BIOD - BACSU - GREMLIN Contacts

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BIOD - ATP-dependent dethiobiotin synthetase BioD

UniProt:	P53558	Sequences: MRGFFVTGTDTEVGKTVISSGLAALLKDNNRHVGVYKPFLSGISRHHPDSDTSLLKDMSQTSLSHEDITPFAFKAPLAPYVAGKLEGKTVTMEEVLSHWGRIREKHECFIVEGAGGISVPLGEDYLVSHVIKALQLPMIIVARPRLGTINHTFLTVKYAESMGLPIAGIIINGISDSPDEDEKTNPEMIERLCGVPILGVTPKLANVTKETVLHMVKDHINLSLLMNQVGV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	231 (209)
Sequences:	4671 (2867)
Seq/√Len:	198.3

ECOLI - BIOD1 BIOD2
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
67_D	101_R	3.169	1.00
26_L	108_C	3.118	1.00
150_N	154_L	2.774	1.00
140_I	155_T	2.753	1.00
74_K	86_E	2.584	1.00
135_Q	165_P	2.575	1.00
157_K	162_M	2.401	1.00
155_T	158_Y	2.281	1.00
84_K	123_E	2.218	1.00
75_A	85_L	2.216	1.00
18_I	201_T	2.193	1.00
132_K	162_M	2.159	1.00
10_D	13_V	2.155	1.00
130_V	134_L	2.126	1.00
32_H	107_E	2.024	1.00
183_K	187_E	1.997	1.00
32_H	106_H	1.996	1.00
18_I	170_I	1.988	1.00
23_A	33_V	1.987	1.00
209_K	212_V	1.928	1.00
151_H	154_L	1.917	1.00
156_V	166_I	1.904	1.00
188_M	192_L	1.899	1.00
122_G	125_Y	1.886	1.00
138_M	159_A	1.827	1.00
100_G	103_R	1.817	1.00
19_S	110_I	1.763	1.00
67_D	105_K	1.756	1.00
43_I	72_A	1.754	1.00
3_G	136_L	1.738	1.00
142_A	148_T	1.638	1.00
91_T	94_E	1.622	1.00
157_K	161_S	1.599	1.00
96_L	133_A	1.588	1.00
187_E	191_R	1.561	1.00
111_V	136_L	1.555	1.00
119_V	188_M	1.533	1.00
7_T	138_M	1.533	1.00
75_A	86_E	1.505	1.00
92_M	133_A	1.504	1.00
142_A	149_I	1.494	1.00
28_D	61_T	1.484	1.00
45_R	74_K	1.457	1.00
73_F	88_K	1.447	1.00
144_P	171_I	1.444	1.00
6_V	22_L	1.442	1.00
4_F	167_A	1.439	1.00
25_L	29_N	1.427	1.00
69_T	72_A	1.419	1.00
36_Y	98_H	1.401	1.00
94_E	97_S	1.394	1.00
132_K	165_P	1.381	1.00
6_V	141_V	1.375	1.00
188_M	191_R	1.372	1.00
27_K	61_T	1.365	1.00
10_D	151_H	1.364	1.00
179_D	183_K	1.341	1.00
128_S	162_M	1.328	1.00
49_D	54_L	1.327	1.00
137_P	167_A	1.310	1.00
149_I	171_I	1.309	1.00
6_V	19_S	1.304	1.00
139_I	198_L	1.301	1.00
96_L	100_G	1.297	1.00
4_F	139_I	1.294	1.00
143_R	148_T	1.290	1.00
190_E	197_I	1.284	1.00
96_L	134_L	1.272	1.00
138_M	164_L	1.254	1.00
36_Y	99_W	1.249	1.00
92_M	125_Y	1.238	1.00
142_A	169_I	1.236	1.00
148_T	152_T	1.234	1.00
99_W	103_R	1.233	1.00
156_V	195_V	1.232	1.00
169_I	197_I	1.232	1.00
31_R	108_C	1.230	1.00
117_I	159_A	1.224	1.00
34_G	106_H	1.221	1.00
154_L	192_L	1.219	1.00
23_A	110_I	1.210	1.00
184_T	187_E	1.199	1.00
10_D	143_R	1.198	1.00
7_T	128_S	1.193	1.00
21_G	25_L	1.180	1.00
122_G	162_M	1.176	1.00
46_H	54_L	1.154	1.00
27_K	33_V	1.151	1.00
149_I	189_I	1.145	1.00
156_V	169_I	1.127	1.00
22_L	26_L	1.124	1.00
76_P	79_P	1.123	1.00
10_D	145_R	1.118	1.00
97_S	101_R	1.106	1.00
77_L	80_Y	1.106	1.00
