PBPX - BACSU - GREMLIN Contacts

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PBPX - Putative penicillin-binding protein PbpX

UniProt:	O31773	Sequences: MTSPTRRRTAKRRRRKLNKRGKLLFGLLAVMVCITIWNALHRNSEENEPSQETAAVSNTDQKKEVKKKTAKKSEEQIKTVDRNQKISNYLKEIGFSGTAMIVRNGEIVTNKGFGYADRKHYIQNNPLTSFYVGSSQKALIATAILQLEEKGKLQTSDPVSTYLPHFPNGQTITLKNLLTHTSGINGHIEGNGAITPDDLIKDIELQGIKRQPGVWDYKDSNYSVLAYIIAEVSGEPYEQYIKNHIFKPAGMTHAGFYKTYEKEPYPAVGYKMEGSKTVTPYIPDLSQLYGAGDIYMSAIDMYKFDQALIDGKLYSQKSYEKMFTPGSSSTYGMGFYVAPGSYSNHGVMPGFNILNSFSKSGQTIVILFSNIQNNAKLGQVNNKIYQLLNQE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	391 (306)
Sequences:	10341 (8185)
Seq/√Len:	467.9

ECOLI - YFEW AMPH AMPC
BACSU - PBPX PBPE YBBE

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
235_E	243_N	3.780	1.00
150_K	244_H	3.668	1.00
242_K	247_K	3.363	1.00
104_N	362_Q	3.338	1.00
143_A	240_Y	3.295	1.00
157_D	161_T	3.000	1.00
146_Q	244_H	2.865	1.00
124_N	130_F	2.815	1.00
146_Q	240_Y	2.804	1.00
154_Q	157_D	2.704	1.00
149_E	315_S	2.700	1.00
156_S	175_K	2.692	1.00
83_N	111_K	2.644	1.00
254_A	296_M	2.630	1.00
236_P	239_Q	2.567	1.00
240_Y	244_H	2.563	1.00
132_V	296_M	2.543	1.00
229_I	240_Y	2.432	1.00
112_G	126_P	2.391	1.00
117_D	120_H	2.367	1.00
142_T	304_F	2.341	1.00
157_D	162_Y	2.307	1.00
149_E	318_S	2.236	1.00
110_N	299_I	2.235	1.00
233_S	240_Y	2.230	1.00
315_S	318_S	2.178	1.00
227_Y	231_E	2.173	1.00
116_A	122_I	2.168	1.00
128_T	267_A	2.137	1.00
138_A	304_F	2.120	1.00
115_Y	121_Y	2.109	1.00
227_Y	230_A	1.950	1.00
226_A	290_G	1.950	1.00
144_I	225_L	1.943	1.00
146_Q	150_K	1.865	1.00
251_M	254_A	1.782	1.00
165_H	231_E	1.768	1.00
195_T	198_D	1.760	1.00
134_S	137_K	1.754	1.00
305_D	364_I	1.737	1.00
143_A	241_I	1.711	1.00
241_I	246_F	1.704	1.00
144_I	153_L	1.696	1.00
148_E	155_T	1.694	1.00
316_Q	320_E	1.692	1.00
109_T	113_F	1.691	1.00
321_K	324_T	1.688	1.00
235_E	240_Y	1.678	1.00
305_D	355_N	1.673	1.00
243_N	247_K	1.673	1.00
87_S	91_K	1.669	1.00
158_P	161_T	1.657	1.00
235_E	244_H	1.609	1.00
115_Y	120_H	1.592	1.00
147_L	229_I	1.591	1.00
83_N	87_S	1.589	1.00
239_Q	243_N	1.581	1.00
83_N	113_F	1.574	1.00
237_Y	290_G	1.558	1.00
358_S	361_G	1.539	1.00
173_T	176_N	1.534	1.00
88_N	92_E	1.523	1.00
97_G	124_N	1.510	1.00
235_E	239_Q	1.505	1.00
102_V	302_Y	1.471	1.00
246_F	251_M	1.468	1.00
182_S	221_N	1.466	1.00
127_L	299_I	1.465	1.00
124_N	128_T	1.447	1.00
133_G	348_M	1.439	1.00
