YBXI - BACSU - GREMLIN Contacts

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YBXI - Probable beta-lactamase YbxI

UniProt:	P54427	Sequences: MKKWIYVVLVLSIAGIGGFSVHAASSAHEKHLNVSKMNVDDEFKDTDGTFILHDLQKDQTFVYNRKRANQRQTPQSTFKVVNALIGLQVKAVRDEYDVKRWDGVKREFESWNRDHTLGSAMRESAIWYYQALARDIGEERMKTWLHTLSYGNEDISGGIDQFWLQSSLTISPLEQETFLEKLAKEELPFDKPVMKIVKRMMIQEEGDHYTLYGKTGTRLTDMGLGWFVGFIKTEHGSYVFVTNVDDSGTKAKNITVDILKKYGLITS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	267 (231)
Sequences:	674 (512)
Seq/√Len:	33.7

BACSU - YBXI

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
71_R	174_E	4.664	1.00
242_T	255_T	4.382	1.00
146_H	153_E	3.534	1.00
88_Q	193_V	3.489	1.00
183_A	239_V	3.293	1.00
121_M	201_M	2.856	1.00
115_H	119_S	2.812	1.00
148_L	189_F	2.727	1.00
126_I	164_L	2.674	1.00
176_E	241_V	2.585	1.00
83_A	197_V	2.508	1.00
71_R	171_S	2.503	1.00
88_Q	190_D	2.494	1.00
115_H	125_A	2.493	1.00
202_I	210_T	2.490	1.00
142_K	146_H	2.387	0.99
192_P	196_I	2.386	0.99
49_T	68_A	2.256	0.99
182_L	194_M	2.190	0.99
185_E	198_K	2.180	0.99
141_M	145_L	2.069	0.98
83_A	129_Y	2.046	0.98
81_V	178_F	2.036	0.98
231_I	264_L	2.014	0.98
67_R	243_N	1.984	0.98
91_A	136_I	1.981	0.98
141_M	155_I	1.944	0.98
134_R	160_D	1.817	0.96
49_T	172_P	1.808	0.96
101_W	106_R	1.765	0.96
88_Q	144_W	1.712	0.95
129_Y	200_M	1.687	0.94
157_G	166_S	1.668	0.94
82_N	133_A	1.661	0.94
203_Q	213_G	1.645	0.94
228_V	241_V	1.640	0.94
143_T	147_T	1.624	0.93
102_D	106_R	1.610	0.93
118_G	199_R	1.600	0.93
81_V	148_L	1.595	0.93
72_Q	243_N	1.593	0.92
145_L	155_I	1.584	0.92
204_E	256_V	1.579	0.92
73_T	167_S	1.576	0.92
89_V	144_W	1.574	0.92
54_D	236_G	1.554	0.92
78_F	162_F	1.542	0.91
201_M	212_Y	1.502	0.90
76_S	79_K	1.497	0.90
213_G	227_F	1.486	0.90
181_K	186_E	1.478	0.89
231_I	259_L	1.454	0.89
42_E	261_K	1.450	0.88
185_E	194_M	1.419	0.87
83_A	121_M	1.415	0.87
133_A	162_F	1.402	0.87
233_T	236_G	1.400	0.87
141_M	162_F	1.395	0.86
86_G	136_I	1.395	0.86
198_K	232_K	1.389	0.86
82_N	141_M	1.383	0.86
75_Q	217_T	1.383	0.86
73_T	166_S	1.370	0.85
130_Q	164_L	1.357	0.85
172_P	243_N	1.353	0.85
40_D	44_K	1.350	0.84
102_D	112_N	1.346	0.84
115_H	123_E	1.346	0.84
113_R	123_E	1.341	0.84
120_A	129_Y	1.332	0.84
98_V	114_D	1.324	0.83
131_A	135_D	1.317	0.83
182_L	197_V	1.310	0.83