111_V	130_V	1.083	1.00
3_G	99_W	1.082	1.00
35_V	59_S	1.071	1.00
83_G	90_V	1.065	1.00
18_I	141_V	1.062	1.00
152_T	169_I	1.060	1.00
38_P	111_V	1.057	1.00
150_N	153_F	1.054	1.00
7_T	113_G	1.051	1.00
8_G	13_V	1.047	1.00
142_A	152_T	1.038	1.00
53_S	56_K	1.024	1.00
179_D	182_E	1.024	1.00
114_A	127_V	1.016	1.00
5_F	131_I	1.013	1.00
125_Y	133_A	1.004	1.00
86_E	98_H	1.003	1.00
208_T	211_T	1.003	1.00
140_I	166_I	1.002	1.00
156_V	193_C	0.999	1.00
132_K	161_S	0.989	1.00
39_F	95_V	0.975	0.99
156_V	160_E	0.974	0.99
34_G	109_F	0.974	0.99
3_G	103_R	0.971	0.99
103_R	109_F	0.957	0.99
54_L	58_M	0.957	0.99
197_I	200_V	0.956	0.99
71_F	94_E	0.950	0.99
12_E	50_S	0.949	0.99
76_P	80_Y	0.947	0.99
93_E	133_A	0.945	0.99
102_I	109_F	0.944	0.99
118_S	158_Y	0.942	0.99
93_E	97_S	0.935	0.99
150_N	155_T	0.935	0.99
143_R	151_H	0.924	0.99
94_E	98_H	0.924	0.99
77_L	185_N	0.922	0.99
78_A	81_V	0.921	0.99
100_G	133_A	0.919	0.99
118_S	128_S	0.917	0.99
20_S	23_A	0.916	0.99
77_L	81_V	0.912	0.99
4_F	110_I	0.910	0.99
85_L	180_E	0.910	0.99
101_R	105_K	0.906	0.99
20_S	54_L	0.904	0.99
98_H	101_R	0.902	0.99
17_V	204_L	0.900	0.99
187_E	190_E	0.895	0.99
41_S	77_L	0.892	0.99
131_I	164_L	0.891	0.99
142_A	153_F	0.891	0.99
41_S	73_F	0.889	0.99
144_P	148_T	0.888	0.99
27_K	60_Q	0.883	0.99
10_D	152_T	0.881	0.99
140_I	156_V	0.876	0.99
141_V	172_N	0.873	0.99
70_P	98_H	0.872	0.99
26_L	33_V	0.872	0.99
54_L	57_D	0.871	0.99
13_V	143_R	0.870	0.99
189_I	193_C	0.869	0.99
36_Y	102_I	0.862	0.99
169_I	193_C	0.855	0.99
34_G	102_I	0.846	0.99
36_Y	70_P	0.840	0.98
33_V	108_C	0.827	0.98
169_I	195_V	0.825	0.98
7_T	117_I	0.820	0.98
101_R	104_E	0.819	0.98
186_P	200_V	0.814	0.98
16_T	54_L	0.808	0.98
23_A	35_V	0.808	0.98
175_S	178_P	0.806	0.98
5_F	113_G	0.804	0.98
166_I	195_V	0.795	0.98
117_I	155_T	0.795	0.98
182_E	186_P	0.790	0.98
73_F	83_G	0.785	0.98
26_L	31_R	0.783	0.98
157_K	163_G	0.781	0.98
95_V	125_Y	0.778	0.97
164_L	195_V	0.775	0.97
159_A	164_L	0.768	0.97
31_R	107_E	0.764	0.97
25_L	28_D	0.764	0.97
208_T	212_V	0.763	0.97
182_E	200_V	0.762	0.97
42_G	76_P	0.761	0.97
27_K	32_H	0.760	0.97
171_I	186_P	0.758	0.97
204_L	207_V	0.755	0.97
73_F	89_T	0.755	0.97
186_P	197_I	0.755	0.97
19_S	55_L	0.749	0.97
118_S	157_K	0.743	0.97
117_I	128_S	0.740	0.97
92_M	130_V	0.736	0.96
67_D	98_H	0.734	0.96
18_I	172_N	0.733	0.96
35_V	55_L	0.732	0.96
71_F	91_T	0.728	0.96
119_V	185_N	0.725	0.96
39_F	121_L	0.723	0.96
168_G	198_L	0.718	0.96
128_S	131_I	0.716	0.96
9_T	148_T	0.715	0.96
149_I	185_N	0.714	0.96
118_S	162_M	0.708	0.96
126_L	192_L	0.706	0.96
160_E	194_G	0.705	0.96
33_V	107_E	0.704	0.95
171_I	200_V	0.703	0.95
190_E	196_P	0.702	0.95
140_I	169_I	0.697	0.95
23_A	60_Q	0.696	0.95
149_I	153_F	0.687	0.95
11_T	146_L	0.687	0.95
