YERB - BACSU - GREMLIN Contacts

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YERB - Putative lipoprotein YerB

UniProt:	O34968	Sequences: MKKWMTVCALCFVFFLLVSCQQKDAVPDTAKKLKAPLTGLKTEQKVTERRPVAVVVNNHPKARPQSGLSKADIVIEALAEGQITRFLAIFQSQMPETVGPVRSAREYFVTLSNGFDSIFVHHGWSPGAKKQLESGAADYMNGLDFDGSLFWRADFSKPPHNSYTSYDYIKKAAEQKGYKLKQETNPLLFQTSDAKPANESYNVRVDYGTNNVTNLVEYNYDKKAEFYTRSSDGVITTDRETGKPVAMQNIFIVEASHHIIDQDGRRDIDLESGGKGLLFQHGNVIETDWKQVNGRIVPVKDGKWLPFVPGKTWINIVPDLDAASISKGEGV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	331 (307)
Sequences:	807 (692)
Seq/√Len:	39.5

BACSU - YERB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
276_G	287_T	6.479	1.00
122_H	162_S	4.940	1.00
158_P	161_N	4.429	1.00
299_V	303_K	3.592	1.00
221_D	228_T	3.508	1.00
55_V	119_F	3.436	1.00
228_T	244_P	3.257	1.00
104_A	119_F	2.860	1.00
69_S	241_T	2.850	1.00
221_D	224_A	2.836	1.00
279_F	284_V	2.653	1.00
226_F	248_Q	2.619	1.00
53_A	87_L	2.587	1.00
248_Q	281_H	2.560	1.00
120_V	150_F	2.555	1.00
230_S	244_P	2.542	1.00
101_V	164_T	2.491	1.00
261_D	264_G	2.483	1.00
125_S	128_A	2.462	1.00
252_I	279_F	2.359	1.00
55_V	108_F	2.354	1.00
219_N	230_S	2.340	1.00
224_A	228_T	2.315	1.00
66_S	163_Y	2.271	1.00
251_F	287_T	2.196	0.99
109_V	132_L	2.164	0.99
74_V	313_W	2.148	0.99
114_G	291_Q	2.031	0.99
235_I	244_P	2.030	0.99
95_P	313_W	2.022	0.99
13_V	16_L	2.007	0.99
275_K	288_D	1.996	0.99
249_N	312_T	1.975	0.99
269_D	272_S	1.954	0.99
236_T	245_V	1.947	0.99
275_K	286_E	1.930	0.99
152_R	161_N	1.914	0.98
218_Y	315_N	1.854	0.98
89_I	115_F	1.845	0.98
53_A	89_I	1.833	0.98
200_S	203_V	1.809	0.98
120_V	169_I	1.803	0.98
114_G	295_R	1.768	0.97
39_G	189_F	1.731	0.97
114_G	253_V	1.713	0.97
199_E	202_N	1.709	0.97
287_T	305_L	1.698	0.97
39_G	309_P	1.696	0.97
288_D	298_P	1.685	0.96
12_F	15_F	1.676	0.96
17_L	20_C	1.662	0.96
54_V	101_V	1.660	0.96
228_T	246_A	1.651	0.96
151_W	165_S	1.646	0.96
253_V	295_R	1.607	0.95
278_L	287_T	1.599	0.95
226_F	246_A	1.590	0.95
200_S	227_Y	1.577	0.95
238_D	241_T	1.566	0.95
202_N	219_N	1.562	0.95
280_Q	308_V	1.548	0.94
116_D	179_K	1.487	0.93
124_W	129_K	1.487	0.93
40_L	309_P	1.486	0.93
199_E	283_N	1.474	0.93
55_V	87_L	1.424	0.91
121_H	164_T	1.419	0.91
259_I	266_R	1.419	0.91
142_G	162_S	1.416	0.91
247_M	311_K	1.403	0.91
229_R	315_N	1.401	0.91
80_E	160_H	1.399	0.91
19_S	22_Q	1.395	0.90
