BIOD1 - ECOLI - GREMLIN Contacts

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BIOD1 - ATP-dependent dethiobiotin synthetase BioD 1

UniProt:	P13000	Sequences: MSKRYFVTGTDTEVGKTVASCALLQAAKAAGYRTAGYKPVASGSEKTPEGLRNSDALALQRNSSLQLDYATVNPYTFAEPTSPHIISAQEGRPIESLVMSAGLRALEQQADWVLVEGAGGWFTPLSDTFTFADWVTQEQLPVILVVGVKLGCINHAMLTAQVIQHAGLTLAGWVANDVTPPGKRHAEYMTTLTRMIPAPLLGEIPWLAENPENAATGKYINLALL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10120
Length:	225 (205)
Sequences:	4673 (2878)
Seq/√Len:	201.0

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
71_T	105_A	3.241	1.00
27_A	112_W	3.213	1.00
144_L	159_T	3.025	1.00
139_Q	169_T	2.741	1.00
78_A	90_E	2.611	1.00
136_T	166_A	2.451	1.00
161_Q	166_A	2.402	1.00
160_A	170_L	2.314	1.00
88_A	127_D	2.271	1.00
134_W	138_E	2.270	1.00
19_A	204_I	2.268	1.00
79_E	89_Q	2.219	1.00
24_L	34_T	2.181	1.00
11_D	14_V	2.149	1.00
19_A	174_V	2.122	1.00
146_V	156_A	2.110	1.00
33_R	110_A	2.103	1.00
33_R	111_D	2.082	1.00
11_D	155_H	2.065	1.00
186_A	190_T	2.035	1.00
191_T	195_M	1.946	1.00
20_S	114_L	1.939	1.00
4_R	140_L	1.914	1.00
142_V	163_I	1.904	1.00
126_S	129_F	1.844	1.00
44_S	76_T	1.812	1.00
104_R	107_E	1.785	1.00
95_E	98_V	1.669	1.00
100_S	137_Q	1.665	1.00
146_V	152_C	1.626	1.00
115_V	140_L	1.617	1.00
154_N	158_L	1.614	1.00
79_E	90_E	1.605	1.00
71_T	109_Q	1.598	1.00
8_T	142_V	1.531	1.00
103_L	107_E	1.531	1.00
46_K	78_A	1.530	1.00
190_T	194_R	1.504	1.00
156_A	173_W	1.494	1.00
77_F	92_R	1.494	1.00
73_N	76_T	1.473	1.00
161_Q	165_H	1.462	1.00
148_V	175_A	1.462	1.00
123_T	191_T	1.461	1.00
160_A	198_A	1.457	1.00
96_S	137_Q	1.449	1.00
28_K	65_L	1.447	1.00
7_V	23_L	1.446	1.00
146_V	153_I	1.419	1.00
37_Y	102_G	1.417	1.00
187_E	190_T	1.412	1.00
5_Y	171_A	1.410	1.00
29_A	65_L	1.408	1.00
143_I	201_L	1.372	1.00
98_V	101_A	1.371	1.00
142_V	168_L	1.363	1.00
173_W	200_L	1.360	1.00
5_Y	143_I	1.358	1.00
53_N	58_A	1.343	1.00
35_A	110_A	1.336	1.00
157_M	195_M	1.319	1.00
141_P	171_A	1.315	1.00
100_S	104_R	1.308	1.00
132_A	166_A	1.306	1.00
136_T	169_T	1.303	1.00
24_L	114_L	1.295	1.00
183_K	186_A	1.288	1.00
28_K	34_T	1.283	1.00
147_G	152_C	1.280	1.00
7_V	20_S	1.259	1.00
37_Y	103_L	1.256	1.00
7_V	145_V	1.251	1.00
4_R	103_L	1.248	1.00
121_W	163_I	1.245	1.00
152_C	156_A	1.239	1.00
191_T	194_R	1.225	1.00
160_A	173_W	1.223	1.00
153_I	175_A	1.217	1.00
100_S	138_E	1.202	1.00
32_Y	112_W	1.182	1.00
193_T	200_L	1.181	1.00
23_L	27_A	1.181	1.00
80_P	83_P	1.170	1.00
8_T	132_A	1.159	1.00
22_A	26_A	1.153	1.00
153_I	192_L	1.150	1.00
146_V	173_W	1.148	1.00
11_D	149_K	1.136	1.00
11_D	147_G	1.132	1.00
157_M	161_Q	1.123	1.00
115_V	134_W	1.119	1.00
39_P	115_V	1.111	1.00
182_G	185_H	1.107	1.00
