UBIX - ECOLI - GREMLIN Contacts

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UBIX - 3-octaprenyl-4-hydroxybenzoate carboxy-lyase partner protein

UniProt:	P0AG03	Sequences: MKRLIVGISGASGAIYGVRLLQVLRDVTDIETHLVMSQAARQTLSLETDFSLREVQALADVTHDARDIAASISSGSFQTLGMVILPCSIKTLSGIVHSYTDGLLTRAADVVLKERRPLVLCVRETPLHLGHLRLMTQAAEIGAVIMPPVPAFYHRPQSLDDVINQTVNRVLDQFAITLPEDLFARWQGA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11044
Length:	189 (183)
Sequences:	1825 (1223)
Seq/√Len:	90.4

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
133_R	140_E	3.286	1.00
129_L	139_A	3.112	1.00
133_R	137_Q	3.025	1.00
92_L	135_M	2.991	1.00
138_A	143_A	2.899	1.00
129_L	136_T	2.654	1.00
19_R	164_N	2.564	1.00
3_R	31_E	2.545	1.00
7_G	104_L	2.445	1.00
129_L	140_E	2.395	1.00
19_R	22_Q	2.384	1.00
168_N	183_F	2.280	1.00
35_V	72_I	2.205	1.00
93_S	99_Y	2.182	1.00
85_L	121_C	2.171	1.00
172_D	185_R	2.164	1.00
33_H	63_H	2.095	1.00
9_S	104_L	2.078	1.00
8_I	17_G	2.073	1.00
132_L	136_T	2.021	1.00
89_I	122_V	1.938	1.00
83_V	170_V	1.911	1.00
39_A	68_I	1.819	1.00
63_H	71_S	1.780	1.00
20_L	83_V	1.734	1.00
37_S	104_L	1.681	1.00
115_R	139_A	1.674	1.00
127_L	149_V	1.645	1.00
159_L	162_V	1.638	1.00
82_M	111_V	1.632	1.00
112_L	143_A	1.580	1.00
92_L	138_A	1.522	1.00
85_L	170_V	1.519	1.00
136_T	140_E	1.518	1.00
129_L	141_I	1.510	1.00
87_C	92_L	1.503	1.00
121_C	170_V	1.502	1.00
160_D	164_N	1.496	1.00
169_R	183_F	1.484	1.00
94_G	99_Y	1.469	1.00
79_T	111_V	1.454	0.99
6_V	21_L	1.450	0.99
133_R	136_T	1.437	0.99
49_D	155_R	1.435	0.99
115_R	144_V	1.393	0.99
14_A	44_L	1.391	0.99
138_A	145_I	1.391	0.99
4_L	174_F	1.388	0.99
65_A	102_G	1.383	0.99
98_S	134_L	1.380	0.99
119_V	174_F	1.369	0.99
38_Q	66_R	1.358	0.99
78_Q	179_P	1.346	0.99
157_Q	161_D	1.336	0.99
81_G	174_F	1.333	0.99
17_G	85_L	1.308	0.99
109_D	131_H	1.274	0.99
144_V	173_Q	1.273	0.99
93_S	134_L	1.258	0.98
20_L	85_L	1.222	0.98
5_I	111_V	1.209	0.98
93_S	97_H	1.205	0.98
33_H	77_F	1.204	0.98
90_K	99_Y	1.201	0.98
146_M	166_T	1.191	0.98
44_L	48_T	1.180	0.98
20_L	167_V	1.166	0.97
152_F	163_I	1.163	0.97
16_Y	150_P	1.154	0.97
130_G	134_L	1.148	0.97
100_T	109_D	1.146	0.97
121_C	166_T	1.140	0.97
122_V	146_M	1.137	0.97
95_I	108_A	1.127	0.97
21_L	32_T	1.125	0.97
117_P	173_Q	1.122	0.97
98_S	130_G	1.116	0.97
16_Y	148_P	1.113	0.97
38_Q	65_A	1.112	0.97
90_K	105_T	1.109	0.97
130_G	141_I	1.105	0.97
5_I	79_T	1.101	0.96
