EX53 - BACSU - GREMLIN Contacts

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EX53 - 5'-3' exonuclease

UniProt:	P54161	Sequences: MNNNKLLLVDGMALLFRAFFATAVHRNFMINDSGVPTNGVNGFLKHLITAVETFQPTHVVCCWDMGSKTYRNDLFQDYKANRSAPPVELIPQFDLAKEAAAELGIMNIGFAGYEADDCIGTLADLFANEADITVVTGDRDLLQLLTDKVSVALLQKGIGNYKVYTKETFYEETGVMPKALIDIKALMGDSSDNYPGVKGIGEKTAYKLIREYETIDRLLENLSLLPKGQQGKIQQGLSDLEMSRKLAEIHCSVPLACTLKDALFTLQMEQAADMLRRHQIKGIERMLEKLNAREIV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	296 (277)
Sequences:	4550 (2859)
Seq/√Len:	171.8

ECOLI - DPO1 XNI
BACSU - EX53 DPO1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
221_N	224_L	4.473	1.00
165_T	168_T	3.903	1.00
32_D	279_Q	3.164	1.00
120_G	249_I	3.122	1.00
231_G	235_Q	3.025	1.00
236_G	239_D	2.913	1.00
74_L	245_K	2.891	1.00
237_L	241_E	2.746	1.00
198_K	236_G	2.724	1.00
127_A	146_T	2.721	1.00
176_M	179_A	2.631	1.00
219_L	241_E	2.423	1.00
5_K	131_D	2.368	1.00
230_Q	234_Q	2.361	1.00
97_K	109_G	2.351	1.00
170_Y	176_M	2.337	1.00
101_A	107_N	2.322	1.00
267_Q	270_Q	2.288	1.00
31_N	279_Q	2.150	1.00
228_G	232_K	2.144	1.00
214_T	217_R	2.117	1.00
228_G	231_G	2.098	1.00
219_L	237_L	2.081	1.00
124_D	251_C	2.081	1.00
217_R	220_E	2.020	1.00
11_G	61_C	1.982	1.00
216_D	241_E	1.959	1.00
98_E	277_R	1.941	1.00
147_D	166_K	1.937	1.00
49_T	53_T	1.873	1.00
183_I	209_I	1.820	1.00
216_D	244_R	1.819	1.00
167_E	171_E	1.810	1.00
258_T	261_D	1.787	1.00
272_A	284_E	1.782	1.00
200_I	229_Q	1.772	1.00
119_I	134_V	1.764	1.00
211_E	224_L	1.759	1.00
166_K	178_K	1.758	1.00
33_S	277_R	1.754	1.00
217_R	221_N	1.734	1.00
44_L	99_A	1.729	1.00
194_Y	247_A	1.683	1.00
227_K	230_Q	1.651	1.00
167_E	170_Y	1.646	1.00
219_L	222_L	1.638	1.00
98_E	101_A	1.626	1.00
245_K	250_H	1.608	1.00
85_P	90_I	1.608	1.00
68_K	73_D	1.603	1.00
197_V	240_L	1.600	1.00
274_M	278_H	1.595	1.00
222_L	234_Q	1.595	1.00
67_S	111_A	1.571	1.00
183_I	187_M	1.567	1.00
31_N	35_V	1.528	1.00
124_D	128_N	1.519	1.00
207_K	211_E	1.519	1.00
65_M	111_A	1.518	1.00
197_V	233_I	1.492	1.00
19_F	88_E	1.481	1.00
123_A	149_V	1.478	1.00
35_V	95_L	1.476	1.00
131_D	148_K	1.476	1.00
225_L	233_I	1.476	1.00
102_E	274_M	1.464	1.00
272_A	276_R	1.455	1.00
199_G	232_K	1.427	1.00
182_D	244_R	1.423	1.00
175_V	206_Y	1.409	1.00
50_A	135_V	1.405	1.00
16_F	20_F	1.383	1.00
87_V	90_I	1.377	1.00
136_T	141_L	1.368	1.00
145_L	169_F	1.357	1.00
166_K	170_Y	1.351	1.00
142_L	151_V	1.346	1.00
187_M	202_E	1.345	1.00
282_G	285_R	1.334	1.00
219_L	233_I	1.332	1.00
244_R	248_E	1.318	1.00
5_K	133_T	1.316	1.00
216_D	220_E	1.306	1.00
127_A	149_V	1.306	1.00
120_G	251_C	1.298	1.00
15_L	96_A	1.298	1.00
181_I	248_E	1.296	1.00
7_L	135_V	1.290	1.00
