BIOB - ECOLI - GREMLIN Contacts

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BIOB - Biotin synthase

UniProt:	P12996	Sequences: MAHRPRWTLSQVTELFEKPLLDLLFEAQQVHRQHFDPRQVQVSTLLSIKTGACPEDCKYCPQSSRYKTGLEAERLMEVEQVLESARKAKAAGSTRFCMGAAWKNPHERDMPYLEQMVQGVKAMGLEACMTLGTLSESQAQRLANAGLDYYNHNLDTSPEFYGNIITTRTYQERLDTLEKVRDAGIKVCSGGIVGLGETVKDRAGLLLQLANLPTPPESVPINMLVKVKGTPLADNDDVDAFDFIRTIAVARIMMPTSYVRLSAGREQMNEQTQAMCFMAGANSIFYGCKLLTTPNPEEDKDLQLFRKLGLNPQQTAVLAGDNEQQQRLEQALMTPDTDEYYNAAAL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10118
Length:	346 (306)
Sequences:	5865 (3417)
Seq/√Len:	195.3

ECOLI - BIOB THIH
BACSU - BIOB
HALSA - COFG COFH

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
114_E	141_R	4.784	1.00
136_E	182_D	4.271	1.00
158_P	171_Q	4.118	1.00
78_V	115_Q	3.271	1.00
121_K	148_D	3.215	1.00
9_L	204_G	3.054	1.00
29_Q	33_Q	3.006	1.00
56_D	65_R	2.884	1.00
31_H	252_I	2.779	1.00
110_M	114_E	2.742	1.00
78_V	119_G	2.702	1.00
77_E	80_Q	2.659	1.00
219_V	254_M	2.586	1.00
260_R	282_N	2.572	1.00
136_E	140_Q	2.570	1.00
81_V	116_M	2.554	1.00
178_E	217_E	2.542	1.00
136_E	179_K	2.445	1.00
13_T	200_K	2.334	1.00
207_L	253_M	2.302	1.00
82_L	119_G	2.299	1.00
111_P	141_R	2.295	1.00
171_Q	175_D	2.221	1.00
175_D	179_K	2.168	1.00
9_L	207_L	2.155	1.00
39_Q	311_N	2.108	1.00
140_Q	144_N	2.073	1.00
15_L	249_V	1.970	1.00
83_E	86_R	1.967	1.00
119_G	122_A	1.959	1.00
199_V	242_D	1.952	1.00
86_R	90_A	1.939	1.00
189_S	209_L	1.930	1.00
154_L	205_L	1.904	1.00
202_R	242_D	1.879	1.00
85_A	120_V	1.855	1.00
143_A	183_A	1.832	1.00
159_E	204_G	1.820	1.00
114_E	145_A	1.801	1.00
27_A	252_I	1.788	1.00
114_E	118_Q	1.758	1.00
12_V	253_M	1.745	1.00
13_T	17_E	1.738	1.00
115_Q	118_Q	1.722	1.00
229_G	232_L	1.696	1.00
137_S	140_Q	1.667	1.00
157_S	201_D	1.660	1.00
8_T	11_Q	1.655	1.00
80_Q	83_E	1.644	1.00
117_V	147_L	1.629	1.00
206_L	250_A	1.625	1.00
82_L	86_R	1.623	1.00
33_Q	38_R	1.620	1.00
38_R	311_N	1.606	1.00
149_Y	186_K	1.576	1.00
274_A	307_K	1.569	1.00
143_A	185_I	1.552	1.00
87_K	90_A	1.550	1.00
178_E	182_D	1.547	1.00
172_E	175_D	1.545	1.00
139_A	183_A	1.534	1.00
229_G	233_A	1.521	1.00
135_S	138_Q	1.520	1.00
303_Q	307_K	1.519	1.00
88_A	93_S	1.515	1.00
299_D	303_Q	1.503	1.00
25_F	279_A	1.500	1.00
9_L	13_T	1.485	1.00
9_L	203_A	1.481	1.00
21_L	245_R	1.480	1.00
113_L	142_L	1.479	1.00
