ADA - ECOLI - GREMLIN Contacts

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ADA - Bifunctional transcriptional activator/DNA repair enzyme Ada

UniProt:	P06134	Sequences: MKKATCLTDDQRWQSVLARDPNADGEFVFAVRTTGIFCRPSCRARHALRENVSFYANASEALAAGFRPCKRCQPEKANAQQHRLDKITHACRLLEQETPVTLEALADQVAMSPFHLHRLFKATTGMTPKAWQQAWRARRLRESLAKGESVTTSILNAGFPDSSSYYRKADETLGMTAKQFRHGGENLAVRYALADCELGRCLVAESERGICAILLGDDDATLISELQQMFPAADNAPADLMFQQHVREVIASLNQRDTPLTLPLDIRGTAFQQQVWQALRTIPCGETVSYQQLANAIGKPKAVRAVASACAANKLAIIIPCHRVVRGDGTLSGYRWGVSRKAQLLRREAENEER	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10029
Length:	354 (288)
Sequences:	1102 (764)
Seq/√Len:	45.0

ECOLI - ADA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
69_C	72_C	5.122	1.00
326_R	332_S	4.667	1.00
90_A	116_L	4.576	1.00
288_V	293_L	4.453	1.00
193_L	223_I	4.399	1.00
117_H	127_T	4.343	1.00
189_V	211_C	4.227	1.00
307_A	311_A	3.941	1.00
195_D	200_R	3.921	1.00
291_Q	327_G	3.724	1.00
73_Q	76_K	3.711	1.00
183_G	231_P	3.503	1.00
69_C	74_P	3.488	1.00
149_S	152_T	3.474	1.00
188_A	234_D	3.359	1.00
274_Q	299_K	3.336	1.00
129_K	133_Q	2.968	1.00
308_S	311_A	2.879	1.00
189_V	206_S	2.821	1.00
205_E	242_F	2.655	1.00
62_L	75_E	2.580	1.00
121_K	127_T	2.517	1.00
95_E	135_W	2.508	1.00
203_V	210_I	2.438	1.00
101_T	104_A	2.412	1.00
343_Q	347_R	2.397	1.00
140_L	165_Y	2.396	1.00
343_Q	346_R	2.344	1.00
205_E	245_H	2.313	1.00
154_I	161_D	2.288	1.00
100_V	132_Q	2.228	1.00
93_L	108_Q	2.202	1.00
287_T	345_L	2.197	1.00
153_S	157_A	2.170	1.00
282_I	288_V	2.154	1.00
331_L	338_V	2.126	1.00
292_Q	295_N	2.099	1.00
220_A	224_S	1.990	0.99
308_S	312_A	1.989	0.99
277_Q	281_T	1.931	0.99
112_S	115_H	1.879	0.99
342_A	346_R	1.814	0.99
333_G	338_V	1.784	0.98
297_I	303_V	1.729	0.98
288_V	296_A	1.661	0.97
278_A	281_T	1.650	0.97
164_S	167_R	1.642	0.97
179_Q	187_L	1.623	0.97
250_I	253_L	1.617	0.97
159_F	168_K	1.603	0.97
277_Q	280_R	1.597	0.97
308_S	332_S	1.592	0.97
214_L	225_E	1.591	0.97
152_T	155_L	1.591	0.97
98_T	101_T	1.581	0.97
197_E	253_L	1.560	0.96
317_I	344_L	1.517	0.96
200_R	219_D	1.516	0.96
175_M	180_F	1.506	0.95
118_R	278_A	1.485	0.95
188_A	236_A	1.465	0.95
317_I	347_R	1.418	0.94
281_T	296_A	1.415	0.94
124_T	127_T	1.403	0.93
93_L	109_V	1.394	0.93
106_A	116_L	1.362	0.92
289_S	307_A	1.344	0.92
245_H	248_E	1.342	0.92
103_E	113_P	1.333	0.91
153_S	156_N	1.325	0.91
224_S	228_Q	1.304	0.90
93_L	105_L	1.301	0.90
288_V	292_Q	1.299	0.90
90_A	109_V	1.297	0.90
225_E	229_M	1.290	0.90
95_E	121_K	1.285	0.90
213_I	318_I	1.282	0.90
310_C	335_R	1.255	0.89
101_T	105_L	1.243	0.88
288_V	308_S	1.233	0.88
66_F	72_C	1.226	0.87
253_L	256_R	1.223	0.87
251_A	257_D	1.223	0.87
189_V	204_A	1.220	0.87
152_T	156_N	1.215	0.87
86_K	111_M	1.191	0.86
194_A	242_F	1.183	0.86
170_D	208_R	1.157	0.84
174_G	183_G	1.152	0.84
266_I	319_I	1.151	0.84
