BIOD2 - ECOLI - GREMLIN Contacts

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BIOD2 - ATP-dependent dethiobiotin synthetase BioD 2

UniProt:	P0A6E9	Sequences: MLKRFFITGTDTSVGKTVVSRALLQALASQGKTVAGYKPVAKGSKETPEGLRNKDALVLQSVSTIELPYEAVNPIALSEEESSVAHSCPINYTLISNGLANLTEKVDHVVVEGTGGWRSLMNDLRPLSEWVVQEQLPVLMVVGIQEGCINHALLTAQAIANDGLPLIGWVANRINPGLAHYAEIIDVLGKKLPAPLIGELPYLPRAEQRELGQYIRLAMLRSVLAVDRVTV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13849
Length:	231 (210)
Sequences:	4751 (2968)
Seq/√Len:	204.8

ECOLI - BIOD2 BIOD1
BACSU - BIOD
HALSA - Q9HQY9 COBQ

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
71_A	101_N	3.345	1.00
27_L	108_H	3.253	1.00
140_M	155_T	2.993	1.00
142_V	148_C	2.636	1.00
135_Q	165_P	2.632	1.00
157_Q	162_D	2.457	1.00
156_A	166_L	2.309	1.00
130_W	134_E	2.308	1.00
132_V	162_D	2.297	1.00
33_T	107_D	2.239	1.00
11_D	14_V	2.210	1.00
24_L	34_V	2.190	1.00
19_V	200_L	2.158	1.00
142_V	152_A	2.126	1.00
33_T	106_V	2.095	1.00
20_S	110_V	2.071	1.00
19_V	170_V	2.062	1.00
11_D	151_H	2.033	1.00
138_V	159_I	2.006	1.00
4_R	136_L	1.965	1.00
187_V	191_K	1.945	1.00
79_E	89_P	1.913	1.00
122_N	125_R	1.879	1.00
100_A	103_T	1.878	1.00
182_A	186_D	1.866	1.00
86_H	89_P	1.864	1.00
47_T	50_G	1.840	1.00
71_A	105_K	1.796	1.00
44_S	76_A	1.780	1.00
186_D	190_K	1.720	1.00
183_E	186_D	1.712	1.00
88_C	123_D	1.664	1.00
111_V	136_L	1.617	1.00
150_N	154_L	1.600	1.00
148_C	152_A	1.593	1.00
94_L	97_N	1.591	1.00
152_A	169_W	1.571	1.00
8_T	138_V	1.565	1.00
208_Q	211_L	1.544	1.00
5_F	167_I	1.531	1.00
48_P	67_L	1.528	1.00
46_E	78_S	1.515	1.00
119_S	187_V	1.499	1.00
73_N	76_A	1.492	1.00
144_I	171_A	1.485	1.00
208_Q	212_G	1.477	1.00
5_F	139_L	1.469	1.00
53_N	58_V	1.464	1.00
7_I	23_L	1.453	1.00
156_A	194_A	1.440	1.00
96_S	100_A	1.429	1.00
96_S	133_Q	1.418	1.00
179_A	182_A	1.417	1.00
28_A	65_I	1.399	1.00
138_V	164_L	1.395	1.00
137_P	167_I	1.391	1.00
35_A	106_V	1.378	1.00
153_L	191_K	1.371	1.00
169_W	196_L	1.366	1.00
32_K	108_H	1.356	1.00
7_I	141_V	1.354	1.00
92_Y	133_Q	1.339	1.00
80_E	83_S	1.331	1.00
29_S	65_I	1.330	1.00
24_L	110_V	1.326	1.00
157_Q	161_N	1.316	1.00
37_Y	99_L	1.309	1.00
149_I	188_L	1.291	1.00
139_L	197_I	1.289	1.00
22_A	26_A	1.283	1.00
37_Y	98_G	1.276	1.00
132_V	165_P	1.274	1.00
128_S	162_D	1.270	1.00
99_L	103_T	1.233	1.00
91_N	94_L	1.232	1.00
96_S	134_E	1.230	1.00
11_D	143_G	1.227	1.00
117_W	159_I	1.223	1.00
11_D	145_Q	1.219	1.00
4_R	99_L	1.218	1.00
189_G	196_L	1.211	1.00
8_T	128_S	1.205	1.00
156_A	169_W	1.199	1.00
187_V	190_K	1.194	1.00
26_A	30_Q	1.186	1.00
122_N	162_D	1.178	1.00
93_T	97_N	1.175	1.00
140_M	166_L	1.172	1.00
90_I	94_L	1.172	1.00
23_L	27_L	1.170	1.00
142_V	169_W	1.169	1.00
28_A	34_V	1.168	1.00
7_I	20_S	1.162	1.00
90_I	95_I	1.154	1.00
