YPGR - BACSU - GREMLIN Contacts

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YPGR - Uncharacterized protein YpgR

UniProt:	P54169	Sequences: MKIKSIEPTPSPNTMKVILTEELPAGKSNNYKPEQAEGAPLVIAEILKIDGVKGVYHVADFLAVERNARYDWKDILPQVRTAFGMESAESAEENRSDQESFGEVKVFVQMFSGIPMQVKLTDGEREERFGLPERFQQAILKLRSEASNVVFERAWKEQGVRFGDFDEIGHDVTEELQAAYSDERLKRLTEAAAQGKGEAKQAVQRKAYKVTLDMLDDEDWKKRYAHLEQMDPKEEDIPVLQKALDDPKVSIRRQAVVYLGMIETPDVLPLLYKALEDKAVSVRRTAGDCLSDIGDPQAIPAMIKSLSDSSKLVRWRAAMFLYEVGDESAIEALRAAEDDPEFEVSLQVKMALERIEHGEEAKGSVWKQMTESRKKGE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	377 (310)
Sequences:	399 (329)
Seq/√Len:	18.7

BACSU - YPGR

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
330_I	352_L	6.740	1.00
182_D	186_K	4.660	1.00
265_P	297_Q	4.299	1.00
245_D	273_K	4.257	1.00
307_S	335_A	4.019	1.00
108_V	176_L	3.730	1.00
334_R	356_E	3.693	1.00
275_L	301_A	3.300	1.00
276_E	304_K	3.039	0.99
290_L	298_A	2.937	0.99
133_E	137_Q	2.879	0.99
217_D	222_K	2.830	0.99
254_Q	258_Y	2.828	0.99
118_V	173_T	2.824	0.98
348_V	352_L	2.813	0.98
211_T	214_M	2.534	0.97
137_Q	141_K	2.331	0.95
73_K	345_S	2.306	0.95
272_Y	290_L	2.247	0.94
141_K	186_K	2.240	0.94
272_Y	301_A	2.201	0.93
129_F	169_G	2.169	0.93
129_F	173_T	2.137	0.92
364_S	367_K	2.094	0.91
303_I	329_A	2.068	0.91
116_M	149_V	2.053	0.90
127_E	166_D	2.043	0.90
186_K	191_A	1.959	0.88
299_I	328_S	1.950	0.88
241_Q	270_L	1.903	0.87
210_V	214_M	1.903	0.87
225_A	232_P	1.885	0.86
216_D	242_K	1.881	0.86
62_L	65_E	1.863	0.85
65_E	68_A	1.861	0.85
146_A	152_E	1.830	0.84
275_L	290_L	1.807	0.84
169_G	173_T	1.803	0.84
194_Q	198_E	1.777	0.83
290_L	301_A	1.714	0.80
59_A	83_F	1.682	0.79
287_G	302_M	1.670	0.78
319_M	367_K	1.649	0.77
180_Y	184_R	1.625	0.76
94_N	99_E	1.613	0.76
166_D	170_H	1.606	0.76
182_D	196_K	1.596	0.75
64_V	337_E	1.590	0.75
257_V	305_S	1.589	0.75
302_M	305_S	1.583	0.74
265_P	295_D	1.571	0.74
230_M	239_V	1.568	0.74
241_Q	273_K	1.538	0.72
194_Q	201_Q	1.533	0.72
267_V	337_E	1.530	0.72
259_L	267_V	1.524	0.72
234_E	264_T	1.520	0.71
73_K	139_I	1.517	0.71
136_Q	140_L	1.516	0.71
190_E	195_G	1.488	0.70
67_N	70_Y	1.473	0.69
148_N	153_R	1.464	0.68
122_D	125_R	1.462	0.68
261_M	289_C	1.460	0.68
198_E	204_Q	1.446	0.67
162_F	175_E	1.444	0.67
272_Y	298_A	1.437	0.67
219_D	304_K	1.429	0.66
107_F	157_E	1.423	0.66
132_P	177_Q	1.417	0.66
319_M	364_S	1.407	0.65
172_V	175_E	1.389	0.64
142_L	156_K	1.387	0.64
