YNCB - BACSU - GREMLIN Contacts

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YNCB - Endonuclease YncB

UniProt:	P94492	Sequences: MKKILISMIAIVLSITLAACGSNHAAKNHSDSNGTEQVSQDTHSNEYNQTEQKAGTPHSKNQKKLVNVTLDRAIDGDTIKVIYNGKKDTVRYLLVDTPETKKPNSCVQPYGEDASKRNKELVNSGKLQLEFDKGDRRDKYGRLLAYVYVDGKSVQETLLKEGLARVAYVYEPNTKYIDQFRLDEQEAKSDKLSIWSKSGYVTNRGFNGCVK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	211 (168)
Sequences:	417 (357)
Seq/√Len:	27.5

BACSU - YNCB YOKF

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
118_N	154_V	3.365	1.00
181_R	184_E	2.862	1.00
92_Y	118_N	2.798	1.00
80_K	89_T	2.731	1.00
122_V	127_L	2.620	0.99
153_S	180_F	2.574	0.99
70_L	127_L	2.573	0.99
91_R	99_E	2.405	0.99
70_L	73_A	2.397	0.99
77_D	99_E	2.338	0.99
159_L	180_F	2.291	0.98
95_V	158_L	2.245	0.98
122_V	154_V	2.150	0.98
156_E	179_Q	2.101	0.97
91_R	142_R	2.056	0.97
185_Q	189_S	2.041	0.97
91_R	96_D	1.994	0.96
184_E	188_K	1.982	0.96
72_R	80_K	1.972	0.96
162_G	187_A	1.971	0.96
81_V	129_L	1.925	0.95
99_E	142_R	1.910	0.95
79_I	92_Y	1.905	0.95
117_R	158_L	1.881	0.95
85_G	88_D	1.873	0.94
121_L	154_V	1.872	0.94
118_N	122_V	1.837	0.94
75_D	96_D	1.825	0.94
77_D	142_R	1.823	0.94
100_T	111_G	1.814	0.93
130_E	175_K	1.757	0.92
117_R	121_L	1.739	0.92
91_R	140_Y	1.714	0.91
99_E	140_Y	1.704	0.91
96_D	99_E	1.663	0.90
75_D	91_R	1.605	0.88
127_L	147_V	1.569	0.87
70_L	79_I	1.542	0.86
68_V	81_V	1.539	0.86
94_L	194_I	1.538	0.86
102_K	105_S	1.506	0.85
75_D	99_E	1.472	0.83
65_L	128_Q	1.448	0.82
88_D	137_R	1.377	0.79
131_F	136_R	1.373	0.79
160_K	186_E	1.359	0.78
73_A	79_I	1.354	0.78
132_D	146_Y	1.337	0.77
92_Y	127_L	1.337	0.77
157_T	160_K	1.320	0.76
75_D	78_T	1.297	0.75
129_L	145_A	1.287	0.74
109_P	166_V	1.285	0.74
165_R	194_I	1.284	0.74
70_L	125_G	1.268	0.73
93_L	168_Y	1.250	0.72
115_S	119_K	1.246	0.72
73_A	123_N	1.245	0.72
96_D	142_R	1.213	0.70
100_T	115_S	1.196	0.68
75_D	140_Y	1.185	0.68
68_V	124_S	1.180	0.67
77_D	91_R	1.176	0.67
118_N	158_L	1.169	0.67
36_E	39_S	1.165	0.66
168_Y	194_I	1.155	0.66
130_E	176_Y	1.132	0.64
131_F	143_L	1.128	0.64
96_D	140_Y	1.127	0.64
164_A	172_P	1.123	0.63
159_L	166_V	1.114	0.63
42_T	50_T	1.111	0.63
158_L	161_E	1.104	0.62
70_L	124_S	1.090	0.61
99_E	138_D	1.076	0.60
137_R	143_L	1.052	0.58
