YHCN - BACSU - GREMLIN Contacts

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YHCN - Lipoprotein YhcN

UniProt:	P54598	Sequences: MFGKKQVLASVLLIPLLMTGCGVADQGEGRRDNNDVRNVNYRNPANDDMRNVNNRDNVDNNVNDNVNNNRVNDDNNNDRKLEVADEAADKVTDLKEVKHADIIVAGNQAYVAVVLTNGNKGAVENNLKKKIAKKVRSTDKNIDNVYVSANPDFVERMQGYGKRIQNGDPIAGLFDEFTQTVQRVFPNAE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	189 (165)
Sequences:	262 (241)
Seq/√Len:	18.7

BACSU - YHCN YLAJ

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
96_E	130_K	3.344	1.00
128_K	149_A	3.234	0.99
92_T	100_A	2.838	0.99
112_A	157_M	2.768	0.98
87_A	135_V	2.725	0.98
105_A	108_Q	2.679	0.98
156_R	179_Q	2.595	0.97
148_S	153_F	2.565	0.97
103_I	157_M	2.565	0.97
110_Y	185_F	2.491	0.97
112_A	148_S	2.367	0.95
113_V	149_A	2.303	0.95
146_Y	185_F	2.285	0.94
156_R	176_E	2.264	0.94
114_V	150_N	2.168	0.93
169_P	176_E	2.047	0.90
12_L	19_T	2.002	0.89
113_V	131_I	1.977	0.89
147_V	156_R	1.924	0.87
113_V	127_L	1.915	0.87
152_D	173_L	1.876	0.86
150_N	153_F	1.862	0.86
148_S	185_F	1.856	0.85
152_D	183_R	1.856	0.85
163_R	168_D	1.840	0.85
88_A	151_P	1.825	0.84
67_N	70_R	1.822	0.84
91_V	97_V	1.770	0.82
169_P	186_P	1.758	0.82
177_F	185_F	1.725	0.81
135_V	145_V	1.684	0.79
110_Y	160_Y	1.681	0.79
160_Y	185_F	1.604	0.76
39_V	61_N	1.594	0.75
169_P	172_G	1.591	0.75
102_I	105_A	1.554	0.73
91_V	94_L	1.539	0.72
151_P	169_P	1.508	0.71
176_E	183_R	1.496	0.70
110_Y	148_S	1.477	0.69
153_F	185_F	1.433	0.67
110_Y	146_Y	1.414	0.66
183_R	186_P	1.393	0.65
147_V	186_P	1.387	0.64
153_F	160_Y	1.384	0.64
96_E	116_T	1.287	0.58
91_V	131_I	1.286	0.58
88_A	102_I	1.273	0.57
63_N	118_G	1.265	0.57
6_Q	9_A	1.265	0.57
149_A	176_E	1.253	0.56
168_D	171_A	1.252	0.56
177_F	181_V	1.244	0.56
83_V	139_D	1.243	0.56
145_V	185_F	1.243	0.56
94_L	187_N	1.242	0.55
98_K	161_G	1.236	0.55
16_L	137_S	1.225	0.54
172_G	186_P	1.224	0.54
124_E	182_Q	1.223	0.54
6_Q	18_M	1.206	0.53
38_N	42_R	1.185	0.52
163_R	172_G	1.177	0.51
69_N	175_D	1.160	0.50
116_T	134_K	1.136	0.49
86_E	148_S	1.127	0.48
102_I	177_F	1.123	0.48
98_K	147_V	1.110	0.47
102_I	108_Q	1.083	0.45
20_G	94_L	1.080	0.45
86_E	129_K	1.074	0.45
6_Q	17_L	1.069	0.45
87_A	128_K	1.067	0.45
148_S	177_F	1.067	0.45
19_T	89_D	1.065	0.44
91_V	115_L	1.020	0.42
112_A	185_F	1.018	0.41
60_N	71_V	1.016	0.41
14_I	82_E	1.015	0.41
15_P	68_N	1.010	0.41
169_P	183_R	1.002	0.41
112_A	130_K	0.999	0.40
8_L	15_P	0.994	0.40
154_V	160_Y	0.993	0.40
82_E	85_D	0.985	0.39
37_R	41_Y	0.980	0.39
13_L	16_L	0.970	0.39
176_E	186_P	0.965	0.38
152_D	169_P	0.948	0.37
128_K	152_D	0.937	0.37
163_R	166_N	0.935	0.37
151_P	186_P	0.929	0.36
154_V	170_I	0.923	0.36
172_G	183_R	0.919	0.36
92_T	184_V	0.914	0.35
79_R	85_D	0.914	0.35
112_A	160_Y	0.905	0.35
159_G	179_Q	0.901	0.35
84_A	104_V	0.901	0.35
146_Y	158_Q	0.901	0.35
23_V	161_G	0.895	0.34
123_V	127_L	0.892	0.34
110_Y	153_F	0.890	0.34
134_K	137_S	0.889	0.34
110_Y	150_N	0.888	0.34
104_V	142_I	0.880	0.33
92_T	116_T	0.875	0.33
131_I	150_N	0.867	0.33
170_I	178_T	0.861	0.32
16_L	20_G	0.860	0.32
83_V	104_V	0.860	0.32
84_A	88_A	0.847	0.32
11_V	127_L	0.846	0.32
116_T	136_R	0.846	0.32
7_V	133_K	0.846	0.32
110_Y	145_V	0.842	0.31
136_R	155_E	0.841	0.31
150_N	182_Q	0.836	0.31
11_V	18_M	0.827	0.31
17_L	125_N	0.821	0.30
102_I	148_S	0.820	0.30
10_S	14_I	0.819	0.30
135_V	142_I	0.813	0.30
106_G	166_N	0.802	0.29