65_R	69_N	1.309	0.83
113_R	191_K	1.294	0.82
203_Q	227_F	1.280	0.81
145_L	164_L	1.263	0.80
193_V	197_V	1.231	0.78
171_S	174_E	1.224	0.78
50_F	255_T	1.216	0.78
106_R	112_N	1.216	0.78
156_S	167_S	1.186	0.76
242_T	251_A	1.166	0.75
113_R	119_S	1.159	0.74
152_N	168_L	1.153	0.74
185_E	195_K	1.145	0.73
185_E	191_K	1.136	0.73
55_L	239_V	1.134	0.72
154_D	157_G	1.134	0.72
51_I	176_E	1.131	0.72
51_I	241_V	1.129	0.72
130_Q	160_D	1.127	0.72
151_G	168_L	1.127	0.72
206_G	209_Y	1.116	0.71
144_W	189_F	1.109	0.71
75_Q	166_S	1.106	0.71
96_Y	116_T	1.104	0.70
130_Q	159_I	1.102	0.70
140_R	143_T	1.101	0.70
78_F	133_A	1.094	0.70
150_Y	175_Q	1.091	0.69
54_D	238_Y	1.089	0.69
82_N	162_F	1.079	0.69
249_T	264_L	1.077	0.68
115_H	127_W	1.076	0.68
70_Q	186_E	1.070	0.68
190_D	193_V	1.062	0.67
67_R	172_P	1.047	0.66
87_L	120_A	1.045	0.66
53_H	92_V	1.045	0.66
205_E	210_T	1.023	0.64
99_K	128_Y	1.007	0.63
53_H	60_T	1.000	0.63
83_A	200_M	0.997	0.62
134_R	164_L	0.994	0.62
67_R	245_D	0.991	0.62
85_I	148_L	0.989	0.62
96_Y	118_G	0.988	0.62
101_W	112_N	0.981	0.61
144_W	148_L	0.975	0.61
127_W	160_D	0.971	0.60
125_A	128_Y	0.965	0.60
141_M	159_I	0.962	0.60
104_V	112_N	0.960	0.59
160_D	164_L	0.959	0.59
131_A	134_R	0.950	0.59
83_A	201_M	0.950	0.59
166_S	169_T	0.937	0.58
72_Q	224_L	0.933	0.57
154_D	158_G	0.930	0.57
202_I	212_Y	0.930	0.57
67_R	72_Q	0.929	0.57
175_Q	228_V	0.928	0.57
157_G	165_Q	0.918	0.56
117_L	120_A	0.914	0.56
56_Q	236_G	0.905	0.55
187_L	194_M	0.904	0.55
172_P	189_F	0.903	0.55
212_Y	218_R	0.902	0.55
126_I	217_T	0.899	0.54
81_V	85_I	0.899	0.54
249_T	253_N	0.892	0.54
72_Q	172_P	0.889	0.54
154_D	166_S	0.886	0.53
121_M	125_A	0.876	0.52
91_A	97_D	0.874	0.52
179_L	228_V	0.873	0.52
41_D	142_K	0.866	0.52
47_D	66_K	0.865	0.52
130_Q	243_N	0.862	0.51
114_D	119_S	0.860	0.51
194_M	230_F	0.859	0.51
85_I	136_I	0.846	0.50
80_V	228_V	0.844	0.50
45_D	105_K	0.844	0.50
154_D	167_S	0.842	0.50
234_E	264_L	0.840	0.49
88_Q	101_W	0.839	0.49
53_H	262_Y	0.836	0.49
128_Y	227_F	0.836	0.49
75_Q	218_R	0.834	0.49
161_Q	165_Q	0.833	0.49
139_E	149_S	0.830	0.49
191_K	195_K	0.830	0.49
95_E	196_I	0.829	0.48
257_D	261_K	0.821	0.48
64_N	227_F	0.817	0.47
100_R	114_D	0.812	0.47
36_K	262_Y	0.811	0.47
166_S	218_R	0.803	0.46
112_N	201_M	0.802	0.46
