LIAF - BACSU - GREMLIN Contacts

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LIAF - Protein LiaF

UniProt:	O32199	Sequences: MTKKQLLGLIIALFGISMFLQIIGIGDLLFWPLFFLIAGYFLKKYSRDWLGSVMYIFAAFLFLKNLFSITFNLFGYAFAAFLIYAGYRLIKGKPIFEPNEKQVNLNKKEHHEPPKDVKHPDMRSFFIGELQMMKQPFDLNDLNVSGFIGDIKIDLSKAMIPEGESTIVISGVIGNVDIYVPSDLEVAVSSAVFIGDINLIGSKKSGLSTKVYAASTDFSESKRRVKVSVSLFIGDVDVKYV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	241 (193)
Sequences:	703 (596)
Seq/√Len:	42.9

BACSU - LIAF

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
148_I	173_I	6.793	1.00
127_I	148_I	5.276	1.00
150_D	175_N	4.957	1.00
175_N	196_D	3.627	1.00
127_I	173_I	3.385	1.00
127_I	194_I	3.248	1.00
129_E	175_N	3.221	1.00
129_E	150_D	3.056	1.00
173_I	194_I	3.032	1.00
150_D	196_D	2.948	1.00
139_L	142_L	2.862	1.00
171_G	176_V	2.745	1.00
147_F	172_V	2.709	1.00
53_V	57_F	2.668	1.00
174_G	195_G	2.616	1.00
12_A	87_Y	2.413	1.00
155_L	178_I	2.407	1.00
20_L	25_I	2.405	1.00
11_I	82_L	2.334	1.00
180_V	186_V	2.123	0.99
145_S	170_S	2.050	0.99
58_A	154_D	2.014	0.99
129_E	196_D	1.990	0.99
35_F	39_G	1.989	0.99
160_I	165_S	1.954	0.99
8_G	90_I	1.850	0.99
36_L	58_A	1.815	0.98
35_F	40_Y	1.774	0.98
142_L	167_I	1.704	0.97
186_V	200_I	1.690	0.97
62_F	188_V	1.642	0.97
32_P	39_G	1.598	0.96
15_G	39_G	1.505	0.95
128_G	149_G	1.502	0.95
144_V	169_I	1.489	0.94
31_W	79_A	1.480	0.94
30_F	61_L	1.461	0.94
28_L	38_A	1.443	0.93
15_G	83_I	1.415	0.93
125_F	146_G	1.406	0.92
15_G	86_G	1.388	0.92
35_F	54_M	1.359	0.91
28_L	46_S	1.338	0.90
139_L	165_S	1.336	0.90
128_G	195_G	1.331	0.90
15_G	58_A	1.320	0.90
63_L	69_I	1.312	0.90
39_G	79_A	1.310	0.90
78_F	81_F	1.290	0.89
76_Y	80_A	1.266	0.88
119_H	138_D	1.265	0.88
69_I	180_V	1.224	0.86
126_F	172_V	1.219	0.86
73_L	76_Y	1.216	0.86
58_A	62_F	1.204	0.85
19_F	80_A	1.202	0.85
8_G	86_G	1.198	0.85
175_N	200_I	1.188	0.84
133_M	154_D	1.187	0.84
99_N	102_Q	1.156	0.83
34_F	38_A	1.143	0.82
175_N	199_L	1.141	0.82
146_G	171_G	1.135	0.81
19_F	34_F	1.114	0.80
35_F	38_A	1.109	0.80
6_L	41_F	1.109	0.80
137_F	141_D	1.105	0.80
149_G	174_G	1.098	0.79
16_I	188_V	1.092	0.79
36_L	55_Y	1.091	0.79
172_V	193_F	1.074	0.78
141_D	174_G	1.074	0.78
51_G	58_A	1.058	0.77
63_L	154_D	1.052	0.76
141_D	199_L	1.038	0.75
61_L	83_I	1.037	0.75
60_F	186_V	1.036	0.75
28_L	101_K	1.016	0.74
143_N	168_V	1.015	0.74
180_V	188_V	1.014	0.74
52_S	83_I	0.997	0.72
81_F	88_R	0.996	0.72
12_A	19_F	0.987	0.72
87_Y	90_I	0.983	0.71
79_A	83_I	0.981	0.71
139_L	206_G	0.976	0.71
152_K	194_I	0.973	0.70
39_G	42_L	0.968	0.70