13_T	203_A	1.479	1.00
29_Q	32_R	1.470	1.00
9_L	200_K	1.449	1.00
226_K	237_D	1.441	1.00
30_V	34_H	1.433	1.00
202_R	246_T	1.426	1.00
244_I	276_C	1.413	1.00
134_L	142_L	1.412	1.00
17_E	199_V	1.401	1.00
160_F	163_N	1.396	1.00
169_T	172_E	1.385	1.00
298_E	302_L	1.364	1.00
29_Q	278_M	1.361	1.00
270_E	307_K	1.355	1.00
198_T	201_D	1.348	1.00
261_L	276_C	1.343	1.00
230_T	233_A	1.342	1.00
42_V	302_L	1.341	1.00
259_V	281_A	1.335	1.00
297_E	300_K	1.334	1.00
141_R	144_N	1.332	1.00
178_E	212_L	1.331	1.00
179_K	182_D	1.329	1.00
110_M	138_Q	1.320	1.00
229_G	234_D	1.319	1.00
83_E	87_K	1.305	1.00
7_W	252_I	1.297	1.00
136_E	183_A	1.288	1.00
16_F	249_V	1.281	1.00
170_Y	174_L	1.279	1.00
207_L	211_N	1.278	1.00
302_L	306_R	1.278	1.00
17_E	200_K	1.276	1.00
230_T	234_D	1.260	1.00
261_L	281_A	1.259	1.00
47_S	50_T	1.249	1.00
278_M	308_L	1.234	1.00
26_E	30_V	1.214	1.00
158_P	162_G	1.211	1.00
82_L	122_A	1.210	1.00
240_A	272_T	1.206	1.00
94_T	314_Q	1.205	1.00
193_V	246_T	1.195	1.00
191_G	205_L	1.193	1.00
89_K	124_G	1.186	1.00
111_P	114_E	1.183	1.00
12_V	203_A	1.180	1.00
12_V	207_L	1.179	1.00
20_L	23_L	1.175	1.00
79_E	83_E	1.171	1.00
7_W	12_V	1.168	1.00
140_Q	143_A	1.167	1.00
21_L	25_F	1.156	1.00
74_R	104_N	1.149	1.00
14_E	18_K	1.146	1.00
113_L	131_L	1.145	1.00
193_V	243_F	1.137	1.00
118_Q	145_A	1.131	1.00
206_L	253_M	1.121	1.00
175_D	178_E	1.120	1.00
303_Q	306_R	1.114	1.00
159_E	201_D	1.106	1.00
50_T	101_A	1.093	1.00
6_R	214_T	1.089	1.00
300_K	303_Q	1.085	1.00
140_Q	183_A	1.085	1.00
117_V	127_A	1.081	1.00
174_L	208_Q	1.075	1.00
158_P	208_Q	1.063	1.00
52_A	74_R	1.056	1.00
177_L	187_V	1.051	1.00
269_N	275_M	1.048	1.00
78_V	112_Y	1.039	1.00
152_H	173_R	1.033	1.00
6_R	210_A	1.025	1.00
154_L	170_Y	1.017	1.00
76_M	81_V	1.016	1.00
203_A	207_L	1.015	1.00
78_V	82_L	1.015	1.00
78_V	116_M	1.004	1.00
12_V	249_V	1.001	1.00
201_D	204_G	1.001	1.00
28_Q	278_M	1.000	1.00
84_S	87_K	1.000	1.00
141_R	145_A	0.997	1.00
204_G	207_L	0.985	0.99
231_P	234_D	0.982	0.99
51_G	62_Q	0.979	0.99
239_D	242_D	0.976	0.99
111_P	115_Q	0.974	0.99
247_I	276_C	0.968	0.99
24_L	245_R	0.967	0.99
16_F	246_T	0.960	0.99
208_Q	211_N	0.956	0.99
103_K	133_T	0.956	0.99
98_M	116_M	0.952	0.99
16_F	199_V	0.950	0.99
170_Y	208_Q	0.947	0.99
89_K	123_M	0.941	0.99
110_M	141_R	0.935	0.99
48_I	81_V	0.932	0.99
277_F	305_F	0.929	0.99
32_R	310_L	0.929	0.99