188_L	192_A	1.383	0.64
187_R	190_E	1.383	0.64
61_F	313_V	1.376	0.63
116_M	131_L	1.367	0.63
153_R	163_G	1.360	0.63
343_E	354_R	1.356	0.62
64_V	226_H	1.342	0.61
188_L	193_A	1.331	0.61
65_E	129_F	1.330	0.61
330_I	348_V	1.322	0.60
195_G	201_Q	1.312	0.60
64_V	83_F	1.306	0.59
112_S	152_E	1.306	0.59
104_V	174_E	1.302	0.59
62_L	181_S	1.289	0.58
105_K	309_S	1.288	0.58
97_D	100_S	1.286	0.58
247_P	256_V	1.282	0.58
256_V	289_C	1.267	0.57
162_F	172_V	1.242	0.55
171_D	174_E	1.239	0.55
148_N	155_W	1.237	0.55
157_E	162_F	1.236	0.55
134_R	177_Q	1.235	0.55
182_D	190_E	1.232	0.55
88_A	92_E	1.232	0.55
186_K	190_E	1.216	0.54
241_Q	245_D	1.206	0.53
206_K	209_K	1.206	0.53
269_P	331_E	1.196	0.52
112_S	147_S	1.188	0.52
118_V	129_F	1.187	0.52
193_A	201_Q	1.184	0.52
154_A	158_Q	1.163	0.50
166_D	174_E	1.162	0.50
62_L	70_Y	1.156	0.50
66_R	341_E	1.156	0.50
146_A	149_V	1.150	0.50
212_L	215_L	1.145	0.49
186_K	202_A	1.143	0.49
193_A	198_E	1.138	0.49
182_D	193_A	1.133	0.49
143_R	179_A	1.123	0.48
62_L	337_E	1.121	0.48
275_L	293_I	1.121	0.48
172_V	192_A	1.120	0.48
79_V	101_F	1.119	0.48
288_D	316_R	1.112	0.47
266_D	337_E	1.104	0.47
334_R	348_V	1.102	0.47
188_L	194_Q	1.102	0.47
153_R	168_I	1.097	0.46
194_Q	202_A	1.088	0.46
345_S	349_K	1.087	0.46
343_E	346_L	1.087	0.46
186_K	198_E	1.086	0.46
59_A	160_V	1.086	0.46
293_I	349_K	1.084	0.45
220_W	252_R	1.083	0.45
362_K	367_K	1.081	0.45
207_A	210_V	1.078	0.45
217_D	226_H	1.077	0.45
308_D	313_V	1.072	0.45
196_K	199_A	1.070	0.45
117_Q	128_R	1.066	0.44
190_E	196_K	1.064	0.44
197_G	204_Q	1.060	0.44
275_L	298_A	1.057	0.44
127_E	142_L	1.053	0.44
135_F	138_A	1.048	0.43
286_A	317_A	1.037	0.43
65_E	169_G	1.031	0.42
200_K	203_V	1.017	0.41
289_C	319_M	1.016	0.41
191_A	195_G	1.016	0.41
184_R	189_T	1.015	0.41
152_E	157_E	1.007	0.41
75_I	136_Q	1.001	0.40
149_V	152_E	1.000	0.40
292_D	316_R	1.000	0.40
131_L	135_F	0.999	0.40
260_G	289_C	0.995	0.40
242_K	247_P	0.993	0.40
154_A	157_E	0.992	0.40
233_K	296_P	0.990	0.40
197_G	200_K	0.989	0.40
150_V	174_E	0.987	0.40
196_K	204_Q	0.983	0.39
237_I	241_Q	0.980	0.39
148_N	163_G	0.979	0.39
276_E	289_C	0.978	0.39
62_L	82_A	0.973	0.39
288_D	291_S	0.972	0.39
64_V	70_Y	0.969	0.38
75_I	152_E	0.968	0.38
292_D	320_F	0.968	0.38
246_D	251_I	0.968	0.38
335_A	338_D	0.963	0.38
194_Q	204_Q	0.962	0.38
108_V	158_Q	0.961	0.38
237_I	267_V	0.959	0.38
145_E	345_S	0.958	0.38
163_G	175_E	0.957	0.38
77_P	124_E	0.955	0.38