73_D	112_G	1.282	1.00
18_A	46_H	1.274	1.00
232_K	235_Q	1.269	1.00
150_S	163_V	1.250	1.00
60_V	262_A	1.250	1.00
168_T	171_E	1.249	1.00
68_K	72_N	1.248	1.00
75_F	246_L	1.231	1.00
222_L	230_Q	1.225	1.00
185_A	247_A	1.225	1.00
22_T	38_N	1.223	1.00
113_Y	250_H	1.216	1.00
74_L	242_M	1.214	1.00
36_P	91_P	1.207	1.00
45_K	286_M	1.206	1.00
121_T	253_V	1.200	1.00
4_N	57_T	1.199	1.00
206_Y	210_R	1.197	1.00
270_Q	273_D	1.193	1.00
212_Y	221_N	1.185	1.00
174_G	210_R	1.158	1.00
81_N	193_N	1.157	1.00
273_D	277_R	1.152	1.00
69_T	72_N	1.146	1.00
62_C	118_C	1.144	1.00
102_E	270_Q	1.133	1.00
145_L	151_V	1.124	1.00
219_L	240_L	1.121	1.00
186_L	204_T	1.119	1.00
113_Y	253_V	1.119	1.00
227_K	231_G	1.105	1.00
47_L	105_I	1.102	1.00
110_F	118_C	1.101	1.00
179_A	213_E	1.098	1.00
194_Y	243_S	1.094	1.00
212_Y	225_L	1.084	1.00
35_V	91_P	1.080	1.00
212_Y	224_L	1.079	1.00
250_H	253_V	1.077	1.00
94_D	98_E	1.073	1.00
208_L	218_L	1.066	1.00
125_L	129_E	1.058	1.00
123_A	132_I	1.058	1.00
35_V	277_R	1.057	1.00
40_V	278_H	1.048	0.99
139_R	184_K	1.045	0.99
169_F	175_V	1.043	0.99
126_F	132_I	1.040	0.99
198_K	239_D	1.040	0.99
232_K	236_G	1.035	0.99
99_A	274_M	1.034	0.99
164_Y	168_T	1.030	0.99
87_V	91_P	1.028	0.99
65_M	109_G	1.027	0.99
63_W	107_N	1.022	0.99
231_G	234_Q	1.013	0.99
127_A	148_K	1.006	0.99
52_E	286_M	1.004	0.99
113_Y	254_P	1.004	0.99
131_D	150_S	1.001	0.99
269_E	273_D	1.000	0.99
276_R	284_E	0.996	0.99
7_L	50_A	0.993	0.99
183_I	202_E	0.980	0.99
132_I	149_V	0.967	0.99
124_D	146_T	0.967	0.99
6_L	126_F	0.965	0.99
273_D	276_R	0.952	0.99
48_I	275_L	0.950	0.99
275_L	283_I	0.942	0.99
7_L	59_V	0.936	0.99
213_E	217_R	0.933	0.99
99_A	278_H	0.928	0.99
20_F	83_S	0.925	0.99
41_N	45_K	0.924	0.99
170_Y	210_R	0.921	0.99
124_D	127_A	0.911	0.99
162_K	172_E	0.910	0.99
15_L	89_L	0.905	0.98
36_P	88_E	0.903	0.98
9_V	61_C	0.903	0.98
103_L	271_A	0.897	0.98
202_E	206_Y	0.897	0.98
226_P	229_Q	0.890	0.98
41_N	280_I	0.886	0.98
268_M	272_A	0.884	0.98
65_M	68_K	0.883	0.98
152_A	163_V	0.880	0.98
181_I	247_A	0.877	0.98
239_D	242_M	0.877	0.98
142_L	164_Y	0.877	0.98
162_K	168_T	0.876	0.98
195_P	243_S	0.871	0.98
243_S	247_A	0.868	0.98
234_Q	237_L	0.863	0.98
168_T	172_E	0.851	0.98
266_L	271_A	0.847	0.98
4_N	58_H	0.843	0.98
39_G	92_Q	0.841	0.98
183_I	206_Y	0.841	0.98
260_K	263_L	0.838	0.97
75_F	195_P	0.836	0.97
133_T	152_A	0.836	0.97
6_L	262_A	0.834	0.97
104_G	267_Q	0.833	0.97
67_S	72_N	0.826	0.97
241_E	244_R	0.826	0.97
222_L	233_I	0.823	0.97
119_I	141_L	0.823	0.97
16_F	85_P	0.822	0.97
40_V	96_A	0.821	0.97
141_L	249_I	0.819	0.97
215_I	240_L	0.818	0.97
281_K	285_R	0.814	0.97
185_A	240_L	0.811	0.97
22_T	42_G	0.809	0.97
88_E	91_P	0.806	0.97