6_R	255_P	0.926	0.99
56_D	63_S	0.920	0.99
51_G	70_L	0.919	0.99
199_V	246_T	0.911	0.99
152_H	176_T	0.911	0.99
87_K	91_A	0.910	0.99
158_P	170_Y	0.907	0.99
38_R	310_L	0.899	0.99
27_A	30_V	0.897	0.99
131_L	150_Y	0.896	0.99
274_A	304_L	0.895	0.99
109_D	112_Y	0.895	0.99
29_Q	310_L	0.881	0.99
31_H	34_H	0.876	0.99
209_L	219_V	0.875	0.99
18_K	24_L	0.873	0.99
5_P	11_Q	0.872	0.99
114_E	144_N	0.869	0.99
116_M	119_G	0.862	0.99
306_R	311_N	0.860	0.99
226_K	234_D	0.860	0.99
73_E	80_Q	0.859	0.99
84_S	96_F	0.852	0.99
39_Q	313_Q	0.851	0.99
244_I	279_A	0.848	0.98
306_R	312_P	0.844	0.98
284_I	301_D	0.841	0.98
63_S	231_P	0.839	0.98
115_Q	119_G	0.836	0.98
104_N	133_T	0.834	0.98
228_K	233_A	0.833	0.98
305_F	310_L	0.833	0.98
161_Y	173_R	0.830	0.98
18_K	21_L	0.822	0.98
181_R	187_V	0.821	0.98
48_I	98_M	0.820	0.98
25_F	244_I	0.819	0.98
42_V	305_F	0.818	0.98
61_P	227_V	0.817	0.98
86_R	89_K	0.816	0.98
118_Q	122_A	0.815	0.98
25_F	248_A	0.812	0.98
174_L	178_E	0.810	0.98
86_R	123_M	0.810	0.98
27_A	31_H	0.803	0.98
32_R	36_D	0.801	0.98
46_L	96_F	0.801	0.98
179_K	183_A	0.800	0.98
19_P	245_R	0.800	0.98
82_L	85_A	0.797	0.98
271_Q	274_A	0.791	0.98
178_E	211_N	0.789	0.98
150_Y	180_V	0.788	0.98
52_A	72_A	0.787	0.98
209_L	254_M	0.787	0.98
207_L	210_A	0.786	0.98
225_V	293_T	0.786	0.98
305_F	312_P	0.785	0.97
18_K	26_E	0.785	0.97
97_C	262_S	0.782	0.97
206_L	209_L	0.782	0.97
69_G	229_G	0.777	0.97
44_T	93_S	0.774	0.97
121_K	127_A	0.767	0.97
107_E	141_R	0.766	0.97
118_Q	144_N	0.765	0.97
221_I	250_A	0.765	0.97
154_L	208_Q	0.762	0.97
262_S	285_F	0.759	0.97
181_R	213_P	0.758	0.97
76_M	84_S	0.752	0.97
104_N	107_E	0.751	0.97
13_T	199_V	0.750	0.97
48_I	101_A	0.748	0.97
74_R	108_R	0.747	0.97
55_E	103_K	0.746	0.97
35_F	259_V	0.743	0.97
240_A	269_N	0.740	0.96
159_E	162_G	0.740	0.96
139_A	185_I	0.739	0.96
55_E	167_T	0.738	0.96
241_F	272_T	0.737	0.96
195_L	235_N	0.735	0.96
21_L	241_F	0.734	0.96
138_Q	141_R	0.733	0.96
227_V	230_T	0.731	0.96
206_L	254_M	0.731	0.96
159_E	163_N	0.727	0.96
79_E	119_G	0.724	0.96
66_Y	231_P	0.723	0.96
214_T	255_P	0.723	0.96
32_R	40_V	0.718	0.96
245_R	249_V	0.714	0.96
247_I	281_A	0.710	0.95
244_I	275_M	0.709	0.95
154_L	157_S	0.708	0.95
298_E	314_Q	0.707	0.95
44_T	88_A	0.707	0.95
171_Q	208_Q	0.707	0.95
276_C	281_A	0.707	0.95
40_V	277_F	0.706	0.95
147_L	185_I	0.706	0.95
14_E	17_E	0.703	0.95
