350_I	353_T	0.799	1.00
142_W	311_L	0.797	1.00
138_T	228_I	0.796	1.00
295_I	344_L	0.793	1.00
195_G	198_Y	0.792	1.00
331_F	334_L	0.788	1.00
216_P	219_Q	0.787	1.00
184_L	187_I	0.784	1.00
143_S	235_T	0.783	1.00
166_F	169_W	0.782	1.00
246_L	289_G	0.780	1.00
263_A	268_V	0.779	1.00
234_A	305_I	0.778	1.00
189_L	233_L	0.777	1.00
109_D	112_R	0.774	1.00
320_E	323_V	0.774	1.00
139_L	311_L	0.770	1.00
162_N	252_L	0.767	1.00
151_S	244_T	0.765	1.00
182_A	237_I	0.765	1.00
208_V	224_Y	0.762	1.00
273_I	278_V	0.761	1.00
133_L	137_I	0.761	1.00
303_L	307_V	0.755	1.00
84_E	87_A	0.754	1.00
151_S	155_G	0.753	1.00
312_N	316_L	0.751	1.00
233_L	236_V	0.750	1.00
247_T	279_F	0.750	1.00
171_S	244_T	0.750	1.00
191_V	195_G	0.748	1.00
169_W	172_A	0.746	1.00
198_Y	201_L	0.746	1.00
142_W	229_T	0.745	1.00
160_V	275_W	0.745	1.00
250_S	282_A	0.741	1.00
129_I	332_G	0.739	1.00
185_F	237_I	0.737	1.00
321_A	330_M	0.735	1.00
317_L	333_T	0.734	1.00
150_V	236_V	0.734	1.00
343_L	347_V	0.733	1.00
240_F	244_T	0.732	1.00
226_W	229_T	0.723	1.00
275_W	278_V	0.719	0.99
205_R	310_S	0.716	0.99
138_T	311_L	0.710	0.99
139_L	228_I	0.708	0.99
215_L	219_Q	0.704	0.99
156_I	279_F	0.703	0.99
143_S	147_I	0.703	0.99
332_G	336_I	0.701	0.99
199_F	202_F	0.699	0.99
322_T	330_M	0.698	0.99
303_L	319_Y	0.696	0.99
339_L	343_L	0.695	0.99
283_M	355_V	0.694	0.99
142_W	228_I	0.692	0.99
194_A	200_D	0.690	0.99
85_V	89_I	0.689	0.99
101_E	108_W	0.688	0.99
307_V	319_Y	0.687	0.99
353_T	361_F	0.686	0.99
129_I	333_T	0.686	0.99
107_L	110_Y	0.683	0.99
177_G	237_I	0.682	0.99
190_I	204_L	0.681	0.99
108_W	113_F	0.680	0.99
247_T	250_S	0.677	0.99
147_I	236_V	0.671	0.99
215_L	220_K	0.670	0.99
263_A	266_K	0.668	0.99
140_G	144_T	0.665	0.99
170_S	174_I	0.664	0.99
287_I	348_S	0.662	0.99
345_N	348_S	0.662	0.99
193_F	230_L	0.660	0.99
172_A	176_I	0.658	0.99
98_P	102_R	0.657	0.99
81_L	86_I	0.656	0.99
191_V	194_A	0.654	0.99
296_S	344_L	0.654	0.99
307_V	320_E	0.653	0.99
182_A	304_L	0.652	0.99
144_T	295_I	0.648	0.99
130_K	133_L	0.644	0.99
250_S	286_V	0.643	0.99
99_I	102_R	0.642	0.99
129_I	314_L	0.638	0.99
146_I	150_V	0.637	0.99
239_G	242_A	0.627	0.99
144_T	148_Y	0.616	0.98
102_R	327_Y	0.614	0.98
148_Y	243_L	0.614	0.98
243_L	294_F	0.611	0.98
341_G	344_L	0.610	0.98
136_S	302_S	0.610	0.98
146_I	233_L	0.608	0.98
306_E	313_G	0.608	0.98
207_L	210_A	0.607	0.98
235_T	305_I	0.606	0.98
352_Y	359_I	0.605	0.98
90_T	96_D	0.605	0.98
203_P	206_G	0.602	0.98
154_L	240_F	0.602	0.98
243_L	289_G	0.600	0.98
251_F	279_F	0.598	0.98
218_Y	221_I	0.595	0.98
174_I	241_A	0.594	0.98
113_F	335_Y	0.591	0.98
158_K	167_D	0.591	0.98
239_G	243_L	0.591	0.98