121_H	128_A	1.383	0.90
68_L	100_P	1.367	0.90
82_Q	266_R	1.356	0.89
278_L	305_L	1.355	0.89
277_L	286_E	1.348	0.89
218_Y	247_M	1.345	0.89
251_F	278_L	1.337	0.88
126_P	265_R	1.336	0.88
299_V	305_L	1.326	0.88
69_S	245_V	1.320	0.88
63_R	160_H	1.318	0.88
202_N	207_Y	1.312	0.87
220_Y	227_Y	1.303	0.87
68_L	86_F	1.297	0.87
30_A	33_L	1.294	0.87
254_E	275_K	1.290	0.87
247_M	315_N	1.283	0.86
256_S	319_D	1.272	0.86
75_I	114_G	1.272	0.86
90_F	96_E	1.266	0.86
191_T	309_P	1.265	0.85
251_F	307_F	1.260	0.85
224_A	246_A	1.249	0.85
129_K	141_N	1.240	0.84
16_L	19_S	1.234	0.84
14_F	17_L	1.232	0.84
75_I	253_V	1.221	0.83
29_T	33_L	1.216	0.83
132_L	139_Y	1.214	0.83
70_K	93_Q	1.210	0.83
251_F	314_I	1.207	0.83
203_V	279_F	1.203	0.82
72_D	92_S	1.200	0.82
70_K	101_V	1.199	0.82
197_A	200_S	1.197	0.82
78_L	268_I	1.196	0.82
72_D	77_A	1.181	0.81
274_G	289_W	1.176	0.81
108_F	119_F	1.174	0.81
75_I	115_F	1.173	0.81
65_Q	100_P	1.170	0.81
216_V	229_R	1.170	0.81
72_D	91_Q	1.163	0.80
277_L	284_V	1.158	0.80
252_I	317_V	1.143	0.79
230_S	235_I	1.143	0.79
281_H	308_V	1.139	0.79
63_R	231_S	1.132	0.78
121_H	124_W	1.131	0.78
251_F	297_V	1.123	0.78
153_A	156_S	1.116	0.77
296_I	304_W	1.111	0.77
90_F	166_Y	1.107	0.77
118_I	173_A	1.104	0.77
152_R	160_H	1.100	0.76
78_L	318_P	1.091	0.76
189_F	245_V	1.090	0.76
247_M	313_W	1.089	0.76
120_V	140_M	1.082	0.75
111_L	316_I	1.078	0.75
95_P	166_Y	1.077	0.75
56_V	88_A	1.074	0.75
77_A	316_I	1.068	0.74
35_A	39_G	1.063	0.74
254_E	277_L	1.058	0.73
151_W	164_T	1.051	0.73
250_I	279_F	1.036	0.72
218_Y	229_R	1.035	0.72
197_A	202_N	1.033	0.72
55_V	77_A	1.025	0.71
203_V	207_Y	1.025	0.71
51_P	184_T	1.022	0.71
57_N	232_D	1.005	0.70
66_S	239_R	0.998	0.69
27_P	30_A	0.998	0.69
82_Q	257_H	0.993	0.69
139_Y	178_Y	0.985	0.68
119_F	260_I	0.983	0.68
17_L	21_Q	0.980	0.68
151_W	169_I	0.977	0.67
52_V	120_V	0.973	0.67
142_G	150_F	0.969	0.67
15_F	18_V	0.963	0.66
146_D	162_S	0.954	0.65
73_I	115_F	0.950	0.65
13_V	17_L	0.946	0.65
197_A	207_Y	0.945	0.65
14_F	34_K	0.940	0.64
254_E	317_V	0.937	0.64
205_V	305_L	0.936	0.64
124_W	291_Q	0.934	0.64
187_L	314_I	0.934	0.64
85_R	102_R	0.930	0.63
227_Y	238_D	0.929	0.63
85_R	103_S	0.928	0.63
269_D	273_G	0.912	0.62
164_T	169_I	0.909	0.62
63_R	86_F	0.903	0.61
261_D	318_P	0.902	0.61
152_R	158_P	0.897	0.61
31_K	34_K	0.897	0.61
25_A	29_T	0.894	0.60