35_A	113_V	1.105	1.00
26_A	30_A	1.092	1.00
101_A	105_A	1.090	1.00
57_L	60_Q	1.088	1.00
160_A	196_I	1.087	1.00
96_S	129_F	1.086	1.00
144_L	170_L	1.083	1.00
36_G	63_S	1.078	1.00
9_G	14_V	1.074	1.00
75_Y	98_V	1.049	1.00
122_F	162_V	1.047	1.00
81_T	84_H	1.043	1.00
6_F	135_V	1.043	1.00
85_I	187_E	1.036	1.00
8_T	117_G	1.029	1.00
19_A	145_V	1.027	1.00
102_G	105_A	1.026	1.00
126_S	166_A	1.021	1.00
182_G	186_A	1.016	1.00
118_A	131_F	1.016	1.00
4_R	107_E	1.013	1.00
89_Q	184_R	1.008	1.00
58_A	62_N	1.007	1.00
200_L	203_E	1.003	1.00
106_L	113_V	1.003	1.00
209_E	212_E	0.999	1.00
18_V	207_L	0.993	1.00
104_R	137_Q	0.990	1.00
190_T	193_T	0.986	1.00
135_V	168_L	0.964	0.99
129_F	137_Q	0.957	0.99
105_A	109_Q	0.957	0.99
80_P	84_H	0.953	0.99
40_V	99_M	0.951	0.99
90_E	102_G	0.948	0.99
42_S	77_F	0.945	0.99
154_N	159_T	0.939	0.99
75_Y	95_E	0.932	0.99
81_T	85_I	0.924	0.99
82_S	85_I	0.921	0.99
192_L	196_I	0.920	0.99
122_F	132_A	0.919	0.99
145_V	176_N	0.918	0.99
21_C	58_A	0.913	0.99
28_K	64_S	0.905	0.99
14_V	147_G	0.903	0.99
97_L	137_Q	0.901	0.99
74_P	102_G	0.896	0.99
97_L	101_A	0.896	0.99
184_R	187_E	0.895	0.99
148_V	152_C	0.894	0.99
144_L	160_A	0.882	0.99
98_V	102_G	0.881	0.99
24_L	36_G	0.872	0.99
107_E	113_V	0.864	0.99
5_Y	114_L	0.862	0.99
36_G	59_L	0.852	0.99
105_A	108_Q	0.851	0.99
126_S	164_Q	0.851	0.99
21_C	24_L	0.848	0.99
207_L	210_N	0.843	0.99
34_T	112_W	0.843	0.99
13_E	54_S	0.842	0.99
37_Y	74_P	0.840	0.99
26_A	29_A	0.838	0.99
132_A	162_V	0.838	0.99
42_S	81_T	0.833	0.98
58_A	61_R	0.821	0.98
147_G	155_H	0.808	0.98
77_F	93_P	0.808	0.98
189_M	203_E	0.806	0.98
121_W	159_T	0.806	0.98
160_A	164_Q	0.805	0.98
47_T	52_R	0.800	0.98
27_A	32_Y	0.795	0.98
27_A	34_T	0.794	0.98
6_F	117_G	0.794	0.98
185_H	203_E	0.786	0.98
173_W	198_A	0.785	0.98
8_T	121_W	0.784	0.98
121_W	132_A	0.781	0.98
163_I	168_L	0.770	0.97
81_T	188_Y	0.762	0.97
157_M	196_I	0.762	0.97
172_G	201_L	0.758	0.97
193_T	199_P	0.754	0.97
77_F	87_S	0.751	0.97
22_A	25_Q	0.746	0.97
43_G	80_P	0.744	0.97
162_V	166_A	0.744	0.97
141_P	169_T	0.744	0.97
170_L	198_A	0.735	0.97
56_A	70_A	0.730	0.96
87_S	94_I	0.729	0.96
122_F	161_Q	0.727	0.96
71_T	102_G	0.720	0.96
28_K	33_R	0.720	0.96
123_T	188_Y	0.719	0.96
46_K	52_R	0.717	0.96
20_S	59_L	0.716	0.96
19_A	176_N	0.715	0.96
161_Q	164_Q	0.713	0.96
96_S	134_W	0.709	0.96
133_D	166_A	0.707	0.96
132_A	135_V	0.706	0.96
131_F	135_V	0.705	0.96
68_D	71_T	0.703	0.96
122_F	157_M	0.695	0.95
173_W	196_I	0.694	0.95
163_I	170_L	0.693	0.95
185_H	189_M	0.692	0.95
175_A	200_L	0.684	0.95
106_L	110_A	0.684	0.95
20_S	36_G	0.676	0.95
41_A	53_N	0.676	0.95
17_T	58_A	0.675	0.95
168_L	198_A	0.673	0.94
158_L	162_V	0.673	0.94
10_T	152_C	0.672	0.94