318_G	337_F	0.589	0.98
319_Y	322_T	0.588	0.98
208_V	219_Q	0.586	0.98
281_N	284_L	0.585	0.98
246_L	250_S	0.579	0.98
138_T	141_L	0.577	0.98
167_D	171_S	0.573	0.97
346_I	350_I	0.572	0.97
325_R	331_F	0.570	0.97
190_I	194_A	0.570	0.97
299_F	337_F	0.569	0.97
134_P	138_T	0.569	0.97
303_L	315_G	0.569	0.97
182_A	234_A	0.568	0.97
245_M	249_N	0.567	0.97
216_P	221_I	0.567	0.97
230_L	234_A	0.567	0.97
329_V	333_T	0.566	0.97
327_Y	331_F	0.565	0.97
140_G	302_S	0.563	0.97
162_N	168_V	0.562	0.97
152_I	286_V	0.562	0.97
284_L	359_I	0.562	0.97
161_Y	270_E	0.557	0.97
283_M	286_V	0.556	0.97
224_Y	227_H	0.555	0.97
296_S	340_I	0.555	0.97
219_Q	222_T	0.554	0.97
268_V	277_H	0.551	0.97
247_T	282_A	0.549	0.97
159_A	167_D	0.549	0.97
275_W	280_R	0.548	0.97
184_L	308_M	0.548	0.97
92_R	122_S	0.547	0.97
90_T	95_F	0.544	0.97
209_S	224_Y	0.541	0.96
162_N	167_D	0.540	0.96
274_L	278_V	0.539	0.96
137_I	141_L	0.538	0.96
277_H	281_N	0.538	0.96
225_L	228_I	0.537	0.96
303_L	318_G	0.537	0.96
208_V	227_H	0.537	0.96
357_P	360_D	0.537	0.96
314_L	337_F	0.536	0.96
216_P	220_K	0.534	0.96
224_Y	228_I	0.531	0.96
209_S	218_Y	0.530	0.96
340_I	344_L	0.529	0.96
275_W	279_F	0.529	0.96
132_S	316_L	0.529	0.96
203_P	226_W	0.529	0.96
318_G	334_L	0.528	0.96
328_P	331_F	0.528	0.96
300_T	304_L	0.527	0.96
283_M	287_I	0.526	0.96
210_A	217_W	0.525	0.96
158_K	171_S	0.522	0.96
142_W	146_I	0.522	0.96
129_I	317_L	0.522	0.96
161_Y	275_W	0.520	0.96
337_F	341_G	0.519	0.96
142_W	225_L	0.519	0.96
115_F	335_Y	0.516	0.95
145_L	149_L	0.516	0.95
154_L	166_F	0.515	0.95
194_A	198_Y	0.515	0.95
321_A	324_S	0.515	0.95
219_Q	223_D	0.514	0.95
135_V	224_Y	0.514	0.95
258_Q	262_T	0.513	0.95
139_L	235_T	0.512	0.95
168_V	171_S	0.512	0.95
133_L	314_L	0.510	0.95
209_S	227_H	0.508	0.95
178_Y	241_A	0.507	0.95
164_S	169_W	0.507	0.95
348_S	351_S	0.506	0.95
99_I	103_Y	0.506	0.95
158_K	244_T	0.504	0.95
269_S	273_I	0.504	0.95
118_S	121_R	0.504	0.95
112_R	127_T	0.504	0.95
156_I	160_V	0.502	0.95
137_I	299_F	0.502	0.95
138_T	225_L	0.501	0.95
203_P	227_H	0.501	0.95
206_G	209_S	0.500	0.95

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
3tuiA	2	0.5742	99.9	0.719	Contact Map
4tquM	1	0.7445	99.9	0.734	Contact Map
3rlfF	1	0.7527	99.9	0.743	Contact Map
2onkC	2	0.6868	99.9	0.747	Contact Map
4ymuD	2	0.5769	99.8	0.753	Contact Map
3d31C	2	0.6731	99.8	0.756	Contact Map
4tquN	1	0.7033	99.8	0.765	Contact Map
3rlfG	1	0.7637	99.8	0.775	Contact Map
3wdoA	1	0.25	21.5	0.965	Contact Map
4pypA	1	0.0852	10.3	0.969	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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