62_A	160_H	0.893	0.60
35_A	189_F	0.886	0.60
225_E	281_H	0.883	0.59
63_R	68_L	0.879	0.59
290_K	298_P	0.875	0.59
196_P	199_E	0.875	0.59
273_G	295_R	0.874	0.59
106_E	260_I	0.874	0.59
237_T	242_G	0.870	0.58
25_A	30_A	0.869	0.58
27_P	32_K	0.868	0.58
144_D	199_E	0.863	0.58
156_S	161_N	0.862	0.58
87_L	104_A	0.853	0.57
68_L	88_A	0.853	0.57
36_P	39_G	0.853	0.57
57_N	83_I	0.850	0.56
102_R	105_R	0.846	0.56
50_R	138_D	0.843	0.56
122_H	143_L	0.841	0.56
253_V	271_E	0.840	0.56
255_A	316_I	0.837	0.55
17_L	22_Q	0.837	0.55
124_W	132_L	0.835	0.55
98_V	148_S	0.830	0.55
57_N	66_S	0.830	0.55
56_V	98_V	0.830	0.55
78_L	207_Y	0.825	0.54
25_A	31_K	0.823	0.54
199_E	235_I	0.822	0.54
51_P	89_I	0.821	0.54
115_F	314_I	0.818	0.54
204_R	217_E	0.813	0.53
280_Q	291_Q	0.812	0.53
272_S	307_F	0.812	0.53
15_F	30_A	0.808	0.53
65_Q	86_F	0.807	0.53
28_D	31_K	0.804	0.52
201_Y	222_K	0.804	0.52
64_P	156_S	0.802	0.52
37_L	189_F	0.800	0.52
155_F	159_P	0.799	0.52
54_V	87_L	0.798	0.52
229_R	247_M	0.797	0.52
122_H	159_P	0.797	0.52
78_L	266_R	0.797	0.52
295_R	298_P	0.794	0.51
156_S	159_P	0.787	0.51
32_K	203_V	0.787	0.51
63_R	242_G	0.787	0.51
55_V	220_Y	0.785	0.51
253_V	297_V	0.785	0.51
248_Q	308_V	0.783	0.50
100_P	232_D	0.781	0.50
264_G	318_P	0.777	0.50
69_S	243_K	0.776	0.50
121_H	143_L	0.774	0.50
33_L	41_K	0.771	0.49
74_V	245_V	0.771	0.49
75_I	87_L	0.768	0.49
190_Q	193_D	0.766	0.49
76_E	216_V	0.764	0.49
50_R	118_I	0.763	0.49
81_G	101_V	0.762	0.49
150_F	162_S	0.758	0.48
53_A	112_S	0.755	0.48
141_N	145_F	0.755	0.48
197_A	314_I	0.754	0.48
91_Q	312_T	0.754	0.48
257_H	268_I	0.753	0.48
205_V	317_V	0.752	0.48
187_L	297_V	0.752	0.48
276_G	286_E	0.749	0.47
107_Y	268_I	0.749	0.47
12_F	16_L	0.748	0.47
291_Q	294_G	0.745	0.47
104_A	260_I	0.745	0.47
52_V	169_I	0.744	0.47
227_Y	282_G	0.744	0.47
152_R	162_S	0.743	0.47
111_L	128_A	0.739	0.46
191_T	194_A	0.739	0.46
74_V	290_K	0.739	0.46
55_V	121_H	0.738	0.46
65_Q	80_E	0.734	0.46
125_S	265_R	0.728	0.45
107_Y	265_R	0.725	0.45
55_V	107_Y	0.723	0.45
57_N	100_P	0.723	0.45
124_W	172_A	0.723	0.45
169_I	316_I	0.722	0.45
124_W	141_N	0.720	0.45
109_V	128_A	0.719	0.45
229_R	313_W	0.718	0.45
149_L	162_S	0.716	0.44
121_H	139_Y	0.715	0.44
98_V	166_Y	0.714	0.44
280_Q	312_T	0.710	0.44
179_K	183_E	0.708	0.44
78_L	257_H	0.708	0.44
35_A	38_T	0.704	0.43
233_G	250_I	0.704	0.43
177_G	241_T	0.703	0.43