10_S	14_E	0.700	0.95
120_V	127_A	0.699	0.95
162_G	165_I	0.698	0.95
226_K	233_A	0.696	0.95
299_D	302_L	0.694	0.95
35_F	255_P	0.693	0.95
56_D	167_T	0.693	0.95
203_A	253_M	0.693	0.95
85_A	125_L	0.690	0.95
40_V	310_L	0.690	0.95
16_F	203_A	0.690	0.95
10_S	200_K	0.689	0.95
133_T	173_R	0.683	0.94
135_S	176_T	0.682	0.94
110_M	142_L	0.681	0.94
50_T	73_E	0.680	0.94
177_L	189_S	0.679	0.94
25_F	29_Q	0.675	0.94
292_T	295_N	0.674	0.94
126_E	148_D	0.674	0.94
254_M	257_S	0.674	0.94
79_E	82_L	0.672	0.94
11_Q	14_E	0.671	0.94
209_L	258_Y	0.668	0.94
58_K	66_Y	0.666	0.94
89_K	94_T	0.665	0.94
135_S	179_K	0.665	0.94
199_V	202_R	0.665	0.94
108_R	112_Y	0.664	0.94
139_A	176_T	0.664	0.94
82_L	123_M	0.660	0.93
19_P	23_L	0.659	0.93
160_F	196_G	0.658	0.93
268_M	272_T	0.658	0.93
160_F	164_I	0.656	0.93
131_L	142_L	0.656	0.93
160_F	195_L	0.655	0.93
12_V	206_L	0.655	0.93
209_L	217_E	0.655	0.93
285_F	290_L	0.655	0.93
223_M	243_F	0.651	0.93
40_V	305_F	0.651	0.93
135_S	172_E	0.649	0.93
64_S	71_E	0.647	0.93
7_W	253_M	0.645	0.93
89_K	125_L	0.644	0.93
265_R	276_C	0.636	0.92
129_M	147_L	0.636	0.92
177_L	181_R	0.636	0.92
59_Y	173_R	0.634	0.92
96_F	127_A	0.633	0.92
203_A	249_V	0.632	0.92
43_S	222_N	0.632	0.92
284_I	305_F	0.631	0.92
30_V	33_Q	0.630	0.92
263_A	281_A	0.627	0.92
35_F	256_T	0.626	0.91
180_V	185_I	0.626	0.91
163_N	196_G	0.625	0.91
113_L	117_V	0.624	0.91
83_E	90_A	0.623	0.91
270_E	300_K	0.621	0.91
54_P	105_P	0.620	0.91
157_S	204_G	0.619	0.91
23_L	26_E	0.618	0.91
107_E	138_Q	0.618	0.91
47_S	264_G	0.615	0.91
134_L	137_S	0.613	0.91
49_K	100_A	0.612	0.91
192_I	195_L	0.612	0.91
18_K	245_R	0.612	0.91
36_D	282_N	0.611	0.90
164_I	232_L	0.610	0.90
240_A	275_M	0.610	0.90
21_L	38_R	0.610	0.90
188_C	222_N	0.609	0.90
41_Q	313_Q	0.608	0.90
47_S	262_S	0.607	0.90
133_T	152_H	0.606	0.90
156_T	160_F	0.605	0.90
240_A	271_Q	0.605	0.90
134_L	138_Q	0.605	0.90
42_V	312_P	0.602	0.90
213_P	257_S	0.600	0.90
48_I	131_L	0.600	0.90
274_A	308_L	0.600	0.90
238_V	243_F	0.600	0.90
304_L	307_K	0.595	0.89
114_E	142_L	0.594	0.89
95_R	128_C	0.594	0.89
91_A	299_D	0.593	0.89
163_N	166_T	0.589	0.89
22_D	25_F	0.589	0.89
247_I	280_G	0.589	0.89
193_V	202_R	0.589	0.89
44_T	314_Q	0.589	0.89
239_D	243_F	0.588	0.89
305_F	308_L	0.585	0.88
180_V	183_A	0.585	0.88
139_A	150_Y	0.584	0.88
258_Y	282_N	0.581	0.88
43_S	153_N	0.581	0.88