195_G	198_E	0.953	0.38
104_V	165_F	0.953	0.38
64_V	73_K	0.949	0.37
265_P	296_P	0.947	0.37
69_R	143_R	0.945	0.37
59_A	73_K	0.935	0.36
346_L	354_R	0.933	0.36
343_E	347_Q	0.931	0.36
319_M	362_K	0.929	0.36
158_Q	173_T	0.926	0.36
228_E	290_L	0.925	0.36
170_H	173_T	0.920	0.36
308_D	354_R	0.918	0.35
345_S	356_E	0.916	0.35
316_R	347_Q	0.915	0.35
163_G	172_V	0.903	0.35
96_S	110_M	0.902	0.35
74_D	304_K	0.899	0.34
218_E	222_K	0.899	0.34
163_G	167_E	0.898	0.34
228_E	256_V	0.887	0.34
115_P	153_R	0.884	0.34
254_Q	323_E	0.884	0.34
74_D	205_R	0.880	0.33
186_K	201_Q	0.879	0.33
147_S	150_V	0.877	0.33
305_S	313_V	0.873	0.33
189_T	196_K	0.872	0.33
337_E	349_K	0.870	0.33
206_K	210_V	0.868	0.33
107_F	310_S	0.863	0.32
242_K	245_D	0.861	0.32
119_K	155_W	0.854	0.32
99_E	233_K	0.851	0.32
272_Y	297_Q	0.846	0.31
65_E	209_K	0.846	0.31
263_E	289_C	0.843	0.31
330_I	337_E	0.839	0.31
345_S	352_L	0.839	0.31
299_I	326_D	0.835	0.31
183_E	353_E	0.833	0.31
214_M	222_K	0.820	0.30
74_D	245_D	0.813	0.30
149_V	157_E	0.811	0.30
184_R	203_V	0.809	0.30
95_R	99_E	0.808	0.29
153_R	162_F	0.805	0.29
86_E	203_V	0.804	0.29
184_R	198_E	0.803	0.29
208_Y	211_T	0.803	0.29
272_Y	300_P	0.793	0.29
289_C	364_S	0.793	0.29
139_I	156_K	0.791	0.29
181_S	189_T	0.791	0.29
285_T	316_R	0.788	0.28
245_D	321_L	0.785	0.28
260_G	291_S	0.783	0.28
279_A	310_S	0.780	0.28
218_E	329_A	0.779	0.28
196_K	203_V	0.777	0.28
186_K	194_Q	0.774	0.28
181_S	186_K	0.773	0.28
336_A	341_E	0.770	0.28
224_Y	290_L	0.769	0.27
189_T	201_Q	0.755	0.27
210_V	215_L	0.752	0.27
309_S	330_I	0.751	0.27
269_P	308_D	0.750	0.27
334_R	337_E	0.747	0.26
208_Y	226_H	0.743	0.26
236_D	248_K	0.743	0.26
115_P	119_K	0.743	0.26
181_S	194_Q	0.742	0.26
189_T	193_A	0.739	0.26
168_I	295_D	0.737	0.26
168_I	172_V	0.736	0.26
162_F	174_E	0.736	0.26
99_E	112_S	0.735	0.26
209_K	352_L	0.732	0.26
324_V	345_S	0.732	0.26
144_S	156_K	0.729	0.26
175_E	178_A	0.727	0.25
58_V	104_V	0.726	0.25
217_D	324_V	0.725	0.25
128_R	132_P	0.724	0.25
58_V	69_R	0.724	0.25
262_I	267_V	0.722	0.25
329_A	353_E	0.721	0.25
68_A	73_K	0.720	0.25
313_V	341_E	0.720	0.25
343_E	365_V	0.720	0.25
221_K	270_L	0.718	0.25
189_T	192_A	0.717	0.25
86_E	97_D	0.717	0.25
298_A	306_L	0.715	0.25
214_M	345_S	0.715	0.25
188_L	196_K	0.711	0.25
191_A	201_Q	0.710	0.25
161_R	180_Y	0.709	0.25
156_K	352_L	0.708	0.25
145_E	152_E	0.707	0.24
288_D	292_D	0.706	0.24
162_F	178_A	0.706	0.24
226_H	229_Q	0.704	0.24
