ADIY - ECOLI - GREMLIN Contacts

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ADIY - HTH-type transcriptional regulator AdiY

UniProt:	P33234	Sequences: MRICSDQPCIVLLTEKDVWIRVNGKEPISLKANHMALLNCENNIIDVSSLNNTLVAHISHDIIKDYLRFLNKDLSQIPVWQRSATPILTLPCLTPDVFRVAAQHSMMPAETESEKERTRALLFTVLSRFLDSKKFVSLMMYMLRNCVSDSVYQIIESDIHKDWNLSMVASCLCLSPSLLKKKLKSENTSYSQIITTCRMRYAVNELMMDGKNISQVSQSCGYNSTSYFISVFKDFYGMTPLHYVSQHRERTVA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11966
Length:	253 (228)
Sequences:	36775 (31661)
Seq/√Len:	2096.8

ECOLI - ADIY ENVY GADX YQHC RHAR YPDC YDIP YBCM GADW APPY CHBR FEAR RHAS ARAC MELR YIDL YDEO YIJO RCLR YEAM EUTR MARA XYLR SOXS YKGA ROB
BACSU - YDEC YISR YFIF YBFI YOBQ BTR YTDP ADAA YESS YDEE YESN

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
203_V	236_Y	3.266	1.00
188_T	196_T	3.196	1.00
156_E	197_C	3.044	1.00
199_M	236_Y	2.922	1.00
211_K	219_S	2.908	1.00
154_I	158_D	2.806	1.00
166_S	176_P	2.721	1.00
201_Y	204_N	2.689	1.00
196_T	235_F	2.548	1.00
232_F	243_Y	2.524	1.00
158_D	161_K	2.331	1.00
151_V	179_L	2.294	1.00
202_A	228_F	2.247	1.00
205_E	219_S	2.243	1.00
183_L	193_I	2.166	1.00
205_E	220_C	2.043	1.00
159_I	197_C	2.001	1.00
211_K	215_Q	1.959	1.00
164_N	167_M	1.932	1.00
154_I	171_C	1.905	1.00
238_M	246_Q	1.881	1.00
19_W	27_P	1.828	1.00
199_M	235_F	1.824	1.00
155_I	194_I	1.819	1.00
9_C	44_I	1.803	1.00
191_S	195_T	1.788	1.00
151_V	172_L	1.781	1.00
205_E	211_K	1.730	1.00
225_T	229_I	1.719	1.00
212_N	215_Q	1.711	1.00
121_L	124_T	1.671	1.00
168_V	190_Y	1.671	1.00
178_L	182_K	1.659	1.00
203_V	243_Y	1.643	1.00
19_W	29_S	1.643	1.00
165_L	180_K	1.626	1.00
231_V	234_D	1.625	1.00
21_R	27_P	1.614	1.00
31_K	34_H	1.607	1.00
204_N	208_M	1.587	1.00
153_Q	157_S	1.583	1.00
201_Y	205_E	1.573	1.00
17_D	29_S	1.543	1.00
176_P	180_K	1.542	1.00
188_T	192_Q	1.529	1.00
214_S	225_T	1.525	1.00
197_C	201_Y	1.520	1.00
124_T	128_R	1.515	1.00
179_L	190_Y	1.508	1.00
190_Y	194_I	1.501	1.00
156_E	193_I	1.501	1.00
15_E	52_N	1.492	1.00
154_I	163_W	1.488	1.00
227_Y	231_V	1.476	1.00
206_L	213_I	1.452	1.00
159_I	201_Y	1.445	1.00
145_N	186_E	1.444	1.00
152_Y	156_E	1.427	1.00
14_T	54_L	1.423	1.00
238_M	242_H	1.413	1.00
214_S	218_Q	1.412	1.00
215_Q	219_S	1.408	1.00
151_V	168_V	1.405	1.00
120_A	127_S	1.397	1.00
178_L	181_K	1.376	1.00
120_A	124_T	1.370	1.00
17_D	31_K	1.369	1.00
155_I	197_C	1.369	1.00
202_A	220_C	1.366	1.00
241_L	245_S	1.363	1.00
215_Q	218_Q	1.359	1.00
189_S	192_Q	1.356	1.00
98_F	104_H	1.341	1.00
196_T	200_R	1.339	1.00