180_F	183_D	1.046	0.58
165_R	200_Y	1.043	0.58
92_Y	184_E	1.040	0.57
155_Q	159_L	1.037	0.57
93_L	151_G	1.036	0.57
102_K	106_C	1.028	0.57
156_E	183_D	1.027	0.56
69_T	125_G	1.024	0.56
138_D	142_R	1.018	0.56
101_K	115_S	1.014	0.55
38_V	43_H	1.014	0.55
100_T	112_E	1.007	0.55
94_L	177_I	1.001	0.54
159_L	190_D	0.997	0.54
93_L	144_L	0.986	0.53
91_R	138_D	0.983	0.53
47_Y	58_H	0.972	0.52
155_Q	180_F	0.957	0.51
103_P	107_V	0.955	0.51
73_A	127_L	0.954	0.51
81_V	124_S	0.940	0.50
77_D	138_D	0.936	0.50
38_V	53_K	0.928	0.49
140_Y	144_L	0.926	0.49
153_S	195_W	0.921	0.48
93_L	132_D	0.913	0.48
39_S	55_G	0.909	0.47
184_E	195_W	0.902	0.47
92_Y	98_P	0.892	0.46
76_G	97_T	0.890	0.46
177_I	181_R	0.884	0.46
133_K	173_N	0.854	0.43
75_D	142_R	0.853	0.43
43_H	49_Q	0.837	0.42
100_T	105_S	0.832	0.42
97_T	118_N	0.831	0.42
42_T	47_Y	0.824	0.41
130_E	159_L	0.824	0.41
77_D	96_D	0.820	0.41
50_T	56_T	0.815	0.40
76_G	91_R	0.815	0.40
101_K	106_C	0.811	0.40
85_G	158_L	0.810	0.40
186_E	192_L	0.807	0.40
85_G	132_D	0.804	0.40
117_R	120_E	0.796	0.39
148_Y	153_S	0.795	0.39
157_T	161_E	0.791	0.39
44_S	47_Y	0.787	0.38
133_K	174_T	0.784	0.38
93_L	146_Y	0.780	0.38
81_V	159_L	0.779	0.38
78_T	99_E	0.779	0.38
117_R	154_V	0.778	0.38
76_G	99_E	0.775	0.38
46_E	53_K	0.775	0.38
36_E	52_Q	0.765	0.37
100_T	129_L	0.763	0.37
54_A	57_P	0.755	0.36
179_Q	182_L	0.755	0.36
96_D	138_D	0.753	0.36
167_A	203_N	0.752	0.36
73_A	118_N	0.751	0.36
97_T	138_D	0.750	0.36
75_D	144_L	0.747	0.36
69_T	151_G	0.745	0.35
41_D	45_N	0.745	0.35
39_S	44_S	0.744	0.35
96_D	144_L	0.737	0.35
146_Y	172_P	0.731	0.34
133_K	171_E	0.731	0.34
97_T	115_S	0.730	0.34
48_N	53_K	0.729	0.34
45_N	52_Q	0.728	0.34
90_V	129_L	0.721	0.34
139_K	168_Y	0.718	0.34
156_E	160_K	0.718	0.34
139_K	170_Y	0.718	0.34
92_Y	155_Q	0.717	0.34
49_Q	53_K	0.717	0.34
73_A	124_S	0.710	0.33
46_E	54_A	0.701	0.32
76_G	98_P	0.696	0.32
49_Q	66_V	0.690	0.32
91_R	97_T	0.689	0.32
159_L	192_L	0.689	0.32
114_A	178_D	0.688	0.32
191_K	197_K	0.684	0.31
199_G	203_N	0.677	0.31
90_V	108_Q	0.675	0.31
84_N	118_N	0.671	0.30
177_I	188_K	0.670	0.30
191_K	198_S	0.666	0.30
153_S	170_Y	0.665	0.30
117_R	161_E	0.662	0.30
47_Y	51_E	0.662	0.30
130_E	148_Y	0.660	0.30
166_V	184_E	0.660	0.30
94_L	169_V	0.652	0.29
124_S	145_A	0.652	0.29