69_C	73_Q	1.149	0.84
87_I	111_M	1.147	0.84
66_F	69_C	1.143	0.84
124_T	130_A	1.143	0.84
70_K	73_Q	1.130	0.83
160_P	164_S	1.130	0.83
194_A	201_C	1.127	0.83
96_Q	108_Q	1.123	0.82
98_T	104_A	1.118	0.82
203_V	213_I	1.099	0.81
102_L	127_T	1.095	0.81
227_Q	237_P	1.093	0.81
316_A	335_R	1.092	0.81
315_L	319_I	1.089	0.80
151_T	174_G	1.077	0.80
293_L	297_I	1.064	0.79
293_L	308_S	1.053	0.78
266_I	273_Q	1.053	0.78
203_V	325_V	1.046	0.78
149_S	210_I	1.043	0.77
248_E	262_L	1.041	0.77
229_M	314_K	1.040	0.77
98_T	103_E	1.035	0.77
176_T	179_Q	1.028	0.76
117_H	121_K	1.026	0.76
218_D	221_T	1.023	0.76
117_H	124_T	1.009	0.75
165_Y	177_A	1.004	0.75
293_L	301_K	1.002	0.75
210_I	318_I	1.001	0.74
147_G	286_E	0.996	0.74
101_T	210_I	0.992	0.74
223_I	227_Q	0.987	0.73
126_M	206_S	0.984	0.73
173_L	316_A	0.983	0.73
303_V	307_A	0.979	0.73
103_E	121_K	0.977	0.73
217_D	340_R	0.969	0.72
89_H	108_Q	0.960	0.71
268_G	272_Q	0.958	0.71
206_S	209_G	0.953	0.71
146_K	196_C	0.951	0.71
135_W	138_R	0.943	0.70
126_M	270_A	0.939	0.70
87_I	168_K	0.936	0.69
68_P	291_Q	0.932	0.69
74_P	77_A	0.928	0.69
174_G	270_A	0.922	0.68
274_Q	297_I	0.918	0.68
191_Y	237_P	0.916	0.68
73_Q	77_A	0.914	0.68
143_S	156_N	0.914	0.68
237_P	243_Q	0.913	0.67
70_K	179_Q	0.912	0.67
227_Q	235_N	0.908	0.67
226_L	231_P	0.907	0.67
116_L	119_L	0.904	0.67
117_H	130_A	0.903	0.67
148_E	152_T	0.900	0.66
292_Q	303_V	0.897	0.66
259_P	274_Q	0.894	0.66
175_M	203_V	0.890	0.65
293_L	324_V	0.883	0.65
175_M	183_G	0.877	0.64
299_K	302_A	0.875	0.64
248_E	252_S	0.865	0.63
145_A	213_I	0.864	0.63
67_R	72_C	0.863	0.63
311_A	333_G	0.862	0.63
74_P	205_E	0.854	0.62
147_G	196_C	0.847	0.62
187_L	207_E	0.839	0.61
249_V	252_S	0.837	0.61
191_Y	195_D	0.835	0.60
104_A	308_S	0.834	0.60
252_S	260_L	0.833	0.60
66_F	74_P	0.828	0.60
214_L	314_K	0.827	0.60
206_S	211_C	0.827	0.60
192_A	265_D	0.826	0.60
227_Q	238_A	0.817	0.59
88_T	92_R	0.813	0.58
239_D	315_L	0.812	0.58
183_G	232_A	0.811	0.58
193_L	200_R	0.810	0.58
189_V	213_I	0.809	0.58
61_A	65_G	0.808	0.58
137_A	141_R	0.805	0.58
238_A	243_Q	0.803	0.57
92_R	95_E	0.802	0.57
117_H	332_S	0.800	0.57
242_F	318_I	0.789	0.56
191_Y	200_R	0.789	0.56
151_T	154_I	0.781	0.55
95_E	131_W	0.780	0.55
140_L	154_I	0.776	0.55
69_C	159_F	0.775	0.55
79_A	83_R	0.775	0.55
61_A	67_R	0.775	0.55
190_R	236_A	0.768	0.54
197_E	254_N	0.766	0.54
282_I	293_L	0.764	0.54
251_A	256_R	0.762	0.53
240_L	243_Q	0.762	0.53
297_I	306_V	0.752	0.53
174_G	192_A	0.751	0.52
98_T	220_A	0.751	0.52
75_E	78_N	0.748	0.52
196_C	335_R	0.745	0.52
291_Q	303_V	0.745	0.52
326_R	330_T	0.745	0.52
89_H	186_N	0.744	0.52
197_E	347_R	0.743	0.52
216_G	222_L	0.743	0.52
346_R	349_A	0.739	0.51
102_L	112_S	0.739	0.51
89_H	109_V	0.737	0.51
255_Q	258_T	0.735	0.51
293_L	303_V	0.735	0.51
181_R	296_A	0.733	0.51
154_I	165_Y	0.733	0.51
289_S	308_S	0.733	0.51