32_Y	111_D	0.671	0.94
37_Y	106_L	0.668	0.94
69_Y	109_Q	0.667	0.94
175_A	189_M	0.662	0.94
130_T	157_M	0.662	0.94
39_P	134_W	0.659	0.94
199_P	202_G	0.657	0.94
12_T	150_L	0.656	0.94
23_L	143_I	0.656	0.94
95_E	129_F	0.653	0.94
130_T	195_M	0.651	0.93
7_V	174_V	0.651	0.93
103_L	138_E	0.651	0.93
43_G	83_P	0.648	0.93
39_P	118_A	0.647	0.93
144_L	173_W	0.647	0.93
27_A	114_L	0.645	0.93
96_S	133_D	0.644	0.93
103_L	115_V	0.638	0.93
80_P	150_L	0.636	0.93
99_M	129_F	0.635	0.93
184_R	188_Y	0.634	0.93
189_M	200_L	0.623	0.92
44_S	54_S	0.622	0.92
123_T	185_H	0.620	0.92
40_V	125_L	0.619	0.92
122_F	166_A	0.619	0.92
136_T	168_L	0.619	0.92
121_W	135_V	0.619	0.92
56_A	73_N	0.617	0.91
13_E	18_V	0.616	0.91
119_G	151_G	0.611	0.91
177_D	206_W	0.610	0.91
117_G	131_F	0.610	0.91
33_R	109_Q	0.607	0.91
165_H	168_L	0.606	0.91
177_D	203_E	0.603	0.91
20_S	23_L	0.600	0.90
99_M	134_W	0.599	0.90
96_S	100_S	0.597	0.90
157_M	160_A	0.596	0.90
24_L	64_S	0.592	0.90
6_F	131_F	0.591	0.90
82_S	150_L	0.590	0.90
18_V	210_N	0.577	0.89
144_L	163_I	0.575	0.88
4_R	115_V	0.574	0.88
186_A	189_M	0.571	0.88
85_I	184_R	0.570	0.88
4_R	138_E	0.569	0.88
41_A	76_T	0.569	0.88
175_A	203_E	0.567	0.88
34_T	111_D	0.565	0.87
179_T	185_H	0.563	0.87
21_C	59_L	0.562	0.87
177_D	185_H	0.562	0.87
136_T	164_Q	0.561	0.87
116_E	119_G	0.555	0.87
66_Q	110_A	0.554	0.86
44_S	52_R	0.553	0.86
132_A	163_I	0.553	0.86
41_A	73_N	0.552	0.86
153_I	188_Y	0.551	0.86
127_D	194_R	0.551	0.86
7_V	143_I	0.550	0.86
103_L	134_W	0.548	0.86
6_F	115_V	0.547	0.86
123_T	131_F	0.542	0.85
132_A	161_Q	0.540	0.85
47_T	55_D	0.540	0.85
35_A	106_L	0.536	0.85
187_E	191_T	0.535	0.85
96_S	99_M	0.533	0.84
207_L	211_P	0.532	0.84
162_V	165_H	0.528	0.84
133_D	137_Q	0.528	0.84
149_K	152_C	0.527	0.84
18_V	22_A	0.526	0.84
172_G	202_G	0.526	0.84
146_V	175_A	0.522	0.83
44_S	73_N	0.518	0.83
103_L	140_L	0.516	0.82
189_M	193_T	0.515	0.82
60_Q	72_V	0.515	0.82
100_S	103_L	0.513	0.82
47_T	54_S	0.511	0.82
161_Q	167_G	0.510	0.82
45_E	54_S	0.509	0.82
22_A	202_G	0.509	0.82
161_Q	195_M	0.507	0.81
10_T	146_V	0.507	0.81
39_P	99_M	0.504	0.81
7_V	155_H	0.504	0.81
121_W	144_L	0.500	0.80
56_A	60_Q	0.500	0.80
164_Q	197_P	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	0.9867	100	0.3	Contact Map
2obnA	2	0.8089	100	0.516	Contact Map
3fgnA	2	0.9556	100	0.524	Contact Map
1s1mA	4	0.9733	100	0.542	Contact Map
3of5A	2	0.96	100	0.566	Contact Map
1byiA	2	0.9911	100	0.569	Contact Map
3zq6A	2	0.9422	100	0.593	Contact Map
3qxcA	2	0.9467	99.9	0.601	Contact Map
3ug7A	4	0.9867	99.9	0.617	Contact Map
4zdjA	4	0.9867	99.9	0.625	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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