110_M	129_M	0.580	0.88
193_V	238_V	0.579	0.88
23_L	27_A	0.579	0.88
49_K	288_C	0.578	0.88
61_P	289_K	0.578	0.88
220_P	223_M	0.578	0.88
251_R	282_N	0.577	0.88
22_D	26_E	0.575	0.88
56_D	64_S	0.575	0.88
241_F	245_R	0.574	0.88
188_C	262_S	0.573	0.87
242_D	246_T	0.572	0.87
47_S	192_I	0.569	0.87
139_A	180_V	0.569	0.87
95_R	260_R	0.569	0.87
263_A	293_T	0.568	0.87
97_C	151_N	0.566	0.87
98_M	120_V	0.564	0.87
112_Y	116_M	0.561	0.86
271_Q	275_M	0.560	0.86
9_L	12_V	0.558	0.86
270_E	304_L	0.557	0.86
174_L	212_L	0.556	0.86
192_I	264_G	0.555	0.86
273_Q	284_I	0.555	0.86
42_V	298_E	0.555	0.86
188_C	264_G	0.553	0.86
272_T	276_C	0.551	0.85
126_E	149_Y	0.550	0.85
52_A	104_N	0.550	0.85
161_Y	165_I	0.549	0.85
181_R	220_P	0.546	0.85
250_A	254_M	0.545	0.85
21_L	24_L	0.545	0.85
7_W	11_Q	0.543	0.85
78_V	81_V	0.540	0.84
48_I	100_A	0.540	0.84
290_L	294_P	0.539	0.84
110_M	131_L	0.537	0.84
191_G	221_I	0.537	0.84
266_E	296_P	0.537	0.84
210_A	214_T	0.536	0.84
82_L	96_F	0.534	0.84
113_L	116_M	0.534	0.84
180_V	187_V	0.534	0.84
47_S	73_E	0.533	0.83
154_L	212_L	0.533	0.83
296_P	300_K	0.532	0.83
61_P	165_I	0.532	0.83
197_E	202_R	0.531	0.83
273_Q	285_F	0.531	0.83
219_V	257_S	0.530	0.83
263_A	273_Q	0.530	0.83
6_R	207_L	0.530	0.83
212_L	218_S	0.529	0.83
45_L	95_R	0.528	0.83
62_Q	97_C	0.527	0.83
189_S	258_Y	0.527	0.83
26_E	29_Q	0.527	0.83
186_K	217_E	0.526	0.83
160_F	191_G	0.524	0.82
51_G	61_P	0.523	0.82
249_V	253_M	0.522	0.82
272_T	275_M	0.520	0.82
181_R	217_E	0.519	0.82
12_V	15_L	0.519	0.82
159_E	198_T	0.518	0.82
84_S	88_A	0.517	0.82
177_L	212_L	0.516	0.81
59_Y	262_S	0.513	0.81
66_Y	107_E	0.512	0.81
85_A	123_M	0.511	0.81
170_Y	201_D	0.509	0.81
9_L	253_M	0.509	0.81
112_Y	115_Q	0.508	0.80
56_D	166_T	0.507	0.80
199_V	249_V	0.503	0.80
29_Q	38_R	0.501	0.80
41_Q	188_C	0.501	0.80
222_N	264_G	0.500	0.79

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
1r30A	2	0.8988	100	0.38	Contact Map
3t7vA	1	0.9046	100	0.448	Contact Map
3iixA	1	0.9133	100	0.46	Contact Map
4r33A	2	0.9133	100	0.466	Contact Map
4wcxA	1	0.9769	100	0.49	Contact Map
4rtbA	2	0.9249	100	0.505	Contact Map
4u0oB	1	0.7081	100	0.683	Contact Map
1oltA	1	0.922	99.8	0.784	Contact Map
4jc0A	1	0.8931	99.8	0.79	Contact Map
2qgqA	1	0.7139	99.8	0.793	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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