222_K	233_G	0.703	0.43
125_S	164_T	0.702	0.43
12_F	26_V	0.700	0.43
243_K	303_K	0.700	0.43
79_A	266_R	0.700	0.43
62_A	152_R	0.699	0.43
217_E	230_S	0.699	0.43
177_G	201_Y	0.699	0.43
35_A	92_S	0.695	0.42
57_N	268_I	0.694	0.42
26_V	154_D	0.694	0.42
276_G	305_L	0.691	0.42
189_F	307_F	0.688	0.42
114_G	294_G	0.686	0.42
298_P	304_W	0.686	0.42
100_P	163_Y	0.685	0.42
237_T	244_P	0.684	0.41
69_S	238_D	0.680	0.41
29_T	32_K	0.679	0.41
200_S	207_Y	0.678	0.41
25_A	28_D	0.672	0.40
10_L	18_V	0.669	0.40
251_F	300_K	0.667	0.40
299_V	304_W	0.666	0.40
96_E	192_S	0.666	0.40
62_A	88_A	0.664	0.40
116_D	209_T	0.663	0.40
58_N	63_R	0.661	0.39
187_L	312_T	0.658	0.39
75_I	251_F	0.657	0.39
71_A	88_A	0.657	0.39
14_F	19_S	0.657	0.39
56_V	68_L	0.655	0.39
126_P	263_D	0.653	0.39
16_L	20_C	0.653	0.39
168_Y	171_K	0.652	0.39
198_N	279_F	0.652	0.39
229_R	257_H	0.649	0.38
10_L	15_F	0.649	0.38
248_Q	311_K	0.648	0.38
63_R	152_R	0.646	0.38
288_D	299_V	0.646	0.38
57_N	86_F	0.646	0.38
27_P	34_K	0.643	0.38
21_Q	24_D	0.640	0.38
90_F	246_A	0.638	0.37
10_L	14_F	0.638	0.37
207_Y	268_I	0.636	0.37
165_S	242_G	0.636	0.37
171_K	198_N	0.634	0.37
130_K	134_S	0.633	0.37
72_D	111_L	0.633	0.37
15_F	20_C	0.633	0.37
63_R	66_S	0.633	0.37
59_H	160_H	0.632	0.37
77_A	268_I	0.631	0.37
307_F	312_T	0.631	0.37
63_R	232_D	0.630	0.37
287_T	290_K	0.630	0.37
139_Y	169_I	0.629	0.37
155_F	161_N	0.627	0.37
28_D	32_K	0.626	0.36
255_A	270_L	0.625	0.36
110_T	131_Q	0.624	0.36
80_E	159_P	0.624	0.36
152_R	159_P	0.624	0.36
56_V	233_G	0.622	0.36
80_E	100_P	0.622	0.36
149_L	164_T	0.620	0.36
156_S	163_Y	0.618	0.36
126_P	130_K	0.618	0.36
128_A	160_H	0.617	0.36
197_A	206_D	0.615	0.36
291_Q	306_P	0.614	0.35
174_E	243_K	0.614	0.35
72_D	268_I	0.613	0.35
114_G	251_F	0.613	0.35
107_Y	160_H	0.610	0.35
76_E	249_N	0.607	0.35
13_V	40_L	0.606	0.35
164_T	168_Y	0.606	0.35
255_A	268_I	0.603	0.35
14_F	89_I	0.601	0.34
14_F	18_V	0.599	0.34
197_A	203_V	0.598	0.34
258_H	269_D	0.598	0.34
89_I	97_T	0.598	0.34
288_D	296_I	0.596	0.34
80_E	161_N	0.596	0.34
36_P	72_D	0.594	0.34
96_E	234_V	0.593	0.34
69_S	242_G	0.592	0.34
10_L	13_V	0.592	0.34
22_Q	222_K	0.591	0.34
26_V	34_K	0.591	0.34
35_A	91_Q	0.591	0.34
71_A	90_F	0.591	0.34
121_H	220_Y	0.590	0.33
73_I	89_I	0.590	0.33
140_M	176_K	0.588	0.33
77_A	108_F	0.587	0.33
24_D	28_D	0.584	0.33
81_G	265_R	0.582	0.33