201_Y	220_C	1.335	1.00
180_K	190_Y	1.335	1.00
177_S	181_K	1.332	1.00
222_Y	231_V	1.329	1.00
174_L	178_L	1.328	1.00
216_V	220_C	1.322	1.00
166_S	170_S	1.250	1.00
226_S	229_I	1.248	1.00
167_M	171_C	1.247	1.00
174_L	179_L	1.231	1.00
197_C	200_R	1.231	1.00
209_D	244_V	1.225	1.00
39_N	42_N	1.223	1.00
195_T	231_V	1.223	1.00
160_H	219_S	1.219	1.00
230_S	234_D	1.200	1.00
229_I	239_T	1.192	1.00
175_S	178_L	1.182	1.00
147_V	174_L	1.166	1.00
203_V	207_M	1.151	1.00
229_I	241_L	1.147	1.00
24_G	42_N	1.141	1.00
99_R	103_Q	1.119	1.00
127_S	131_D	1.115	1.00
165_L	190_Y	1.113	1.00
117_R	121_L	1.104	1.00
224_S	230_S	1.102	1.00
154_I	172_L	1.102	1.00
15_E	32_A	1.092	1.00
200_R	203_V	1.069	1.00
195_T	234_D	1.066	1.00
211_K	216_V	1.061	1.00
169_A	176_P	1.057	1.00
182_K	186_E	1.056	1.00
123_F	127_S	1.042	1.00
19_W	46_D	1.028	1.00
182_K	185_S	1.019	1.00
116_E	119_R	1.018	1.00
34_H	89_T	1.017	1.00
96_D	99_R	1.017	1.00
147_V	172_L	1.007	1.00
146_C	150_S	1.000	1.00
177_S	180_K	0.987	1.00
98_F	102_A	0.985	1.00
242_H	245_S	0.985	1.00
14_T	52_N	0.982	1.00
192_Q	195_T	0.981	1.00
161_K	167_M	0.980	1.00
163_W	168_V	0.978	1.00
162_D	167_M	0.972	1.00
239_T	242_H	0.969	1.00
241_L	244_V	0.969	1.00
149_D	153_Q	0.969	1.00
152_Y	193_I	0.968	1.00
168_V	171_C	0.965	1.00
213_I	216_V	0.965	1.00
229_I	233_K	0.954	1.00
117_R	124_T	0.953	1.00
154_I	168_V	0.945	1.00
96_D	100_V	0.942	1.00
205_E	216_V	0.938	1.00
167_M	170_S	0.936	1.00
105_S	108_P	0.935	1.00
116_E	120_A	0.932	1.00
165_L	176_P	0.928	1.00
147_V	182_K	0.927	1.00
120_A	123_F	0.926	1.00
13_L	18_V	0.925	1.00
150_S	171_C	0.922	1.00
100_V	103_Q	0.919	1.00
100_V	104_H	0.914	1.00
115_K	119_R	0.913	1.00
231_V	235_F	0.912	1.00
162_D	223_N	0.908	1.00
203_V	232_F	0.903	1.00
160_H	201_Y	0.897	1.00
174_L	182_K	0.896	1.00
150_S	153_Q	0.894	1.00
236_Y	243_Y	0.888	1.00
119_R	123_F	0.884	1.00
227_Y	230_S	0.882	1.00
192_Q	196_T	0.880	1.00
233_K	239_T	0.877	1.00
195_T	235_F	0.876	1.00
110_E	114_E	0.875	1.00
155_I	190_Y	0.873	1.00
148_S	182_K	0.868	1.00
124_T	127_S	0.864	1.00
22_V	26_E	0.861	1.00
199_M	231_V	0.857	1.00
183_L	190_Y	0.854	1.00
18_V	30_L	0.851	1.00
148_S	186_E	0.849	1.00
148_S	151_V	0.845	1.00
172_L	179_L	0.844	1.00
95_P	99_R	0.841	1.00
191_S	227_Y	0.840	1.00
149_D	152_Y	0.840	1.00
148_S	152_Y	0.837	1.00
150_S	172_L	0.833	1.00
242_H	246_Q	0.832	1.00
209_D	216_V	0.831	1.00
198_R	220_C	0.831	1.00
111_T	114_E	0.829	1.00
159_I	194_I	0.822	1.00
159_I	163_W	0.822	1.00
158_D	171_C	0.821	1.00
103_Q	107_M	0.819	1.00
21_R	25_K	0.808	1.00