95_V	164_A	0.652	0.29
131_F	145_A	0.651	0.29
42_T	54_A	0.649	0.29
76_G	111_G	0.648	0.29
159_L	181_R	0.646	0.29
159_L	183_D	0.638	0.28
40_Q	43_H	0.635	0.28
108_Q	174_T	0.630	0.28
52_Q	58_H	0.630	0.28
83_Y	131_F	0.628	0.28
177_I	192_L	0.627	0.28
183_D	188_K	0.625	0.28
89_T	189_S	0.621	0.27
51_E	58_H	0.619	0.27
78_T	142_R	0.618	0.27
48_N	52_Q	0.615	0.27
95_V	182_L	0.613	0.27
155_Q	170_Y	0.607	0.27
117_R	169_V	0.605	0.26
50_T	58_H	0.602	0.26
191_K	203_N	0.599	0.26
133_K	172_P	0.599	0.26
114_A	163_L	0.599	0.26
40_Q	46_E	0.597	0.26
35_T	43_H	0.594	0.26
35_T	40_Q	0.592	0.26
55_G	58_H	0.591	0.26
77_D	140_Y	0.589	0.25
105_S	159_L	0.588	0.25
146_Y	195_W	0.584	0.25
125_G	149_V	0.582	0.25
95_V	121_L	0.582	0.25
107_V	112_E	0.579	0.25
165_R	202_T	0.579	0.25
98_P	164_A	0.572	0.24
80_K	87_K	0.572	0.24
32_S	49_Q	0.570	0.24
112_E	116_K	0.569	0.24
39_S	42_T	0.569	0.24
73_A	125_G	0.568	0.24
129_L	147_V	0.567	0.24
62_Q	67_N	0.564	0.24
148_Y	174_T	0.563	0.24
49_Q	55_G	0.561	0.24
40_Q	48_N	0.561	0.24
76_G	129_L	0.559	0.24
183_D	186_E	0.555	0.24
185_Q	188_K	0.552	0.23
71_D	193_S	0.550	0.23
67_N	126_K	0.550	0.23
76_G	164_A	0.548	0.23
91_R	144_L	0.547	0.23
146_Y	155_Q	0.542	0.23
168_Y	188_K	0.539	0.23
78_T	96_D	0.533	0.22
77_D	111_G	0.530	0.22
76_G	96_D	0.529	0.22
167_A	172_P	0.529	0.22
122_V	147_V	0.529	0.22
47_Y	56_T	0.529	0.22
68_V	127_L	0.525	0.22
178_D	198_S	0.525	0.22
132_D	144_L	0.523	0.22
93_L	97_T	0.523	0.22
46_E	51_E	0.522	0.22
126_K	151_G	0.522	0.22
79_I	147_V	0.522	0.22
44_S	58_H	0.521	0.22
191_K	194_I	0.512	0.21
92_Y	157_T	0.509	0.21
75_D	138_D	0.507	0.21
32_S	36_E	0.504	0.21
167_A	173_N	0.503	0.21
32_S	38_V	0.502	0.21
137_R	177_I	0.500	0.21
37_Q	52_Q	0.500	0.21

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
4eqpA	1	0.6066	100	0.402	Contact Map
3bdlA	2	0.7062	100	0.409	Contact Map
4qmgA	3	0.6919	100	0.414	Contact Map
2wacA	1	0.8863	99.9	0.494	Contact Map
2hqxA	2	0.3033	99.9	0.502	Contact Map
4b9wA	2	0.7299	98.9	0.771	Contact Map
4q5yA	2	0.6919	98.6	0.8	Contact Map
3ntkA	1	0.7251	98.4	0.809	Contact Map
4b9xA	1	0.7583	98.3	0.814	Contact Map
4q5wA	1	0.763	97.8	0.835	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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