126_P	299_I	1.436	1.00
308_L	323_F	1.424	1.00
175_K	333_M	1.415	1.00
176_N	181_T	1.410	1.00
145_L	155_T	1.403	1.00
102_V	364_I	1.403	1.00
253_H	265_Y	1.403	1.00
83_N	109_T	1.396	1.00
147_L	233_S	1.395	1.00
97_G	130_F	1.389	1.00
99_A	298_A	1.372	1.00
112_G	124_N	1.369	1.00
197_D	201_K	1.350	1.00
139_L	294_I	1.350	1.00
176_N	213_G	1.340	1.00
135_S	355_N	1.334	1.00
141_A	222_Y	1.331	1.00
148_E	153_L	1.329	1.00
99_A	124_N	1.327	1.00
246_F	294_I	1.325	1.00
141_A	178_L	1.322	1.00
171_T	211_Q	1.317	1.00
237_Y	241_I	1.311	1.00
174_L	228_I	1.301	1.00
145_L	148_E	1.287	1.00
144_I	178_L	1.281	1.00
175_K	321_K	1.273	1.00
254_A	300_D	1.272	1.00
301_M	368_F	1.258	1.00
116_A	128_T	1.256	1.00
251_M	300_D	1.243	1.00
103_R	363_T	1.239	1.00
139_L	304_F	1.238	1.00
148_E	321_K	1.231	1.00
332_G	337_V	1.216	1.00
125_N	128_T	1.214	1.00
309_I	357_F	1.205	1.00
137_K	217_Y	1.198	1.00
152_K	232_V	1.193	1.00
347_V	352_N	1.185	1.00
84_Q	88_N	1.183	1.00
135_S	353_I	1.179	1.00
219_D	291_A	1.169	1.00
103_R	106_E	1.159	1.00
102_V	107_I	1.157	1.00
134_S	217_Y	1.147	1.00
256_F	294_I	1.138	1.00
306_Q	309_I	1.133	1.00
218_K	221_N	1.131	1.00
146_Q	313_L	1.128	1.00
158_P	171_T	1.125	1.00
100_M	367_L	1.121	1.00
305_D	357_F	1.121	1.00
144_I	229_I	1.120	1.00
139_L	241_I	1.119	1.00
357_F	364_I	1.115	1.00
145_L	318_S	1.100	1.00
269_G	351_F	1.097	1.00
110_N	126_P	1.096	1.00
143_A	229_I	1.096	1.00
238_E	288_L	1.092	1.00
198_D	201_K	1.089	1.00
143_A	244_H	1.079	1.00
142_T	314_Y	1.076	1.00
176_N	179_T	1.076	1.00
249_A	307_A	1.072	1.00
140_I	237_Y	1.067	1.00
117_D	122_I	1.066	1.00
301_M	366_I	1.066	1.00
139_L	251_M	1.063	1.00
135_S	301_M	1.063	1.00
145_L	322_M	1.054	1.00
136_Q	294_I	1.052	1.00
222_Y	225_L	1.044	1.00
298_A	368_F	1.036	1.00
142_T	308_L	1.033	1.00
96_S	118_R	1.021	1.00
143_A	233_S	1.016	1.00
299_I	303_K	1.012	1.00
146_Q	245_I	1.008	1.00
90_L	113_F	1.000	1.00
211_Q	214_V	0.999	1.00
86_I	100_M	0.999	1.00
162_Y	232_V	0.997	1.00
356_S	365_V	0.993	1.00
157_D	174_L	0.992	1.00
160_S	170_Q	0.986	1.00
85_K	89_Y	0.979	1.00
159_V	228_I	0.978	1.00
210_R	216_D	0.976	1.00
311_G	320_E	0.973	1.00
153_L	232_V	0.968	1.00
228_I	232_V	0.968	1.00
99_A	130_F	0.966	1.00
308_L	335_F	0.966	1.00
132_V	136_Q	0.964	1.00
147_L	152_K	0.963	1.00
131_Y	295_Y	0.960	1.00
86_I	98_T	0.953	1.00
139_L	246_F	0.949	1.00
246_F	254_A	0.948	1.00
87_S	113_F	0.948	1.00
251_M	296_M	0.947	1.00