126_F	147_F	0.966	0.70
15_G	79_A	0.960	0.69
39_G	80_A	0.956	0.69
161_P	164_E	0.948	0.68
36_L	39_G	0.944	0.68
124_S	145_S	0.938	0.68
143_N	151_I	0.923	0.66
25_I	153_I	0.921	0.66
146_G	151_I	0.918	0.66
33_L	41_F	0.915	0.66
13_L	28_L	0.905	0.65
28_L	194_I	0.900	0.64
132_M	184_L	0.899	0.64
54_M	58_A	0.899	0.64
137_F	156_S	0.899	0.64
67_F	74_F	0.898	0.64
11_I	205_S	0.897	0.64
159_M	183_D	0.896	0.64
22_I	82_L	0.890	0.63
11_I	112_E	0.887	0.63
31_W	36_L	0.884	0.63
17_S	59_A	0.874	0.62
13_L	63_L	0.873	0.62
10_I	93_K	0.866	0.61
180_V	189_S	0.862	0.61
54_M	188_V	0.861	0.61
39_G	58_A	0.859	0.61
160_I	163_G	0.859	0.61
82_L	179_Y	0.855	0.60
7_L	156_S	0.854	0.60
139_L	158_A	0.852	0.60
39_G	54_M	0.848	0.60
167_I	178_I	0.843	0.59
48_D	76_Y	0.837	0.59
126_F	166_T	0.833	0.58
85_A	89_L	0.831	0.58
82_L	148_I	0.829	0.58
19_F	79_A	0.824	0.57
35_F	42_L	0.817	0.57
142_L	150_D	0.810	0.56
139_L	150_D	0.805	0.56
80_A	83_I	0.805	0.56
164_E	184_L	0.801	0.55
124_S	170_S	0.798	0.55
8_G	22_I	0.796	0.55
158_A	161_P	0.791	0.54
37_I	203_K	0.784	0.54
137_F	154_D	0.778	0.53
155_L	167_I	0.777	0.53
137_F	159_M	0.776	0.53
42_L	53_V	0.775	0.53
39_G	51_G	0.775	0.53
5_Q	180_V	0.772	0.53
15_G	62_F	0.770	0.52
34_F	90_I	0.769	0.52
19_F	22_I	0.767	0.52
8_G	163_G	0.767	0.52
150_D	182_S	0.765	0.52
139_L	155_L	0.765	0.52
80_A	142_L	0.746	0.50
6_L	176_V	0.744	0.50
89_L	95_I	0.741	0.50
32_P	35_F	0.734	0.49
13_L	45_Y	0.733	0.49
18_M	192_V	0.731	0.49
39_G	154_D	0.730	0.49
168_V	171_G	0.728	0.48
79_A	82_L	0.719	0.48
17_S	81_F	0.718	0.47
67_F	77_A	0.716	0.47
29_L	93_K	0.716	0.47
135_Q	157_K	0.714	0.47
130_L	178_I	0.714	0.47
5_Q	9_L	0.714	0.47
40_Y	46_S	0.712	0.47
95_I	186_V	0.710	0.47
11_I	85_A	0.710	0.47
30_F	39_G	0.707	0.46
149_G	195_G	0.706	0.46
48_D	87_Y	0.705	0.46
44_K	183_D	0.703	0.46
34_F	116_D	0.701	0.46
12_A	195_G	0.697	0.45
126_F	174_G	0.694	0.45
37_I	59_A	0.694	0.45
8_G	12_A	0.690	0.45
115_K	187_A	0.689	0.45
20_L	184_L	0.684	0.44
85_A	178_I	0.682	0.44
59_A	178_I	0.672	0.43
19_F	189_S	0.672	0.43
34_F	114_P	0.670	0.43
119_H	205_S	0.667	0.43
139_L	184_L	0.658	0.42
192_V	197_I	0.652	0.41
9_L	13_L	0.651	0.41
137_F	160_I	0.646	0.41
9_L	52_S	0.645	0.41
40_Y	117_V	0.644	0.41
43_K	90_I	0.642	0.40
77_A	117_V	0.641	0.40
9_L	57_F	0.639	0.40
60_F	87_Y	0.638	0.40
87_Y	98_P	0.638	0.40
152_K	179_Y	0.637	0.40
86_G	90_I	0.637	0.40
170_S	191_A	0.636	0.40
76_Y	185_E	0.636	0.40
127_I	206_G	0.635	0.40
33_L	78_F	0.634	0.40
16_I	201_G	0.632	0.39
152_K	178_I	0.620	0.38
44_K	91_K	0.616	0.38
