BSDB - BACSU - GREMLIN Contacts

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BSDB - Phenolic acid decarboxylase subunit B

UniProt:	P94404	Sequences: MKAEFKRKGGGKVKLVVGMTGATGAIFGVRLLQWLKAAGVETHLVVSPWANVTIKHETGYTLQEVEQLATYTYSHKDQAAAISSGSFDTDGMIVAPCSMKSLASIRTGMADNLLTRAADVMLKERKKLVLLTRETPLNQIHLENMLALTKMGTIILPPMPAFYNRPRSLEEMVDHIVFRTLDQFGIRLPEAKRWNGIEKQKGGA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	204 (184)
Sequences:	1872 (1238)
Seq/√Len:	91.2

ECOLI - UBIX
BACSU - BSDB
SULSO - PAAD

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
143_E	150_K	3.265	1.00
139_Q	149_T	3.151	1.00
143_E	147_A	2.979	1.00
102_L	145_M	2.975	1.00
148_L	153_T	2.903	1.00
14_K	41_E	2.772	1.00
30_R	174_D	2.627	1.00
139_Q	146_L	2.626	1.00
139_Q	150_K	2.373	1.00
30_R	33_Q	2.370	1.00
18_G	114_L	2.346	1.00
178_F	191_A	2.296	1.00
182_D	193_R	2.257	1.00
103_A	109_M	2.191	1.00
95_A	131_L	2.155	1.00
43_H	73_Y	2.142	1.00
45_V	82_I	2.130	1.00
19_M	28_G	2.099	1.00
20_T	114_L	2.025	1.00
142_L	146_L	2.017	1.00
93_I	180_T	1.969	1.00
99_M	132_T	1.926	1.00
49_W	78_Q	1.827	1.00
73_Y	81_A	1.811	1.00
137_L	159_M	1.771	1.00
31_L	93_I	1.731	1.00
125_R	149_T	1.655	1.00
169_L	172_M	1.628	1.00
92_M	121_M	1.616	1.00
47_S	114_L	1.615	1.00
88_D	187_R	1.567	1.00
139_Q	151_M	1.538	1.00
97_C	102_L	1.521	1.00
122_L	153_T	1.516	1.00
170_E	174_D	1.514	1.00
104_S	109_M	1.504	1.00
146_L	150_K	1.485	1.00
95_A	180_T	1.480	1.00
89_T	121_M	1.475	1.00
17_V	32_L	1.471	1.00
102_L	148_L	1.467	1.00
131_L	180_T	1.450	0.99
179_R	191_A	1.429	0.99
148_L	155_I	1.426	0.99
25_A	54_I	1.407	0.99
125_R	154_I	1.402	0.99
143_E	146_L	1.395	0.99
48_P	76_K	1.386	0.99
75_H	112_N	1.375	0.99
15_L	184_F	1.372	0.99
59_G	165_R	1.363	0.99
129_V	184_F	1.362	0.99
167_R	171_E	1.343	0.99
108_G	144_N	1.329	0.99
91_G	184_F	1.312	0.99
28_G	95_A	1.276	0.99
154_I	183_Q	1.269	0.99
119_D	141_H	1.267	0.99
31_L	95_A	1.216	0.98
103_A	107_T	1.203	0.98
54_I	58_T	1.197	0.98
43_H	87_F	1.197	0.98
103_A	144_N	1.192	0.98
100_K	109_M	1.188	0.98
105_I	118_A	1.187	0.98
110_A	119_D	1.171	0.98
156_L	176_I	1.168	0.98
31_L	177_V	1.165	0.98
16_V	121_M	1.163	0.98
94_V	105_I	1.159	0.97
13_V	90_D	1.156	0.97
48_P	75_H	1.155	0.97
162_F	173_V	1.148	0.97
88_D	185_G	1.141	0.97
131_L	176_I	1.136	0.97
17_V	95_A	1.134	0.97
27_F	160_P	1.132	0.97
93_I	184_F	1.125	0.97
36_K	70_T	1.117	0.97
140_I	144_N	1.110	0.97
16_V	89_T	1.103	0.97
140_I	151_M	1.103	0.97