250_G	303_K	0.946	1.00
84_Q	87_S	0.932	1.00
99_A	112_G	0.931	1.00
153_L	174_L	0.926	1.00
159_V	177_L	0.926	1.00
201_K	205_L	0.925	1.00
140_I	290_G	0.924	1.00
251_M	304_F	0.920	1.00
273_E	276_K	0.920	1.00
210_R	214_V	0.917	1.00
131_Y	348_M	0.915	1.00
107_I	306_Q	0.914	1.00
331_Y	336_Y	0.914	1.00
335_F	357_F	0.911	1.00
303_K	306_Q	0.909	1.00
242_K	246_F	0.908	1.00
148_E	318_S	0.900	1.00
229_I	233_S	0.892	1.00
200_I	227_Y	0.891	1.00
117_D	268_V	0.886	1.00
239_Q	242_K	0.882	1.00
311_G	316_Q	0.878	1.00
118_R	270_Y	0.877	1.00
229_I	237_Y	0.876	1.00
226_A	237_Y	0.874	1.00
129_S	295_Y	0.871	1.00
180_H	221_N	0.868	1.00
355_N	366_I	0.864	1.00
233_S	244_H	0.859	1.00
209_K	216_D	0.858	1.00
87_S	90_L	0.857	1.00
110_N	298_A	0.847	1.00
251_M	303_K	0.846	1.00
163_L	231_E	0.845	1.00
129_S	265_Y	0.843	1.00
115_Y	123_Q	0.841	1.00
233_S	236_P	0.839	1.00
302_Y	364_I	0.838	1.00
237_Y	256_F	0.836	1.00
87_S	111_K	0.836	1.00
178_L	225_L	0.835	1.00
129_S	253_H	0.833	1.00
101_I	365_V	0.833	1.00
162_Y	174_L	0.831	1.00
344_N	360_S	0.829	1.00
100_M	111_K	0.829	1.00
132_V	353_I	0.827	1.00
142_T	146_Q	0.824	1.00
129_S	255_G	0.823	1.00
139_L	301_M	0.822	1.00
140_I	226_A	0.820	1.00
241_I	256_F	0.819	1.00
306_Q	310_D	0.819	1.00
342_Y	361_G	0.814	1.00
96_S	371_I	0.813	1.00
279_T	282_I	0.812	1.00
86_I	90_L	0.811	1.00
162_Y	228_I	0.811	1.00
253_H	297_S	0.809	1.00
280_P	284_D	0.802	1.00
215_W	331_Y	0.801	1.00
174_L	232_V	0.800	1.00
165_H	201_K	0.795	1.00
201_K	204_E	0.794	1.00
320_E	324_T	0.793	1.00
98_T	367_L	0.793	1.00
241_I	254_A	0.790	1.00
117_D	121_Y	0.790	1.00
181_T	213_G	0.787	1.00
147_L	150_K	0.786	1.00
196_P	227_Y	0.786	1.00
192_G	198_D	0.786	1.00
302_Y	366_I	0.782	1.00
141_A	334_G	0.779	1.00
159_V	163_L	0.778	1.00
153_L	228_I	0.777	1.00
308_L	322_M	0.777	1.00
279_T	284_D	0.777	1.00
331_Y	335_F	0.775	1.00
259_T	262_K	0.772	1.00
325_P	330_T	0.772	1.00
319_Y	323_F	0.772	1.00
155_T	333_M	0.771	1.00
90_L	98_T	0.770	1.00
143_A	245_I	0.769	1.00
107_I	110_N	0.766	1.00
176_N	212_P	0.764	1.00
105_G	306_Q	0.763	1.00
172_I	182_S	0.762	1.00
135_S	138_A	0.760	1.00
102_V	306_Q	0.759	1.00
253_H	300_D	0.754	1.00
319_Y	322_M	0.753	1.00
230_A	233_S	0.752	1.00
86_I	113_F	0.752	1.00
280_P	283_P	0.750	1.00
274_G	277_T	0.749	1.00
311_G	319_Y	0.745	1.00
196_P	230_A	0.743	1.00
197_D	227_Y	0.742	1.00
127_L	253_H	0.741	1.00
175_K	179_T	0.738	1.00
138_A	355_N	0.737	1.00