145_E	181_S	0.703	0.24
211_T	362_K	0.701	0.24
163_G	168_I	0.700	0.24
114_I	117_Q	0.697	0.24
163_G	169_G	0.697	0.24
256_V	274_A	0.695	0.24
185_L	189_T	0.694	0.24
138_A	154_A	0.690	0.24
245_D	338_D	0.687	0.24
99_E	278_K	0.686	0.24
198_E	201_Q	0.685	0.23
167_E	171_D	0.684	0.23
299_I	324_V	0.683	0.23
304_K	307_S	0.683	0.23
148_N	151_F	0.682	0.23
58_V	119_K	0.681	0.23
288_D	315_W	0.680	0.23
264_T	293_I	0.680	0.23
91_A	97_D	0.679	0.23
221_K	237_I	0.677	0.23
256_V	348_V	0.673	0.23
161_R	172_V	0.673	0.23
241_Q	263_E	0.670	0.23
160_V	168_I	0.668	0.23
291_S	344_V	0.663	0.22
240_L	262_I	0.661	0.22
187_R	196_K	0.660	0.22
159_G	163_G	0.659	0.22
195_G	204_Q	0.659	0.22
189_T	194_Q	0.654	0.22
207_A	225_A	0.653	0.22
168_I	178_A	0.652	0.22
212_L	234_E	0.649	0.22
120_L	174_E	0.649	0.22
208_Y	214_M	0.648	0.22
300_P	328_S	0.646	0.22
357_H	362_K	0.646	0.22
128_R	153_R	0.646	0.22
183_E	191_A	0.645	0.22
154_A	189_T	0.644	0.22
223_R	246_D	0.643	0.22
236_D	319_M	0.643	0.22
205_R	266_D	0.640	0.22
182_D	203_V	0.639	0.21
209_K	348_V	0.638	0.21
228_E	254_Q	0.638	0.21
81_T	165_F	0.637	0.21
350_M	354_R	0.636	0.21
234_E	353_E	0.632	0.21
347_Q	361_A	0.631	0.21
338_D	350_M	0.627	0.21
122_D	166_D	0.627	0.21
145_E	154_A	0.626	0.21
118_V	128_R	0.626	0.21
103_E	111_F	0.626	0.21
68_A	156_K	0.625	0.21
150_V	153_R	0.625	0.21
106_V	109_Q	0.625	0.21
334_R	367_K	0.625	0.21
315_W	354_R	0.624	0.21
61_F	341_E	0.622	0.21
223_R	314_R	0.621	0.21
237_I	259_L	0.619	0.21
129_F	139_I	0.618	0.21
347_Q	350_M	0.618	0.21
291_S	347_Q	0.616	0.21
64_V	71_D	0.616	0.21
332_A	342_F	0.616	0.21
343_E	358_G	0.614	0.20
247_P	279_A	0.612	0.20
291_S	358_G	0.611	0.20
297_Q	334_R	0.609	0.20
260_G	288_D	0.609	0.20
145_E	158_Q	0.608	0.20
176_L	186_K	0.606	0.20
193_A	196_K	0.605	0.20
154_A	163_G	0.605	0.20
207_A	211_T	0.602	0.20
329_A	336_A	0.599	0.20
94_N	97_D	0.599	0.20
329_A	332_A	0.598	0.20
75_I	259_L	0.597	0.20
323_E	351_A	0.597	0.20
161_R	175_E	0.595	0.20
88_A	96_S	0.595	0.20
171_D	175_E	0.595	0.20
213_D	216_D	0.595	0.20
294_G	356_E	0.594	0.20
191_A	194_Q	0.594	0.20
346_L	361_A	0.593	0.20
265_P	272_Y	0.593	0.20
153_R	180_Y	0.593	0.20
93_E	190_E	0.593	0.20
112_S	143_R	0.589	0.19
207_A	293_I	0.588	0.19
208_Y	215_L	0.588	0.19
291_S	316_R	0.588	0.19
220_W	313_V	0.585	0.19
253_R	314_R	0.585	0.19
277_D	358_G	0.584	0.19
328_S	360_E	0.583	0.19
154_A	161_R	0.583	0.19
316_R	344_V	0.582	0.19
194_Q	199_A	0.582	0.19