178_F	188_L	1.097	0.96
17_V	42_T	1.096	0.96
104_S	111_D	1.091	0.96
127_K	183_Q	1.087	0.96
108_G	140_I	1.084	0.96
132_T	156_L	1.076	0.96
131_L	158_P	1.072	0.96
27_F	158_P	1.072	0.96
100_K	115_T	1.067	0.96
32_L	42_T	1.056	0.96
135_T	156_L	1.035	0.95
122_L	151_M	1.031	0.95
92_M	117_A	1.029	0.95
99_M	144_N	1.028	0.95
148_L	151_M	1.021	0.95
16_V	82_I	1.011	0.94
34_W	190_E	1.004	0.94
48_P	51_N	1.002	0.94
122_L	138_N	0.996	0.94
100_K	104_S	0.993	0.94
161_A	175_H	0.979	0.93
14_K	90_D	0.969	0.93
34_W	37_A	0.965	0.93
51_N	66_E	0.960	0.93
127_K	185_G	0.948	0.92
135_T	176_I	0.945	0.92
73_Y	77_D	0.943	0.92
99_M	103_A	0.942	0.92
31_L	180_T	0.935	0.92
94_V	118_A	0.930	0.92
149_T	153_T	0.929	0.92
30_R	170_E	0.927	0.91
29_V	54_I	0.926	0.91
26_I	173_V	0.924	0.91
92_M	118_A	0.914	0.91
111_D	115_T	0.906	0.90
44_L	69_A	0.906	0.90
99_M	141_H	0.882	0.89
104_S	115_T	0.881	0.89
156_L	180_T	0.873	0.89
40_V	186_I	0.869	0.89
19_M	50_A	0.863	0.88
55_K	61_T	0.857	0.88
131_L	156_L	0.853	0.88
156_L	179_R	0.853	0.88
85_G	123_K	0.852	0.88
27_F	176_I	0.852	0.88
166_P	171_E	0.851	0.88
121_M	128_L	0.850	0.87
102_L	144_N	0.843	0.87
158_P	176_I	0.836	0.87
52_V	78_Q	0.835	0.87
79_A	83_S	0.829	0.86
139_Q	153_T	0.829	0.86
149_T	155_I	0.827	0.86
56_H	79_A	0.823	0.86
147_A	151_M	0.821	0.86
29_V	58_T	0.820	0.86
18_G	92_M	0.816	0.85
129_V	183_Q	0.815	0.85
64_E	67_Q	0.815	0.85
32_L	44_L	0.813	0.85
138_N	144_N	0.804	0.84
65_V	69_A	0.803	0.84
130_L	148_L	0.802	0.84
52_V	55_K	0.802	0.84
83_S	113_L	0.802	0.84
19_M	25_A	0.799	0.84
85_G	124_E	0.798	0.84
144_N	148_L	0.793	0.84
85_G	120_V	0.789	0.83
100_K	119_D	0.788	0.83
46_V	50_A	0.781	0.83
105_I	130_L	0.775	0.82
53_T	100_K	0.775	0.82
40_V	90_D	0.772	0.82
106_R	147_A	0.764	0.81
110_A	115_T	0.764	0.81
117_A	121_M	0.762	0.81
48_P	52_V	0.762	0.81
112_N	115_T	0.756	0.81
52_V	56_H	0.754	0.80
15_L	40_V	0.750	0.80
88_D	126_K	0.746	0.80
92_M	128_L	0.741	0.79
175_H	191_A	0.738	0.79
107_T	144_N	0.738	0.79
142_L	148_L	0.736	0.79
23_T	49_W	0.736	0.79
147_A	150_K	0.735	0.79
97_C	130_L	0.734	0.79
156_L	183_Q	0.732	0.78
132_T	159_M	0.730	0.78
94_V	130_L	0.724	0.78
120_V	123_K	0.724	0.78
109_M	112_N	0.719	0.77
34_W	177_V	0.714	0.77
38_A	186_I	0.714	0.77
121_M	126_K	0.686	0.74
34_W	174_D	0.686	0.74
44_L	72_T	0.682	0.73
132_T	137_L	0.675	0.73
41_E	87_F	0.674	0.72
30_R	177_V	0.670	0.72
179_R	183_Q	0.668	0.72
158_P	175_H	0.663	0.71
52_V	79_A	0.663	0.71
63_Q	66_E	0.662	0.71