138_A	305_D	0.736	1.00
138_A	335_F	0.735	1.00
172_I	184_I	0.734	1.00
223_S	291_A	0.732	1.00
103_R	362_Q	0.729	1.00
115_Y	122_I	0.725	1.00
296_M	301_M	0.724	1.00
345_H	354_L	0.723	1.00
115_Y	118_R	0.716	1.00
323_F	346_G	0.713	1.00
80_V	84_Q	0.713	1.00
178_L	222_Y	0.710	1.00
81_D	84_Q	0.710	1.00
238_E	242_K	0.709	1.00
309_I	362_Q	0.706	1.00
309_I	364_I	0.705	1.00
103_R	108_V	0.703	1.00
323_F	359_K	0.696	1.00
346_G	357_F	0.692	1.00
146_Q	149_E	0.690	1.00
314_Y	319_Y	0.690	1.00
129_S	297_S	0.690	1.00
163_L	228_I	0.689	1.00
98_T	369_S	0.689	1.00
137_K	219_D	0.685	1.00
148_E	154_Q	0.682	1.00
147_L	240_Y	0.680	1.00
116_A	125_N	0.680	1.00
187_H	220_S	0.679	1.00
255_G	295_Y	0.679	1.00
154_Q	174_L	0.678	1.00
330_T	337_V	0.678	1.00
222_Y	334_G	0.677	1.00
144_I	228_I	0.670	1.00
100_M	109_T	0.670	1.00
289_Y	292_G	0.669	1.00
230_A	236_P	0.668	1.00
298_A	366_I	0.667	1.00
341_S	361_G	0.666	1.00
305_D	366_I	0.664	1.00
142_T	245_I	0.664	1.00
115_Y	119_K	0.662	1.00
245_I	313_L	0.659	1.00
89_Y	95_F	0.658	1.00
154_Q	175_K	0.655	1.00
166_F	172_I	0.653	1.00
322_M	335_F	0.652	1.00
184_I	220_S	0.651	1.00
198_D	202_D	0.651	1.00
219_D	346_G	0.650	1.00
133_G	351_F	0.649	1.00
307_A	313_L	0.648	1.00
353_I	368_F	0.647	1.00
317_K	320_E	0.647	1.00
275_S	278_V	0.647	1.00
318_S	321_K	0.646	1.00
342_Y	358_S	0.646	1.00
148_E	157_D	0.645	1.00
131_Y	136_Q	0.641	1.00
154_Q	162_Y	0.639	1.00
147_L	232_V	0.636	1.00
302_Y	306_Q	0.632	1.00
132_V	135_S	0.631	0.99
132_V	368_F	0.631	0.99
163_L	227_Y	0.629	0.99
323_F	335_F	0.629	0.99
132_V	301_M	0.627	0.99
133_G	352_N	0.625	0.99
88_N	91_K	0.625	0.99
298_A	302_Y	0.625	0.99
95_F	369_S	0.623	0.99
326_G	329_S	0.623	0.99
320_E	323_F	0.623	0.99
80_V	83_N	0.622	0.99
160_S	169_G	0.621	0.99
130_F	368_F	0.620	0.99
308_L	346_G	0.619	0.99
77_I	80_V	0.617	0.99
267_A	270_Y	0.613	0.99
182_S	218_K	0.610	0.99
302_Y	305_D	0.609	0.99
194_I	198_D	0.608	0.99
78_K	81_D	0.607	0.99
145_L	335_F	0.606	0.99
342_Y	346_G	0.605	0.99
156_S	173_T	0.604	0.99
179_T	333_M	0.604	0.99
132_V	254_A	0.603	0.99
322_M	332_G	0.600	0.99
263_E	266_P	0.600	0.99
180_H	222_Y	0.598	0.99
196_P	199_L	0.598	0.99
174_L	225_L	0.598	0.99
249_A	303_K	0.597	0.99
256_F	293_D	0.594	0.99
107_I	302_Y	0.593	0.99
129_S	262_K	0.590	0.99
95_F	98_T	0.586	0.99
133_G	292_G	0.580	0.99
186_G	291_A	0.580	0.99
313_L	318_S	0.579	0.99
316_Q	319_Y	0.578	0.99
245_I	248_P	0.577	0.99