83_V	174_F	1.096	0.96
84_I	95_I	1.090	0.96
89_I	134_L	1.085	0.96
94_G	101_D	1.084	0.96
78_Q	175_A	1.082	0.96
6_V	32_T	1.073	0.96
6_V	85_L	1.065	0.96
112_L	141_I	1.061	0.96
121_C	148_P	1.049	0.95
82_M	107_A	1.048	0.95
23_V	182_L	1.042	0.95
138_A	141_I	1.034	0.95
38_Q	41_R	1.020	0.95
27_V	176_I	0.994	0.94
89_I	93_S	0.984	0.93
5_I	72_I	0.980	0.93
125_T	146_M	0.980	0.93
139_A	143_A	0.980	0.93
90_K	94_G	0.973	0.93
151_A	165_Q	0.971	0.93
112_L	128_H	0.970	0.93
15_I	163_I	0.960	0.93
41_R	56_Q	0.954	0.92
23_V	26_D	0.948	0.92
63_H	67_D	0.946	0.92
20_L	170_V	0.943	0.92
18_V	44_L	0.940	0.92
25_R	60_D	0.930	0.91
125_T	166_T	0.928	0.91
82_M	108_A	0.922	0.91
19_R	160_D	0.919	0.91
84_I	108_A	0.915	0.91
75_G	113_K	0.899	0.90
94_G	105_T	0.899	0.90
101_D	105_T	0.890	0.89
89_I	131_H	0.887	0.89
117_P	175_A	0.884	0.89
16_Y	166_T	0.879	0.89
156_P	161_D	0.869	0.88
148_P	166_T	0.868	0.88
129_L	143_A	0.868	0.88
139_A	145_I	0.863	0.88
69_A	73_S	0.860	0.88
8_I	40_A	0.857	0.88
137_Q	141_I	0.856	0.88
146_M	170_V	0.856	0.88
92_L	134_L	0.856	0.88
45_S	51_S	0.852	0.87
36_M	40_A	0.843	0.87
30_I	176_I	0.839	0.87
121_C	146_M	0.838	0.86
7_G	82_M	0.837	0.86
53_R	56_Q	0.837	0.86
128_H	134_L	0.836	0.86
75_G	110_V	0.834	0.86
42_Q	68_I	0.833	0.86
111_V	118_L	0.830	0.86
146_M	169_R	0.829	0.86
18_V	48_T	0.823	0.85
119_V	173_Q	0.820	0.85
46_L	69_A	0.800	0.84
75_G	114_E	0.797	0.84
134_L	138_A	0.797	0.84
8_I	14_A	0.787	0.83
165_Q	183_F	0.787	0.83
43_T	90_K	0.784	0.83
30_I	80_L	0.782	0.82
90_K	109_D	0.781	0.82
73_S	103_L	0.780	0.82
21_L	34_L	0.777	0.82
120_L	138_A	0.776	0.82
54_E	57_A	0.774	0.82
38_Q	42_Q	0.769	0.81
110_V	113_K	0.766	0.81
42_Q	45_S	0.764	0.81
34_L	59_A	0.762	0.81
146_M	173_Q	0.759	0.81
96_V	137_Q	0.757	0.80
137_Q	140_E	0.754	0.80
132_L	138_A	0.749	0.80
42_Q	46_L	0.749	0.80
100_T	105_T	0.746	0.79
12_S	39_A	0.746	0.79
168_N	180_E	0.741	0.79
95_I	120_L	0.738	0.79
4_L	30_I	0.738	0.79
23_V	167_V	0.734	0.78
122_V	149_V	0.730	0.78
107_A	111_V	0.729	0.78
102_G	105_T	0.726	0.77
148_P	165_Q	0.718	0.77
34_L	62_T	0.717	0.77
122_V	127_L	0.716	0.77
111_V	116_R	0.714	0.76
97_H	134_L	0.706	0.76
31_E	77_F	0.701	0.75
84_I	120_L	0.699	0.75
87_C	120_L	0.699	0.75
82_M	118_L	0.698	0.75
78_Q	116_R	0.689	0.74
99_Y	102_G	0.688	0.74
23_V	164_N	0.688	0.74
19_R	167_V	0.682	0.73
169_R	173_Q	0.676	0.72
3_R	80_L	0.675	0.72
83_V	119_V	0.674	0.72
61_V	71_S	0.668	0.71