155_L	166_T	0.615	0.38
97_E	100_E	0.612	0.38
26_G	37_I	0.612	0.38
50_L	95_I	0.611	0.38
31_W	83_I	0.609	0.37
36_L	79_A	0.608	0.37
92_G	193_F	0.606	0.37
155_L	164_E	0.605	0.37
42_L	46_S	0.603	0.37
164_E	183_D	0.600	0.37
40_Y	188_V	0.599	0.36
58_A	63_L	0.599	0.36
158_A	190_S	0.597	0.36
161_P	169_I	0.597	0.36
136_P	165_S	0.595	0.36
154_D	176_V	0.592	0.36
69_I	161_P	0.592	0.36
140_N	144_V	0.591	0.36
55_Y	158_A	0.591	0.36
37_I	115_K	0.591	0.36
43_K	51_G	0.589	0.36
19_F	44_K	0.589	0.36
103_V	115_K	0.586	0.35
84_Y	187_A	0.585	0.35
68_S	73_L	0.584	0.35
129_E	163_G	0.583	0.35
12_A	24_G	0.581	0.35
147_F	193_F	0.579	0.35
16_I	174_G	0.578	0.35
87_Y	117_V	0.574	0.34
8_G	70_T	0.571	0.34
22_I	155_L	0.571	0.34
34_F	62_F	0.568	0.34
66_L	76_Y	0.568	0.34
146_G	176_V	0.567	0.34
171_G	192_V	0.566	0.34
136_P	157_K	0.566	0.34
32_P	80_A	0.566	0.34
180_V	197_I	0.563	0.33
126_F	193_F	0.562	0.33
93_K	164_E	0.562	0.33
43_K	87_Y	0.562	0.33
11_I	16_I	0.561	0.33
30_F	34_F	0.561	0.33
66_L	177_D	0.560	0.33
180_V	196_D	0.558	0.33
79_A	86_G	0.556	0.33
112_E	115_K	0.555	0.33
155_L	165_S	0.553	0.33
39_G	86_G	0.553	0.33
147_F	153_I	0.553	0.33
196_D	200_I	0.551	0.32
34_F	96_F	0.551	0.32
16_I	29_L	0.549	0.32
120_P	140_N	0.548	0.32
33_L	55_Y	0.547	0.32
12_A	94_P	0.544	0.32
10_I	128_G	0.544	0.32
98_P	115_K	0.543	0.32
148_I	194_I	0.543	0.32
141_D	175_N	0.540	0.31
153_I	169_I	0.539	0.31
11_I	19_F	0.539	0.31
77_A	81_F	0.534	0.31
121_D	184_L	0.534	0.31
15_G	32_P	0.531	0.31
5_Q	47_R	0.531	0.31
150_D	199_L	0.531	0.31
14_F	177_D	0.530	0.31
158_A	183_D	0.529	0.31
128_G	151_I	0.528	0.30
81_F	96_F	0.526	0.30
93_K	156_S	0.525	0.30
50_L	127_I	0.525	0.30
135_Q	201_G	0.523	0.30
116_D	198_N	0.521	0.30
87_Y	91_K	0.520	0.30
169_I	198_N	0.519	0.30
176_V	180_V	0.517	0.30
73_L	102_Q	0.515	0.29
30_F	44_K	0.514	0.29
47_R	55_Y	0.513	0.29
79_A	167_I	0.512	0.29
141_D	165_S	0.509	0.29
147_F	197_I	0.502	0.28
22_I	79_A	0.501	0.28
13_L	182_S	0.500	0.28
123_R	195_G	0.500	0.28
75_G	87_Y	0.500	0.28

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
4qrkA	1	0.751	99.4	0.758	Contact Map
3giaA	1	0.4357	27	0.946	Contact Map
3l1lA	2	0.4315	13.9	0.953	Contact Map
4i0uA	4	0.2448	13.2	0.953	Contact Map
2rddB	1	0.1452	9.4	0.956	Contact Map
4ev6A	3	0.2531	8.4	0.957	Contact Map
1wazA	1	0.1909	7.8	0.958	Contact Map
2i68A	2	0.2407	7.7	0.958	Contact Map
4tphA	2	0.3651	6.8	0.959	Contact Map
4mndA	2	0.3693	6.7	0.959	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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