275_L	280_I	0.804	0.97
7_L	54_F	0.799	0.97
44_L	96_A	0.798	0.97
204_T	207_K	0.798	0.97
75_F	242_M	0.796	0.97
98_E	270_Q	0.796	0.97
54_F	133_T	0.793	0.96
39_G	96_A	0.791	0.96
59_V	264_F	0.788	0.96
127_A	132_I	0.785	0.96
257_C	262_A	0.784	0.96
166_K	176_M	0.782	0.96
43_F	100_A	0.781	0.96
272_A	288_E	0.777	0.96
200_I	208_L	0.777	0.96
48_I	283_I	0.773	0.96
179_A	209_I	0.773	0.96
93_F	97_K	0.772	0.96
248_E	251_C	0.767	0.96
40_V	95_L	0.766	0.96
41_N	282_G	0.764	0.96
211_E	226_P	0.763	0.96
54_F	163_V	0.761	0.96
142_L	145_L	0.759	0.96
207_K	229_Q	0.758	0.95
77_D	80_A	0.757	0.95
175_V	183_I	0.755	0.95
186_L	233_I	0.754	0.95
208_L	229_Q	0.751	0.95
7_L	133_T	0.749	0.95
20_F	86_P	0.748	0.95
229_Q	232_K	0.748	0.95
199_G	228_G	0.748	0.95
164_Y	172_E	0.747	0.95
237_L	240_L	0.741	0.95
175_V	179_A	0.741	0.95
238_S	241_E	0.741	0.95
101_A	270_Q	0.740	0.95
68_K	112_G	0.730	0.94
80_A	193_N	0.730	0.94
61_C	100_A	0.729	0.94
6_L	132_I	0.728	0.94
169_F	180_L	0.728	0.94
271_A	275_L	0.727	0.94
43_F	96_A	0.725	0.94
222_L	237_L	0.723	0.94
8_L	132_I	0.722	0.94
9_V	14_L	0.719	0.94
153_L	156_K	0.718	0.94
175_V	180_L	0.717	0.94
221_N	225_L	0.717	0.94
23_A	38_N	0.715	0.94
204_T	229_Q	0.715	0.94
133_T	163_V	0.715	0.94
185_A	243_S	0.711	0.94
225_L	229_Q	0.711	0.94
241_E	245_K	0.710	0.94
13_A	154_L	0.710	0.94
126_F	130_A	0.709	0.94
240_L	243_S	0.707	0.93
180_L	247_A	0.707	0.93
200_I	204_T	0.706	0.93
95_L	278_H	0.702	0.93
169_F	172_E	0.701	0.93
8_L	122_L	0.700	0.93
44_L	48_I	0.697	0.93
132_I	148_K	0.695	0.93
65_M	118_C	0.694	0.93
70_Y	250_H	0.693	0.93
173_T	180_L	0.693	0.93
223_S	234_Q	0.692	0.93
91_P	94_D	0.687	0.92
142_L	153_L	0.686	0.92
108_I	122_L	0.686	0.92
95_L	98_E	0.683	0.92
59_V	105_I	0.683	0.92
24_V	38_N	0.678	0.92
19_F	23_A	0.677	0.92
23_A	42_G	0.676	0.92
16_F	86_P	0.676	0.92
106_M	261_D	0.674	0.92
84_A	87_V	0.671	0.92
133_T	150_S	0.669	0.91
139_R	153_L	0.668	0.91
153_L	184_K	0.666	0.91
150_S	165_T	0.658	0.91
197_V	236_G	0.655	0.91
185_A	215_I	0.655	0.91
61_C	105_I	0.646	0.90
99_A	275_L	0.646	0.90
185_A	244_R	0.645	0.90
31_N	278_H	0.642	0.90
282_G	286_M	0.642	0.90
197_V	232_K	0.641	0.90
125_L	258_T	0.640	0.90
215_I	218_L	0.640	0.90
16_F	83_S	0.639	0.90
180_L	184_K	0.638	0.89
13_A	136_T	0.634	0.89
146_T	149_V	0.632	0.89
186_L	215_I	0.632	0.89
66_G	90_I	0.630	0.89
58_H	263_L	0.630	0.89
62_C	122_L	0.629	0.89
215_I	241_E	0.625	0.88
48_I	286_M	0.624	0.88
125_L	128_N	0.623	0.88
236_G	240_L	0.621	0.88
54_F	152_A	0.620	0.88
276_R	281_K	0.620	0.88
222_L	225_L	0.619	0.88
218_L	225_L	0.616	0.88
223_S	230_Q	0.614	0.88
102_E	271_A	0.614	0.88
183_I	205_A	0.608	0.87
179_A	182_D	0.607	0.87
135_V	152_A	0.606	0.87