42_Q	69_A	0.664	0.71
110_V	114_E	0.660	0.71
16_Y	163_I	0.659	0.70
129_L	138_A	0.657	0.70
5_I	82_M	0.652	0.70
36_M	62_T	0.646	0.69
96_V	138_A	0.643	0.69
66_R	69_A	0.642	0.68
14_A	17_G	0.640	0.68
36_M	52_L	0.640	0.68
90_K	100_T	0.640	0.68
36_M	55_V	0.636	0.68
5_I	107_A	0.636	0.68
122_V	132_L	0.634	0.67
59_A	62_T	0.626	0.66
55_V	59_A	0.626	0.66
94_G	102_G	0.623	0.66
158_S	161_D	0.620	0.66
50_F	54_E	0.616	0.65
94_G	131_H	0.613	0.65
32_T	59_A	0.609	0.64
56_Q	62_T	0.607	0.64
18_V	22_Q	0.605	0.64
5_I	35_V	0.604	0.64
150_P	162_V	0.603	0.64
93_S	96_V	0.603	0.64
31_E	61_V	0.602	0.63
20_L	171_L	0.599	0.63
150_P	169_R	0.599	0.63
3_R	78_Q	0.597	0.63
164_N	167_V	0.595	0.63
71_S	188_G	0.594	0.62
16_Y	152_F	0.593	0.62
14_A	40_A	0.591	0.62
68_I	73_S	0.590	0.62
9_S	88_S	0.587	0.62
109_D	128_H	0.585	0.61
119_V	170_V	0.582	0.61
41_R	65_A	0.581	0.61
98_S	128_H	0.581	0.61
88_S	149_V	0.577	0.60
77_F	81_G	0.577	0.60
113_K	131_H	0.576	0.60
71_S	187_Q	0.570	0.59
115_R	173_Q	0.570	0.59
4_L	81_G	0.570	0.59
180_E	183_F	0.569	0.59
108_A	118_L	0.568	0.59
55_V	58_L	0.568	0.59
36_M	44_L	0.564	0.59
100_T	128_H	0.564	0.59
31_E	80_L	0.564	0.59
8_I	36_M	0.560	0.58
19_R	163_I	0.555	0.57
81_G	116_R	0.553	0.57
136_T	139_A	0.548	0.56
37_S	183_F	0.547	0.56
89_I	109_D	0.546	0.56
83_V	171_L	0.543	0.56
4_L	176_I	0.540	0.55
120_L	145_I	0.540	0.55
127_L	135_M	0.537	0.55
22_Q	58_L	0.535	0.55
3_R	33_H	0.531	0.54
66_R	157_Q	0.530	0.54
149_V	166_T	0.526	0.53
87_C	91_T	0.523	0.53
43_T	148_P	0.523	0.53
50_F	55_V	0.521	0.53
78_Q	185_R	0.521	0.53
161_D	164_N	0.521	0.53
33_H	61_V	0.517	0.52
16_Y	96_V	0.517	0.52
64_D	71_S	0.514	0.52
43_T	87_C	0.511	0.51
22_Q	50_F	0.511	0.51
75_G	109_D	0.506	0.51
8_I	21_L	0.506	0.51
164_N	182_L	0.506	0.51
40_A	46_L	0.505	0.50
82_M	116_R	0.504	0.50
159_L	163_I	0.504	0.50
44_L	52_L	0.503	0.50
36_M	39_A	0.502	0.50
125_T	147_P	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	0.9735	100	0.329	Contact Map
4zavA	6	0.9841	100	0.332	Contact Map
2ejbA	6	0.9101	100	0.334	Contact Map
1sbzA	6	0.9841	100	0.342	Contact Map
3lqkA	5	0.963	100	0.482	Contact Map
3mcuA	5	0.9048	100	0.513	Contact Map
1g63A	6	0.8095	100	0.523	Contact Map
1qzuA	3	0.7513	100	0.526	Contact Map
1p3y1	6	0.8413	100	0.541	Contact Map
3wisA	4	0.836	100	0.549	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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