112_G	298_A	0.576	0.99
296_M	300_D	0.574	0.99
318_S	322_M	0.572	0.99
134_S	219_D	0.572	0.99
181_T	215_W	0.572	0.99
145_L	149_E	0.571	0.99
254_A	297_S	0.570	0.99
100_M	113_F	0.570	0.99
125_N	265_Y	0.569	0.99
158_P	173_T	0.569	0.99
160_S	164_P	0.566	0.99
241_I	245_I	0.564	0.99
196_P	200_I	0.563	0.99
159_V	162_Y	0.563	0.99
159_V	166_F	0.562	0.99
165_H	204_E	0.558	0.99
97_G	370_N	0.556	0.99
251_M	307_A	0.555	0.99
168_N	211_Q	0.554	0.99
297_S	300_D	0.554	0.99
185_N	206_Q	0.553	0.99
159_V	224_V	0.552	0.99
159_V	172_I	0.552	0.99
140_I	241_I	0.551	0.99
301_M	355_N	0.551	0.99
127_L	265_Y	0.550	0.99
236_P	240_Y	0.550	0.99
140_I	225_L	0.548	0.99
307_A	319_Y	0.546	0.99
170_Q	176_N	0.546	0.99
186_G	220_S	0.544	0.99
215_W	336_Y	0.539	0.98
310_D	362_Q	0.538	0.98
166_F	224_V	0.538	0.98
281_Y	284_D	0.537	0.98
177_L	225_L	0.537	0.98
219_D	344_N	0.537	0.98
122_I	128_T	0.537	0.98
116_A	124_N	0.535	0.98
144_I	232_V	0.535	0.98
307_A	312_K	0.534	0.98
202_D	205_L	0.532	0.98
172_I	176_N	0.531	0.98
346_G	359_K	0.529	0.98
272_M	277_T	0.528	0.98
237_Y	246_F	0.526	0.98
279_T	283_P	0.525	0.98
99_A	102_V	0.525	0.98
144_I	174_L	0.521	0.98
255_G	259_T	0.521	0.98
358_S	363_T	0.520	0.98
274_G	278_V	0.520	0.98
238_E	256_F	0.520	0.98
208_I	212_P	0.520	0.98
166_F	169_G	0.520	0.98
313_L	319_Y	0.518	0.98
289_Y	293_D	0.517	0.98
321_K	325_P	0.516	0.98
337_V	342_Y	0.516	0.98
90_L	95_F	0.515	0.98
168_N	171_T	0.514	0.98
86_I	89_Y	0.513	0.98
118_R	121_Y	0.512	0.98
240_Y	243_N	0.512	0.98
79_T	111_K	0.511	0.98
343_S	346_G	0.511	0.98
379_Q	382_N	0.510	0.98
247_K	252_T	0.510	0.98
241_I	294_I	0.507	0.98
140_I	222_Y	0.507	0.98
138_A	142_T	0.506	0.98
252_T	300_D	0.505	0.98
312_K	316_Q	0.505	0.98
166_F	231_E	0.505	0.98
169_G	172_I	0.503	0.98
303_K	307_A	0.503	0.98
317_K	321_K	0.503	0.98
177_L	221_N	0.502	0.98
138_A	141_A	0.500	0.97
139_L	142_T	0.500	0.97

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
3tg9A	2	0.7724	100	0.291	Contact Map
1yqsA	1	0.8107	100	0.292	Contact Map
2qmiA	5	0.8005	100	0.301	Contact Map
4netA	1	0.8056	100	0.301	Contact Map
2qz6A	1	0.7724	100	0.302	Contact Map
3wrzA	1	0.798	100	0.302	Contact Map
2ffyA	1	0.7928	100	0.303	Contact Map
4gdnA	1	0.8056	100	0.305	Contact Map
4ivkA	4	0.8414	100	0.305	Contact Map
1ei5A	2	0.7928	100	0.305	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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