133_A	141_M	0.801	0.46
76_S	214_K	0.800	0.46
109_E	211_L	0.794	0.46
120_A	162_F	0.793	0.45
132_L	164_L	0.791	0.45
42_E	62_V	0.786	0.45
161_Q	182_L	0.784	0.45
252_K	256_V	0.783	0.45
117_L	129_Y	0.781	0.44
79_K	214_K	0.780	0.44
127_W	230_F	0.777	0.44
149_S	153_E	0.777	0.44
84_L	189_F	0.774	0.44
248_G	251_A	0.772	0.44
78_F	126_I	0.770	0.44
43_F	48_G	0.757	0.42
81_V	189_F	0.752	0.42
79_K	215_T	0.751	0.42
55_L	180_E	0.750	0.42
87_L	129_Y	0.748	0.42
40_D	257_D	0.743	0.41
175_Q	179_L	0.742	0.41
170_I	198_K	0.740	0.41
55_L	237_S	0.738	0.41
82_N	129_Y	0.718	0.39
142_K	153_E	0.717	0.39
45_D	69_N	0.716	0.39
62_V	127_W	0.716	0.39
256_V	260_K	0.715	0.39
128_Y	251_A	0.715	0.39
105_K	109_E	0.714	0.39
159_I	164_L	0.714	0.39
141_M	160_D	0.710	0.39
217_T	251_A	0.704	0.38
191_K	235_H	0.702	0.38
140_R	144_W	0.702	0.38
51_I	68_A	0.702	0.38
166_S	217_T	0.701	0.38
212_Y	230_F	0.696	0.38
183_A	212_Y	0.696	0.38
79_K	129_Y	0.695	0.37
112_N	115_H	0.692	0.37
121_M	197_V	0.691	0.37
116_T	119_S	0.689	0.37
52_L	176_E	0.687	0.37
54_D	95_E	0.687	0.37
119_S	123_E	0.687	0.37
75_Q	251_A	0.687	0.37
103_G	114_D	0.687	0.37
80_V	122_R	0.686	0.37
211_L	244_V	0.681	0.36
51_I	173_L	0.678	0.36
183_A	198_K	0.674	0.36
37_M	262_Y	0.670	0.36
99_K	135_D	0.668	0.35
92_V	200_M	0.667	0.35
41_D	207_D	0.662	0.35
208_H	256_V	0.662	0.35
210_T	232_K	0.662	0.35
176_E	212_Y	0.656	0.34
85_I	135_D	0.656	0.34
126_I	133_A	0.653	0.34
111_W	126_I	0.650	0.34
176_E	179_L	0.647	0.34
152_N	156_S	0.645	0.34
253_N	257_D	0.644	0.34
85_I	141_M	0.643	0.33
119_S	125_A	0.642	0.33
182_L	230_F	0.638	0.33
127_W	168_L	0.636	0.33
90_K	140_R	0.635	0.33
55_L	115_H	0.631	0.33
166_S	213_G	0.625	0.32
95_E	199_R	0.624	0.32
199_R	202_I	0.624	0.32
69_N	173_L	0.624	0.32
122_R	193_V	0.624	0.32
130_Q	134_R	0.624	0.32
84_L	182_L	0.621	0.32
55_L	238_Y	0.620	0.32
180_E	184_K	0.617	0.32
41_D	57_K	0.616	0.31
239_V	255_T	0.613	0.31
165_Q	224_L	0.613	0.31
129_Y	162_F	0.610	0.31
107_E	111_W	0.609	0.31
81_V	145_L	0.609	0.31
86_G	128_Y	0.608	0.31
93_R	248_G	0.607	0.31
73_T	169_T	0.605	0.31
103_G	112_N	0.605	0.31
92_V	97_D	0.604	0.31
108_F	121_M	0.599	0.30
62_V	65_R	0.597	0.30
35_S	261_K	0.595	0.30
93_R	234_E	0.594	0.30
56_Q	235_H	0.593	0.30
224_L	243_N	0.591	0.30
66_K	177_T	0.590	0.30