260_I	265_R	0.582	0.33
52_V	166_Y	0.582	0.33
108_F	121_H	0.582	0.33
15_F	32_K	0.581	0.33
56_V	75_I	0.579	0.33
75_I	314_I	0.579	0.33
261_D	265_R	0.578	0.33
74_V	86_F	0.576	0.32
278_L	297_V	0.573	0.32
288_D	301_D	0.571	0.32
36_P	92_S	0.569	0.32
125_S	143_L	0.568	0.32
98_V	167_D	0.567	0.32
128_A	143_L	0.565	0.31
82_Q	121_H	0.565	0.31
112_S	117_S	0.561	0.31
290_K	316_I	0.561	0.31
157_K	258_H	0.560	0.31
256_S	269_D	0.560	0.31
156_S	160_H	0.556	0.31
78_L	265_R	0.556	0.31
107_Y	119_F	0.554	0.31
92_S	159_P	0.554	0.31
25_A	33_L	0.551	0.30
285_I	300_K	0.551	0.30
132_L	172_A	0.551	0.30
78_L	125_S	0.547	0.30
118_I	138_D	0.547	0.30
47_T	290_K	0.546	0.30
121_H	214_N	0.544	0.30
280_Q	305_L	0.543	0.30
174_E	177_G	0.543	0.30
124_W	143_L	0.538	0.29
115_F	267_D	0.537	0.29
96_E	256_S	0.536	0.29
113_N	137_A	0.535	0.29
78_L	218_Y	0.533	0.29
89_I	117_S	0.533	0.29
114_G	121_H	0.533	0.29
258_H	293_N	0.533	0.29
256_S	320_L	0.531	0.29
57_N	62_A	0.530	0.29
66_S	255_A	0.529	0.29
122_H	161_N	0.528	0.29
38_T	294_G	0.527	0.29
193_D	225_E	0.526	0.29
114_G	297_V	0.525	0.28
118_I	140_M	0.524	0.28
149_L	172_A	0.524	0.28
58_N	80_E	0.521	0.28
245_V	301_D	0.521	0.28
12_F	22_Q	0.520	0.28
98_V	168_Y	0.520	0.28
56_V	130_K	0.520	0.28
38_T	189_F	0.520	0.28
23_K	32_K	0.519	0.28
10_L	24_D	0.518	0.28
11_C	29_T	0.518	0.28
207_Y	233_G	0.517	0.28
11_C	21_Q	0.516	0.28
48_E	96_E	0.516	0.28
22_Q	32_K	0.515	0.28
198_N	202_N	0.514	0.28
116_D	121_H	0.511	0.27
78_L	208_G	0.511	0.27
121_H	151_W	0.510	0.27
255_A	266_R	0.510	0.27
30_A	293_N	0.508	0.27
73_I	232_D	0.508	0.27
28_D	191_T	0.507	0.27
125_S	165_S	0.506	0.27
100_P	214_N	0.506	0.27
100_P	124_W	0.506	0.27
124_W	128_A	0.504	0.27
57_N	172_A	0.503	0.27
125_S	129_K	0.503	0.27
125_S	268_I	0.503	0.27
82_Q	128_A	0.500	0.27
108_F	316_I	0.500	0.27

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
2psbA	1	0.8731	100	0.145	Contact Map
3zbiC	1	0.0846	81.1	0.958	Contact Map
4yv7A	1	0.7674	72.5	0.961	Contact Map
4utoA	1	0.7221	72.2	0.961	Contact Map
1xt8A	1	0.6284	64	0.963	Contact Map
4wzzA	1	0.7704	58.4	0.965	Contact Map
4jg9A	2	0.3505	56.9	0.965	Contact Map
1yr2A	1	0.5952	56.5	0.965	Contact Map
2hyxA	2	0.852	51.5	0.966	Contact Map
2wtpA	2	0.2508	50.1	0.966	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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