179_Q	182_Q	0.796	0.29
81_L	88_A	0.791	0.29
102_I	111_V	0.783	0.28
112_A	131_I	0.782	0.28
101_D	155_E	0.774	0.28
139_D	164_I	0.767	0.27
88_A	101_D	0.767	0.27
66_V	69_N	0.766	0.27
108_Q	153_F	0.764	0.27
9_A	77_N	0.763	0.27
24_A	148_S	0.760	0.27
132_A	150_N	0.751	0.27
81_L	102_I	0.751	0.27
7_V	106_G	0.749	0.27
125_N	128_K	0.745	0.26
113_V	130_K	0.743	0.26
20_G	23_V	0.743	0.26
94_L	130_K	0.739	0.26
88_A	131_I	0.738	0.26
104_V	143_D	0.736	0.26
112_A	150_N	0.735	0.26
106_G	180_T	0.734	0.26
96_E	127_L	0.731	0.26
149_A	156_R	0.722	0.25
128_K	169_P	0.721	0.25
102_I	145_V	0.719	0.25
76_N	96_E	0.718	0.25
24_A	27_G	0.714	0.25
132_A	140_K	0.714	0.25
173_L	176_E	0.712	0.25
10_S	17_L	0.705	0.24
95_K	171_A	0.701	0.24
10_S	19_T	0.699	0.24
17_L	42_R	0.698	0.24
154_V	163_R	0.694	0.24
97_V	101_D	0.693	0.24
102_I	106_G	0.691	0.24
89_D	95_K	0.690	0.24
131_I	185_F	0.689	0.24
103_I	164_I	0.682	0.23
9_A	20_G	0.682	0.23
174_F	179_Q	0.673	0.23
81_L	156_R	0.668	0.23
88_A	186_P	0.667	0.23
90_K	144_N	0.653	0.22
112_A	177_F	0.652	0.22
36_V	39_V	0.651	0.22
11_V	59_D	0.648	0.22
110_Y	177_F	0.647	0.22
156_R	186_P	0.647	0.22
84_A	123_V	0.644	0.22
87_A	138_T	0.644	0.22
22_G	137_S	0.644	0.22
175_D	181_V	0.642	0.22
85_D	104_V	0.642	0.22
177_F	180_T	0.632	0.21
66_V	70_R	0.632	0.21
94_L	157_M	0.630	0.21
40_N	133_K	0.624	0.21
97_V	176_E	0.623	0.21
94_L	173_L	0.621	0.21
132_A	136_R	0.620	0.21
60_N	170_I	0.620	0.21
13_L	84_A	0.620	0.21
128_K	183_R	0.619	0.21
152_D	167_G	0.618	0.21
155_E	175_D	0.617	0.21
131_I	149_A	0.616	0.21
167_G	183_R	0.615	0.20
104_V	182_Q	0.613	0.20
59_D	73_D	0.613	0.20
82_E	99_H	0.612	0.20
8_L	13_L	0.605	0.20
37_R	141_N	0.604	0.20
146_Y	177_F	0.598	0.20
151_P	183_R	0.596	0.20
129_K	145_V	0.596	0.20
91_V	130_K	0.594	0.20
108_Q	160_Y	0.585	0.19
152_D	186_P	0.584	0.19
12_L	24_A	0.579	0.19
104_V	156_R	0.579	0.19
108_Q	148_S	0.574	0.19
131_I	160_Y	0.573	0.19
22_G	101_D	0.566	0.19
176_E	181_V	0.565	0.19
27_G	59_D	0.563	0.18
129_K	147_V	0.562	0.18
62_V	65_N	0.557	0.18
106_G	142_I	0.556	0.18
38_N	133_K	0.556	0.18
91_V	112_A	0.553	0.18
101_D	137_S	0.550	0.18
107_N	144_N	0.547	0.18
87_A	91_V	0.545	0.18
153_F	181_V	0.543	0.18
67_N	91_V	0.543	0.18
9_A	139_D	0.542	0.18
61_N	147_V	0.542	0.18
23_V	38_N	0.541	0.18
150_N	185_F	0.540	0.18
74_D	126_N	0.536	0.17
78_D	127_L	0.534	0.17
71_V	161_G	0.533	0.17
81_L	185_F	0.532	0.17
18_M	152_D	0.530	0.17
17_L	22_G	0.529	0.17
12_L	77_N	0.525	0.17
12_L	85_D	0.525	0.17
91_V	187_N	0.522	0.17
112_A	153_F	0.522	0.17
113_V	116_T	0.521	0.17
13_L	184_V	0.518	0.17
10_S	15_P	0.516	0.17
8_L	19_T	0.513	0.17
169_P	173_L	0.511	0.17
103_I	161_G	0.511	0.17
62_V	68_N	0.509	0.16
119_N	129_K	0.509	0.16
84_A	174_F	0.507	0.16
95_K	179_Q	0.506	0.16
165_Q	173_L	0.503	0.16
81_L	97_V	0.502	0.16
19_T	78_D	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
3vxbA	1	0.5132	87.4	0.911	Contact Map
3ombA	1	0.5344	86.9	0.912	Contact Map
2qgmA	1	0.5079	86.6	0.912	Contact Map
4n01A	1	0.6349	81.1	0.918	Contact Map
4yv7A	1	0.545	76.6	0.921	Contact Map
3b55A	1	0.582	76.3	0.921	Contact Map
4utoA	1	0.7143	74.4	0.922	Contact Map
3qaxA	1	0.7037	74.2	0.923	Contact Map
3zbiC	1	0.1481	73.8	0.923	Contact Map
4kysA	1	0.4497	73.3	0.923	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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