310_C	336_W	0.732	0.51
241_M	245_H	0.730	0.50
314_K	343_Q	0.728	0.50
94_L	131_W	0.727	0.50
225_E	314_K	0.726	0.50
172_T	210_I	0.725	0.50
105_L	108_Q	0.724	0.50
178_K	185_E	0.723	0.50
259_P	319_I	0.721	0.50
221_T	234_D	0.717	0.49
138_R	156_N	0.716	0.49
270_A	296_A	0.715	0.49
175_M	222_L	0.714	0.49
96_Q	311_A	0.713	0.49
288_V	324_V	0.711	0.49
62_L	76_K	0.711	0.49
68_P	168_K	0.711	0.49
155_L	162_S	0.709	0.48
245_H	345_L	0.706	0.48
212_A	335_R	0.706	0.48
156_N	281_T	0.702	0.48
216_G	307_A	0.701	0.48
204_A	267_R	0.700	0.47
299_K	303_V	0.699	0.47
133_Q	182_H	0.698	0.47
174_G	230_F	0.697	0.47
69_C	311_A	0.697	0.47
308_S	333_G	0.696	0.47
131_W	272_Q	0.694	0.47
259_P	315_L	0.692	0.47
163_S	311_A	0.692	0.47
287_T	325_V	0.692	0.47
138_R	142_E	0.689	0.46
222_L	335_R	0.688	0.46
175_M	233_A	0.681	0.46
110_A	113_P	0.681	0.46
67_R	71_R	0.680	0.46
332_S	338_V	0.678	0.45
186_N	295_N	0.676	0.45
163_S	178_K	0.675	0.45
65_G	69_C	0.674	0.45
61_A	69_C	0.669	0.44
201_C	213_I	0.666	0.44
195_D	227_Q	0.664	0.44
63_A	143_S	0.658	0.43
262_L	265_D	0.658	0.43
190_R	207_E	0.657	0.43
264_L	319_I	0.657	0.43
181_R	342_A	0.653	0.43
182_H	185_E	0.653	0.43
291_Q	325_V	0.652	0.43
211_C	242_F	0.652	0.43
180_F	245_H	0.648	0.42
243_Q	246_V	0.647	0.42
185_E	232_A	0.643	0.42
118_R	121_K	0.642	0.42
224_S	237_P	0.640	0.42
140_L	169_A	0.640	0.42
103_E	236_A	0.640	0.42
97_E	100_V	0.639	0.42
255_Q	284_C	0.638	0.42
87_I	302_A	0.638	0.42
282_I	324_V	0.635	0.41
77_A	133_Q	0.635	0.41
144_L	153_S	0.633	0.41
64_A	69_C	0.628	0.41
137_A	224_S	0.628	0.41
201_C	215_L	0.627	0.40
243_Q	247_R	0.627	0.40
192_A	246_V	0.627	0.40
127_T	317_I	0.626	0.40
307_A	345_L	0.623	0.40
161_D	177_A	0.622	0.40
331_L	342_A	0.619	0.40
107_D	157_A	0.616	0.39
195_D	219_D	0.616	0.39
275_V	293_L	0.615	0.39
159_F	165_Y	0.611	0.39
70_K	141_R	0.611	0.39
87_I	116_L	0.610	0.39
207_E	225_E	0.608	0.39
85_D	232_A	0.607	0.39
140_L	177_A	0.606	0.39
154_I	162_S	0.604	0.38
204_A	265_D	0.604	0.38
84_L	123_T	0.604	0.38
159_F	253_L	0.602	0.38
201_C	319_I	0.600	0.38
311_A	332_S	0.600	0.38
74_P	229_M	0.600	0.38
156_N	257_D	0.599	0.38
209_G	265_D	0.598	0.38
325_V	328_D	0.596	0.38
209_G	230_F	0.595	0.38
302_A	327_G	0.595	0.38
273_Q	280_R	0.594	0.37
273_Q	308_S	0.593	0.37
237_P	324_V	0.592	0.37
123_T	126_M	0.591	0.37
91_C	124_T	0.588	0.37
194_A	319_I	0.586	0.37
301_K	350_E	0.585	0.37
85_D	147_G	0.583	0.36
87_I	119_L	0.583	0.36
102_L	117_H	0.583	0.36
73_Q	177_A	0.582	0.36
255_Q	259_P	0.582	0.36
140_L	163_S	0.582	0.36
219_D	223_I	0.580	0.36
303_V	314_K	0.578	0.36
191_Y	227_Q	0.577	0.36
101_T	301_K	0.577	0.36
291_Q	307_A	0.576	0.36
213_I	324_V	0.575	0.36
178_K	207_E	0.575	0.36
175_M	202_L	0.574	0.36
198_L	317_I	0.573	0.36
126_M	249_V	0.573	0.36
87_I	123_T	0.573	0.36
109_V	119_L	0.573	0.36
203_V	246_V	0.570	0.35