55_L	58_D	0.589	0.30
49_T	62_V	0.588	0.30
87_L	162_F	0.585	0.29
121_M	200_M	0.584	0.29
87_L	193_V	0.582	0.29
87_L	117_L	0.581	0.29
171_S	175_Q	0.580	0.29
168_L	172_P	0.579	0.29
104_V	131_A	0.577	0.29
146_H	155_I	0.577	0.29
186_E	237_S	0.576	0.29
246_D	251_A	0.575	0.29
100_R	207_D	0.574	0.29
195_K	198_K	0.572	0.28
83_A	186_E	0.571	0.28
48_G	63_Y	0.569	0.28
51_I	203_Q	0.569	0.28
48_G	87_L	0.567	0.28
211_L	231_I	0.564	0.28
89_V	136_I	0.563	0.28
85_I	162_F	0.563	0.28
188_P	191_K	0.562	0.28
101_W	115_H	0.562	0.28
156_S	254_I	0.562	0.28
37_M	42_E	0.560	0.28
175_Q	229_G	0.560	0.28
134_R	162_F	0.560	0.28
153_E	173_L	0.559	0.28
61_F	233_T	0.558	0.27
173_L	190_D	0.558	0.27
231_I	247_S	0.557	0.27
91_A	135_D	0.557	0.27
77_T	80_V	0.556	0.27
80_V	192_P	0.554	0.27
148_L	203_Q	0.554	0.27
101_W	104_V	0.553	0.27
142_K	155_I	0.553	0.27
116_T	250_K	0.552	0.27
103_G	106_R	0.551	0.27
94_D	196_I	0.547	0.27
86_G	95_E	0.546	0.27
229_G	240_F	0.545	0.27
77_T	229_G	0.543	0.26
150_Y	228_V	0.541	0.26
123_E	127_W	0.539	0.26
226_W	229_G	0.535	0.26
148_L	194_M	0.533	0.26
113_R	143_T	0.532	0.26
204_E	263_G	0.530	0.26
75_Q	165_Q	0.529	0.26
83_A	120_A	0.529	0.26
121_M	251_A	0.527	0.25
179_L	239_V	0.526	0.25
148_L	178_F	0.524	0.25
128_Y	258_I	0.522	0.25
97_D	227_F	0.522	0.25
91_A	140_R	0.521	0.25
103_G	111_W	0.520	0.25
217_T	246_D	0.520	0.25
209_Y	230_F	0.518	0.25
254_I	258_I	0.516	0.25
59_Q	64_N	0.516	0.25
85_I	89_V	0.514	0.25
106_R	111_W	0.513	0.25
204_E	209_Y	0.513	0.25
133_A	187_L	0.513	0.25
82_N	132_L	0.511	0.24
50_F	201_M	0.510	0.24
76_S	215_T	0.510	0.24
97_D	156_S	0.507	0.24
166_S	251_A	0.507	0.24
166_S	227_F	0.506	0.24
150_Y	229_G	0.506	0.24
91_A	132_L	0.502	0.24
136_I	140_R	0.501	0.24
53_H	238_Y	0.500	0.24

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
4s2pA	2	0.8801	100	0.573	Contact Map
4iedA	1	0.8914	100	0.574	Contact Map
4zdxA	1	0.8727	100	0.575	Contact Map
1xkzA	2	0.9139	100	0.582	Contact Map
1nrfA	1	0.8914	100	0.586	Contact Map
1k38A	2	0.8614	100	0.588	Contact Map
2iwbA	1	0.8951	100	0.59	Contact Map
4oh0A	1	0.8764	100	0.592	Contact Map
2x02A	2	0.8876	100	0.599	Contact Map
4jf5A	1	0.8764	100	0.602	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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