254_Q	290_L	0.581	0.19
339_D	361_A	0.581	0.19
221_K	230_M	0.579	0.19
309_S	340_P	0.575	0.19
233_K	264_T	0.575	0.19
237_I	345_S	0.573	0.19
117_Q	153_R	0.573	0.19
69_R	85_M	0.573	0.19
312_L	346_L	0.572	0.19
111_F	188_L	0.572	0.19
269_P	281_S	0.572	0.19
260_G	316_R	0.568	0.19
204_Q	219_D	0.567	0.19
122_D	337_E	0.566	0.19
299_I	303_I	0.566	0.19
243_A	302_M	0.565	0.18
291_S	315_W	0.564	0.18
190_E	203_V	0.563	0.18
87_S	99_E	0.560	0.18
161_R	164_D	0.560	0.18
209_K	235_E	0.559	0.18
333_L	351_A	0.554	0.18
228_E	236_D	0.553	0.18
107_F	121_T	0.553	0.18
230_M	247_P	0.550	0.18
292_D	315_W	0.550	0.18
154_A	172_V	0.550	0.18
208_Y	345_S	0.549	0.18
305_S	365_V	0.548	0.18
83_F	179_A	0.547	0.18
139_I	151_F	0.546	0.18
159_G	170_H	0.546	0.18
128_R	308_D	0.543	0.18
136_Q	157_E	0.541	0.18
115_P	120_L	0.541	0.18
190_E	201_Q	0.541	0.18
214_M	236_D	0.541	0.18
92_E	98_Q	0.540	0.18
73_K	127_E	0.539	0.18
269_P	330_I	0.538	0.17
156_K	166_D	0.535	0.17
330_I	350_M	0.535	0.17
158_Q	172_V	0.535	0.17
107_F	116_M	0.533	0.17
264_T	295_D	0.531	0.17
102_G	114_I	0.531	0.17
187_R	199_A	0.530	0.17
209_K	349_K	0.529	0.17
103_E	115_P	0.529	0.17
253_R	318_A	0.528	0.17
139_I	142_L	0.528	0.17
154_A	162_F	0.527	0.17
128_R	135_F	0.527	0.17
313_V	361_A	0.525	0.17
164_D	194_Q	0.525	0.17
319_M	344_V	0.525	0.17
330_I	367_K	0.525	0.17
147_S	152_E	0.525	0.17
118_V	183_E	0.520	0.17
291_S	361_A	0.520	0.17
308_D	343_E	0.520	0.17
181_S	190_E	0.519	0.17
145_E	149_V	0.517	0.17
303_I	332_A	0.517	0.17
288_D	302_M	0.516	0.17
153_R	161_R	0.514	0.17
89_E	278_K	0.514	0.17
312_L	316_R	0.514	0.17
165_F	174_E	0.513	0.17
256_V	290_L	0.513	0.17
222_K	337_E	0.510	0.17
360_E	365_V	0.510	0.17
208_Y	217_D	0.509	0.16
186_K	197_G	0.508	0.16
257_V	302_M	0.508	0.16
257_V	324_V	0.507	0.16
62_L	124_E	0.504	0.16
250_S	341_E	0.504	0.16
124_E	136_Q	0.502	0.16
137_Q	144_S	0.500	0.16

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
1pqxA	1	0.2414	99.9	0.812	Contact Map
2k1hA	1	0.2281	99.9	0.812	Contact Map
3ltjA	2	0.4695	99.8	0.819	Contact Map
2ltmA	1	0.2573	99.8	0.825	Contact Map
2ltlA	1	0.2573	99.8	0.825	Contact Map
3ltmA	1	0.4828	99.8	0.826	Contact Map
4lacA	1	0.5172	99.8	0.83	Contact Map
1wa5B	1	0.5517	99.8	0.831	Contact Map
3tpoA	1	0.5013	99.8	0.831	Contact Map
4jw3C	1	0.2573	99.7	0.84	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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