51_V	264_F	0.606	0.87
140_D	192_D	0.606	0.87
242_M	245_K	0.606	0.87
8_L	119_I	0.604	0.87
24_V	88_E	0.602	0.87
46_H	154_L	0.602	0.87
170_Y	174_G	0.600	0.86
51_V	59_V	0.600	0.86
129_E	260_K	0.599	0.86
29_M	34_G	0.599	0.86
11_G	15_L	0.598	0.86
123_A	127_A	0.594	0.86
179_A	214_T	0.593	0.86
181_I	244_R	0.593	0.86
13_A	137_G	0.593	0.86
5_K	57_T	0.591	0.86
5_K	54_F	0.590	0.85
63_W	109_G	0.589	0.85
169_F	206_Y	0.589	0.85
123_A	251_C	0.586	0.85
198_K	235_Q	0.585	0.85
233_I	240_L	0.585	0.85
55_Q	264_F	0.584	0.85
110_F	254_P	0.583	0.85
69_T	73_D	0.583	0.85
33_S	279_Q	0.582	0.85
209_I	213_E	0.582	0.85
276_R	288_E	0.579	0.84
266_L	287_L	0.578	0.84
184_K	191_S	0.577	0.84
180_L	183_I	0.576	0.84
12_M	63_W	0.574	0.84
218_L	221_N	0.574	0.84
175_V	210_R	0.572	0.84
176_M	213_E	0.571	0.84
142_L	180_L	0.570	0.83
24_V	30_I	0.569	0.83
12_M	93_F	0.566	0.83
41_N	283_I	0.566	0.83
48_I	103_L	0.562	0.83
150_S	166_K	0.561	0.83
19_F	24_V	0.561	0.83
104_G	266_L	0.561	0.83
166_K	177_P	0.560	0.82
152_A	161_Y	0.558	0.82
145_L	166_K	0.557	0.82
181_I	249_I	0.556	0.82
174_G	206_Y	0.555	0.82
181_I	185_A	0.554	0.82
225_L	230_Q	0.554	0.82
227_K	234_Q	0.553	0.82
72_N	191_S	0.552	0.81
104_G	270_Q	0.551	0.81
8_L	60_V	0.551	0.81
245_K	248_E	0.551	0.81
169_F	173_T	0.545	0.81
19_F	36_P	0.544	0.81
209_I	214_T	0.543	0.80
95_L	277_R	0.542	0.80
218_L	222_L	0.541	0.80
60_V	108_I	0.539	0.80
70_Y	113_Y	0.538	0.80
110_F	113_Y	0.536	0.80
14_L	141_L	0.535	0.79
8_L	134_V	0.535	0.79
108_I	262_A	0.534	0.79
183_I	200_I	0.534	0.79
198_K	232_K	0.532	0.79
145_L	168_T	0.529	0.79
280_I	283_I	0.529	0.79
186_L	218_L	0.529	0.79
187_M	209_I	0.529	0.79
110_F	253_V	0.525	0.78
274_M	277_R	0.525	0.78
14_L	161_Y	0.524	0.78
46_H	49_T	0.522	0.78
85_P	89_L	0.521	0.78
189_D	192_D	0.521	0.78
44_L	275_L	0.517	0.77
186_L	197_V	0.517	0.77
214_T	220_E	0.515	0.77
285_R	288_E	0.515	0.77
207_K	227_K	0.513	0.77
63_W	97_K	0.512	0.76
272_A	281_K	0.511	0.76
141_L	180_L	0.511	0.76
235_Q	239_D	0.510	0.76
14_L	135_V	0.510	0.76
9_V	135_V	0.508	0.76
226_P	231_G	0.506	0.76
84_A	90_I	0.505	0.75
206_Y	209_I	0.503	0.75
212_Y	217_R	0.501	0.75
40_V	99_A	0.500	0.75

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
1bgxT	1	0.9628	100	0.197	Contact Map
1exnA	1	0.8682	100	0.275	Contact Map
3zdbA	1	0.8209	100	0.283	Contact Map
3h7iA	1	0.8986	100	0.284	Contact Map
2izoA	1	0.7601	100	0.411	Contact Map
4q0wA	1	0.9155	100	0.42	Contact Map
1rxwA	1	0.8615	100	0.421	Contact Map
3oryA	3	0.9155	100	0.424	Contact Map
3q8kA	1	0.9392	100	0.435	Contact Map
4wa8A	1	0.8547	100	0.441	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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