72_C	159_F	0.569	0.35
152_T	170_D	0.569	0.35
70_K	76_K	0.569	0.35
295_N	315_L	0.568	0.35
188_A	219_D	0.567	0.35
179_Q	186_N	0.565	0.35
303_V	327_G	0.565	0.35
179_Q	297_I	0.564	0.35
107_D	350_E	0.563	0.35
143_S	153_S	0.563	0.35
72_C	311_A	0.562	0.35
83_R	123_T	0.562	0.35
217_D	234_D	0.560	0.34
115_H	124_T	0.560	0.34
69_C	76_K	0.558	0.34
211_C	264_L	0.558	0.34
240_L	295_N	0.557	0.34
252_S	259_P	0.554	0.34
68_P	192_A	0.554	0.34
293_L	296_A	0.553	0.34
88_T	315_L	0.552	0.34
272_Q	278_A	0.551	0.34
175_M	209_G	0.550	0.34
191_Y	239_D	0.550	0.34
196_C	234_D	0.550	0.34
83_R	119_L	0.550	0.34
66_F	168_K	0.549	0.33
100_V	105_L	0.547	0.33
113_P	311_A	0.546	0.33
253_L	260_L	0.545	0.33
132_Q	136_R	0.544	0.33
66_F	144_L	0.544	0.33
144_L	227_Q	0.543	0.33
211_C	272_Q	0.541	0.33
213_I	310_C	0.540	0.33
61_A	131_W	0.539	0.33
145_A	232_A	0.538	0.32
97_E	139_R	0.536	0.32
278_A	283_P	0.536	0.32
237_P	251_A	0.533	0.32
163_S	308_S	0.532	0.32
207_E	298_G	0.532	0.32
92_R	98_T	0.532	0.32
297_I	301_K	0.532	0.32
204_A	223_I	0.531	0.32
240_L	261_T	0.530	0.32
256_R	270_A	0.530	0.32
196_C	201_C	0.530	0.32
164_S	177_A	0.529	0.32
269_T	272_Q	0.527	0.32
64_A	71_R	0.526	0.31
107_D	114_F	0.526	0.31
210_I	315_L	0.526	0.31
165_Y	237_P	0.525	0.31
310_C	333_G	0.524	0.31
222_L	310_C	0.523	0.31
135_W	178_K	0.522	0.31
173_L	269_T	0.521	0.31
142_E	190_R	0.520	0.31
90_A	210_I	0.519	0.31
248_E	261_T	0.518	0.31
327_G	330_T	0.518	0.31
207_E	277_Q	0.517	0.31
72_C	205_E	0.517	0.31
130_A	174_G	0.517	0.31
61_A	64_A	0.516	0.31
136_R	159_F	0.515	0.31
91_C	94_L	0.513	0.30
130_A	134_A	0.513	0.30
178_K	268_G	0.513	0.30
198_L	347_R	0.512	0.30
272_Q	319_I	0.512	0.30
196_C	214_L	0.512	0.30
73_Q	138_R	0.512	0.30
194_A	250_I	0.510	0.30
148_E	339_S	0.510	0.30
112_S	117_H	0.510	0.30
224_S	227_Q	0.508	0.30
256_R	259_P	0.508	0.30
211_C	235_N	0.507	0.30
246_V	253_L	0.506	0.30
163_S	211_C	0.506	0.30
237_P	244_Q	0.506	0.30
79_A	319_I	0.505	0.30
86_K	93_L	0.504	0.30
80_Q	315_L	0.504	0.30
173_L	318_I	0.504	0.30
175_M	272_Q	0.504	0.30
188_A	207_E	0.504	0.30
94_L	105_L	0.504	0.30
202_L	298_G	0.503	0.30
64_A	80_Q	0.503	0.30
92_R	269_T	0.503	0.30
159_F	230_F	0.502	0.29
183_G	328_D	0.501	0.29
85_D	88_T	0.501	0.29
146_K	299_K	0.501	0.29
189_V	205_E	0.500	0.29
219_D	237_P	0.500	0.29

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
1sfeA	1	0.4661	100	0.619	Contact Map
3l00A	1	0.4209	100	0.675	Contact Map
4bhbA	1	0.4492	100	0.678	Contact Map
1eh6A	1	0.4463	100	0.679	Contact Map
1wrjA	1	0.4209	100	0.688	Contact Map
1u8bA	1	0.3729	100	0.712	Contact Map
1mgtA	1	0.435	100	0.725	Contact Map
2g7hA	1	0.4181	100	0.737	Contact Map
2kifA	1	0.2458	100	0.777	Contact Map
3gvaA	1	0.2486	100	0.779	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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