153_L	157_Q	1.151	1.00
8_T	113_G	1.130	1.00
118_R	158_A	1.125	1.00
57_L	60_Q	1.124	1.00
35_A	109_V	1.123	1.00
94_L	98_G	1.122	1.00
156_A	192_L	1.112	1.00
74_P	98_G	1.107	1.00
36_G	63_S	1.107	1.00
81_E	84_V	1.080	1.00
143_G	148_C	1.064	1.00
19_V	141_V	1.061	1.00
6_F	131_V	1.053	1.00
9_G	14_V	1.045	1.00
97_N	101_N	1.042	1.00
100_A	133_Q	1.034	1.00
111_V	130_W	1.029	1.00
4_R	103_T	1.026	1.00
114_T	127_L	1.026	1.00
101_N	105_K	1.020	1.00
58_V	62_V	1.019	1.00
188_L	192_L	1.010	1.00
81_E	85_A	1.010	1.00
82_S	85_A	1.009	1.00
102_L	109_V	1.001	1.00
210_E	213_Q	0.991	1.00
80_E	84_V	0.988	1.00
208_Q	213_Q	0.977	1.00
186_D	189_G	0.969	1.00
39_P	111_V	0.969	1.00
150_N	155_T	0.950	0.99
118_R	128_S	0.946	0.99
85_A	183_E	0.943	0.99
125_R	133_Q	0.935	0.99
196_L	199_E	0.926	0.99
141_V	172_N	0.926	0.99
180_H	183_E	0.925	0.99
14_V	143_G	0.925	0.99
37_Y	102_L	0.924	0.99
207_E	212_G	0.922	0.99
206_A	211_L	0.908	0.99
37_Y	74_P	0.901	0.99
98_G	101_N	0.900	0.99
103_T	109_V	0.889	0.99
81_E	184_I	0.887	0.99
42_K	77_L	0.880	0.99
10_T	148_C	0.880	0.99
21_R	24_L	0.876	0.99
140_M	156_A	0.869	0.99
21_R	58_V	0.867	0.99
205_R	211_L	0.867	0.99
40_V	95_I	0.864	0.99
5_F	110_V	0.851	0.99
148_C	171_A	0.850	0.99
28_A	64_T	0.849	0.99
169_W	194_A	0.848	0.99
18_V	203_L	0.835	0.99
207_E	211_L	0.833	0.99
6_F	113_G	0.830	0.99
26_A	29_S	0.824	0.98
122_N	160_A	0.824	0.98
159_I	164_L	0.823	0.98
131_V	164_L	0.822	0.98
34_V	108_H	0.821	0.98
42_K	81_E	0.819	0.98
205_R	212_G	0.818	0.98
203_L	206_A	0.815	0.98
137_P	165_P	0.813	0.98
144_I	148_C	0.811	0.98
19_V	172_N	0.804	0.98
206_A	210_E	0.803	0.98
24_L	36_G	0.795	0.98
166_L	194_A	0.793	0.98
149_I	184_I	0.792	0.98
156_A	160_A	0.790	0.98
153_L	192_L	0.789	0.98
92_Y	125_R	0.788	0.98
75_I	94_L	0.786	0.98
143_G	151_H	0.784	0.98
28_A	33_T	0.772	0.98
185_I	196_L	0.771	0.98
91_N	95_I	0.771	0.98
117_W	128_S	0.763	0.97
40_V	121_M	0.761	0.97
71_A	98_G	0.761	0.97
169_W	192_L	0.761	0.97
95_I	125_R	0.761	0.97
32_K	107_D	0.759	0.97
35_A	102_L	0.759	0.97
118_R	157_Q	0.757	0.97
36_G	59_L	0.753	0.97
8_T	117_W	0.753	0.97
12_T	146_E	0.751	0.97
96_S	125_R	0.749	0.97
209_R	213_Q	0.748	0.97
117_W	155_T	0.744	0.97
27_L	34_V	0.744	0.97
43_G	80_E	0.738	0.97
181_Y	185_I	0.736	0.97
58_V	61_S	0.725	0.97
207_E	210_E	0.724	0.96
209_R	212_G	0.723	0.96
173_R	181_Y	0.723	0.96
171_A	196_L	0.719	0.96
181_Y	199_E	0.715	0.96
128_S	158_A	0.715	0.96
92_Y	96_S	0.714	0.96
185_I	199_E	0.706	0.96
99_L	134_E	0.696	0.96
27_L	32_K	0.693	0.95
75_I	91_N	0.692	0.95
127_L	131_V	0.692	0.95
129_E	162_D	0.688	0.95
83_S	86_H	0.684	0.95
206_A	212_G	0.683	0.95
124_L	190_K	0.683	0.95
41_A	53_N	0.682	0.95
99_L	130_W	0.681	0.95
189_G	195_P	0.681	0.95
149_I	187_V	0.680	0.95
126_P	191_K	0.679	0.95
102_L	106_V	0.679	0.95