52_T	66_E	0.686	0.95
137_P	165_P	0.686	0.95
38_P	130_V	0.685	0.95
20_S	55_L	0.684	0.95
92_M	129_H	0.680	0.95
127_V	131_I	0.677	0.94
32_H	105_K	0.674	0.94
6_V	170_I	0.674	0.94
129_H	162_M	0.672	0.94
22_L	139_I	0.672	0.94
171_I	197_I	0.668	0.94
128_S	158_Y	0.666	0.94
40_L	49_D	0.664	0.94
159_A	166_I	0.664	0.94
6_V	139_I	0.657	0.93
92_M	96_L	0.654	0.93
118_S	153_F	0.652	0.93
43_I	50_S	0.652	0.93
119_V	182_E	0.651	0.93
17_V	207_V	0.649	0.93
102_I	106_H	0.648	0.93
48_P	53_S	0.646	0.93
26_L	110_I	0.646	0.93
42_G	79_P	0.640	0.93
99_W	134_L	0.638	0.92
52_T	69_T	0.637	0.92
99_W	111_V	0.637	0.92
3_G	111_V	0.637	0.92
113_G	127_V	0.636	0.92
112_E	115_G	0.636	0.92
12_E	17_V	0.633	0.92
117_I	131_I	0.629	0.92
86_E	94_E	0.624	0.92
99_W	136_L	0.622	0.92
158_Y	162_M	0.621	0.91
207_V	212_V	0.620	0.91
76_P	146_L	0.618	0.91
3_G	134_L	0.618	0.91
155_T	160_E	0.617	0.91
168_G	196_P	0.614	0.91
95_V	130_V	0.609	0.91
64_S	67_D	0.607	0.91
173_G	182_E	0.606	0.90
43_I	48_P	0.605	0.90
38_P	114_A	0.604	0.90
173_G	203_K	0.603	0.90
21_G	24_A	0.603	0.90
49_D	57_D	0.602	0.90
153_F	169_I	0.601	0.90
40_L	69_T	0.601	0.90
45_R	48_P	0.600	0.90
81_V	184_T	0.597	0.90
157_K	160_E	0.594	0.90
168_G	199_G	0.593	0.89
40_L	72_A	0.586	0.89
5_F	127_V	0.586	0.89
118_S	126_L	0.583	0.89
19_S	35_V	0.581	0.89
154_L	157_K	0.578	0.88
132_K	164_L	0.572	0.88
140_I	159_A	0.570	0.88
99_W	130_V	0.570	0.88
154_L	158_Y	0.570	0.88
85_L	184_T	0.569	0.87
19_S	22_L	0.569	0.87
56_K	68_I	0.568	0.87
96_L	130_V	0.566	0.87
173_G	200_V	0.565	0.87
145_R	148_T	0.565	0.87
78_A	146_L	0.564	0.87
126_L	153_F	0.563	0.87
119_V	127_V	0.559	0.87
186_P	190_E	0.559	0.87
158_Y	161_S	0.554	0.86
206_N	211_T	0.546	0.85
7_T	140_I	0.546	0.85
25_L	201_T	0.544	0.85
86_E	101_R	0.544	0.85
96_L	99_W	0.544	0.85
92_M	95_V	0.543	0.85
183_K	186_P	0.537	0.84
117_I	140_I	0.534	0.84
10_D	189_I	0.531	0.84
117_I	164_L	0.528	0.83
178_P	183_K	0.527	0.83
100_G	104_E	0.525	0.83
207_V	210_E	0.519	0.82
38_P	71_F	0.517	0.82
65_H	105_K	0.513	0.82
128_S	157_K	0.510	0.81
129_H	133_A	0.506	0.81
44_S	50_S	0.506	0.81
171_I	189_I	0.504	0.80
128_S	138_M	0.503	0.80
43_I	69_T	0.503	0.80
145_R	185_N	0.500	0.80
123_E	191_R	0.500	0.80
169_I	189_I	0.500	0.80

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	0.974	100	0.314	Contact Map
3fgnA	2	0.9654	100	0.521	Contact Map
2obnA	2	0.7835	100	0.535	Contact Map
1s1mA	4	0.9697	100	0.549	Contact Map
3of5A	2	0.9307	100	0.593	Contact Map
1byiA	2	0.9567	100	0.594	Contact Map
3zq6A	2	0.9134	100	0.605	Contact Map
3qxcA	2	0.9134	99.9	0.612	Contact Map
3ug7A	4	0.9264	99.9	0.619	Contact Map
4zdjA	4	0.9784	99.9	0.629	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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