93_I	129_V	0.662	0.71
16_V	92_M	0.662	0.71
46_V	72_T	0.660	0.71
120_V	124_E	0.660	0.71
106_R	148_L	0.653	0.70
60_Y	64_E	0.650	0.70
76_K	79_A	0.647	0.69
27_F	173_V	0.643	0.69
100_K	110_A	0.640	0.69
139_Q	148_L	0.638	0.68
13_V	39_G	0.637	0.68
104_S	112_N	0.637	0.68
103_A	106_R	0.631	0.67
14_K	88_D	0.629	0.67
15_L	91_G	0.626	0.67
25_A	28_G	0.623	0.67
168_S	171_E	0.622	0.66
132_T	142_L	0.619	0.66
174_D	177_V	0.618	0.66
29_V	33_Q	0.616	0.66
34_W	188_L	0.615	0.66
16_V	45_V	0.613	0.65
66_E	70_T	0.612	0.65
160_P	172_M	0.611	0.65
110_A	138_N	0.606	0.64
19_M	46_V	0.606	0.64
98_S	159_M	0.595	0.63
51_N	75_H	0.591	0.62
46_V	62_L	0.587	0.62
46_V	54_I	0.587	0.62
20_T	98_S	0.583	0.61
123_K	141_H	0.580	0.61
125_R	183_Q	0.579	0.61
104_S	141_H	0.578	0.61
118_A	128_L	0.578	0.61
188_L	193_R	0.577	0.61
65_V	70_T	0.576	0.60
81_A	195_N	0.574	0.60
91_G	126_K	0.573	0.60
60_Y	65_V	0.573	0.60
129_V	180_T	0.572	0.60
81_A	196_G	0.572	0.60
25_A	50_A	0.571	0.60
160_P	179_R	0.571	0.60
119_D	138_N	0.570	0.60
27_F	162_F	0.569	0.60
108_G	138_N	0.569	0.60
62_L	66_E	0.567	0.59
14_K	43_H	0.566	0.59
31_L	181_L	0.565	0.59
69_A	72_T	0.564	0.59
78_Q	83_S	0.557	0.58
16_V	117_A	0.556	0.58
33_Q	60_Y	0.556	0.58
87_F	91_G	0.550	0.57
30_R	173_V	0.545	0.56
66_E	72_T	0.544	0.56
42_T	69_A	0.543	0.56
97_C	101_S	0.539	0.55
46_V	49_W	0.537	0.55
65_V	68_L	0.534	0.55
45_V	79_A	0.532	0.55
29_V	65_V	0.530	0.54
146_L	149_T	0.528	0.54
171_E	174_D	0.528	0.54
166_P	169_L	0.527	0.54
41_E	90_D	0.526	0.54
79_A	98_S	0.526	0.54
76_K	167_R	0.524	0.53
93_I	181_L	0.523	0.53
41_E	71_Y	0.522	0.53
71_Y	81_A	0.521	0.53
46_V	65_V	0.520	0.53
137_L	145_M	0.520	0.53
135_T	157_P	0.519	0.53
88_D	193_R	0.519	0.53
99_M	119_D	0.515	0.52
15_L	186_I	0.513	0.52
89_T	126_K	0.513	0.52
19_M	32_L	0.513	0.52
32_L	39_G	0.511	0.52
51_N	62_L	0.510	0.51
97_C	145_M	0.508	0.51
127_K	154_I	0.506	0.51
50_A	56_H	0.504	0.51
55_K	58_T	0.500	0.50

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
4rhfA	6	0.9118	100	0.353	Contact Map
4zavA	6	0.951	100	0.354	Contact Map
2ejbA	6	0.8431	100	0.364	Contact Map
1sbzA	6	0.9069	100	0.364	Contact Map
3lqkA	5	0.9118	100	0.504	Contact Map
3mcuA	5	0.8578	100	0.532	Contact Map
1g63A	6	0.7549	100	0.541	Contact Map
1qzuA	3	0.7059	100	0.544	Contact Map
1p3y1	6	0.8039	100	0.56	Contact Map
3wisA	4	0.7843	100	0.57	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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