68_P	71_A	0.673	0.95
182_A	185_I	0.673	0.95
13_S	54_K	0.671	0.95
171_A	185_I	0.671	0.95
140_M	169_W	0.668	0.95
173_R	202_Y	0.665	0.94
92_Y	95_I	0.665	0.94
119_S	184_I	0.665	0.94
128_S	131_V	0.665	0.94
171_A	199_E	0.660	0.94
161_N	164_L	0.660	0.94
119_S	149_I	0.655	0.94
205_R	208_Q	0.652	0.94
39_P	130_W	0.650	0.94
159_I	166_L	0.650	0.94
4_R	111_V	0.648	0.94
7_I	170_V	0.646	0.93
93_T	133_Q	0.645	0.93
92_Y	130_W	0.642	0.93
168_G	197_I	0.639	0.93
101_N	104_E	0.635	0.93
205_R	213_Q	0.633	0.93
118_R	162_D	0.633	0.93
96_S	130_W	0.632	0.93
20_S	59_L	0.631	0.93
118_R	153_L	0.627	0.92
115_G	147_G	0.623	0.92
180_H	184_I	0.620	0.92
43_G	83_S	0.617	0.92
22_A	25_Q	0.614	0.92
7_I	139_L	0.614	0.92
164_L	194_A	0.611	0.91
24_L	64_T	0.611	0.91
119_S	181_Y	0.607	0.91
92_Y	129_E	0.607	0.91
4_R	134_E	0.606	0.91
39_P	114_T	0.606	0.91
23_L	139_L	0.603	0.91
154_L	158_A	0.602	0.91
17_T	58_V	0.599	0.91
89_P	180_H	0.596	0.90
81_E	180_H	0.595	0.90
83_S	87_S	0.594	0.90
173_R	199_E	0.593	0.90
132_V	164_L	0.592	0.90
160_A	193_P	0.592	0.90
56_A	70_E	0.591	0.90
206_A	213_Q	0.587	0.90
69_Y	105_K	0.584	0.90
97_N	100_A	0.583	0.89
153_L	156_A	0.579	0.89
34_V	107_D	0.579	0.89
113_G	127_L	0.577	0.89
99_L	111_V	0.575	0.89
33_T	105_K	0.573	0.89
82_S	146_E	0.572	0.89
157_Q	160_A	0.571	0.88
175_N	181_Y	0.569	0.88
20_S	36_G	0.568	0.88
168_G	195_P	0.567	0.88
126_P	153_L	0.567	0.88
18_V	206_A	0.559	0.87
158_A	162_D	0.555	0.87
56_A	60_Q	0.551	0.87
115_G	146_E	0.551	0.87
140_M	159_I	0.550	0.87
6_F	127_L	0.550	0.87
95_I	98_G	0.542	0.86
99_L	136_L	0.542	0.86
157_Q	191_K	0.542	0.86
49_E	69_Y	0.540	0.86
55_D	59_L	0.539	0.86
41_A	76_A	0.537	0.85
117_W	131_V	0.534	0.85
85_A	180_H	0.534	0.85
6_F	111_V	0.534	0.85
21_R	59_L	0.533	0.85
207_E	213_Q	0.533	0.85
27_L	110_V	0.528	0.84
84_V	187_V	0.527	0.84
41_A	73_N	0.520	0.83
80_E	146_E	0.518	0.83
157_Q	163_G	0.517	0.83
14_V	151_H	0.516	0.83
203_L	207_E	0.516	0.83
13_S	80_E	0.516	0.83
152_A	171_A	0.516	0.83
13_S	18_V	0.516	0.83
112_E	115_G	0.516	0.83
132_V	160_A	0.515	0.83
158_A	161_N	0.512	0.82
67_L	71_A	0.511	0.82
41_A	114_T	0.510	0.82
156_A	163_G	0.510	0.82
44_S	73_N	0.508	0.82
45_K	78_S	0.506	0.82
46_E	49_E	0.505	0.82
94_L	101_N	0.502	0.81
26_A	200_L	0.500	0.81

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
4a0gA	2	0.987	100	0.331	Contact Map
2obnA	2	0.7879	100	0.532	Contact Map
3fgnA	2	0.9524	100	0.54	Contact Map
1s1mA	4	0.974	100	0.557	Contact Map
1byiA	2	0.9481	100	0.583	Contact Map
3of5A	2	0.9307	100	0.59	Contact Map
3zq6A	2	0.9004	99.9	0.605	Contact Map
3qxcA	2	0.9048	99.9	0.608	Contact Map
3ug7A	4	0.9437	99.9	0.629	Contact Map
1vcoA	4	0.9957	99.9	0.638	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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