191_S	194_I	0.807	1.00
102_A	108_P	0.799	1.00
193_I	197_C	0.798	1.00
192_Q	235_F	0.785	1.00
152_Y	183_L	0.784	1.00
206_L	244_V	0.782	1.00
9_C	57_H	0.779	1.00
199_M	228_F	0.777	1.00
206_L	216_V	0.776	1.00
60_H	63_I	0.774	1.00
180_K	189_S	0.767	1.00
181_K	185_S	0.765	1.00
159_I	220_C	0.762	1.00
202_A	205_E	0.759	1.00
18_V	29_S	0.758	1.00
238_M	243_Y	0.758	1.00
218_Q	223_N	0.755	1.00
20_I	36_A	0.754	1.00
117_R	120_A	0.750	1.00
224_S	227_Y	0.750	1.00
147_V	150_S	0.748	1.00
60_H	64_K	0.746	1.00
159_I	198_R	0.743	1.00
180_K	191_S	0.743	1.00
207_M	243_Y	0.742	1.00
180_K	184_K	0.740	1.00
99_R	102_A	0.739	1.00
144_R	185_S	0.731	1.00
38_L	44_I	0.731	1.00
145_N	182_K	0.726	1.00
102_A	106_M	0.726	1.00
96_D	103_Q	0.721	1.00
101_A	104_H	0.719	1.00
223_N	227_Y	0.717	1.00
155_I	193_I	0.717	1.00
158_D	167_M	0.715	1.00
151_V	190_Y	0.713	1.00
121_L	125_V	0.712	1.00
12_L	35_M	0.709	1.00
87_I	90_L	0.707	1.00
116_E	127_S	0.704	1.00
217_S	225_T	0.703	1.00
104_H	107_M	0.703	1.00
151_V	154_I	0.701	1.00
163_W	167_M	0.701	1.00
30_L	36_A	0.700	1.00
11_V	55_V	0.699	1.00
84_A	87_I	0.698	1.00
48_S	51_N	0.693	1.00
233_K	242_H	0.693	1.00
151_V	183_L	0.693	1.00
103_Q	106_M	0.692	1.00
228_F	232_F	0.680	1.00
195_T	227_Y	0.680	1.00
86_P	89_T	0.678	1.00
98_F	101_A	0.677	1.00
225_T	228_F	0.675	1.00
11_V	20_I	0.674	1.00
188_T	193_I	0.664	1.00
232_F	238_M	0.657	1.00
168_V	179_L	0.655	1.00
116_E	123_F	0.655	1.00
121_L	128_R	0.648	1.00
124_T	129_F	0.645	1.00
102_A	105_S	0.637	1.00
104_H	108_P	0.635	1.00
184_K	189_S	0.633	1.00
144_R	147_V	0.632	1.00
65_D	68_R	0.628	1.00
145_N	149_D	0.628	1.00
200_R	236_Y	0.625	1.00
226_S	239_T	0.624	1.00
228_F	240_P	0.624	1.00
212_N	216_V	0.623	1.00
226_S	230_S	0.623	1.00
95_P	98_F	0.623	1.00
128_R	131_D	0.614	1.00
199_M	222_Y	0.613	1.00
165_L	191_S	0.611	1.00
62_I	65_D	0.611	1.00
67_L	70_L	0.609	1.00
169_A	172_L	0.606	1.00
97_V	105_S	0.604	1.00
210_G	216_V	0.603	1.00
163_W	198_R	0.602	1.00
11_V	36_A	0.601	1.00
13_L	53_T	0.597	1.00
118_T	121_L	0.594	1.00
216_V	244_V	0.591	1.00
195_T	199_M	0.590	1.00
97_V	101_A	0.589	1.00
11_V	38_L	0.587	1.00
148_S	179_L	0.585	1.00
144_R	186_E	0.585	1.00
205_E	208_M	0.583	1.00
11_V	53_T	0.582	1.00
168_V	172_L	0.582	1.00
101_A	105_S	0.580	1.00
151_V	171_C	0.578	1.00
224_S	234_D	0.574	1.00
13_L	30_L	0.574	1.00
64_K	68_R	0.574	1.00
154_I	167_M	0.573	1.00
47_V	51_N	0.572	1.00
222_Y	227_Y	0.571	1.00
17_D	48_S	0.571	1.00
68_R	72_K	0.569	1.00
54_L	57_H	0.567	1.00
20_I	38_L	0.566	1.00
22_V	25_K	0.564	1.00
97_V	108_P	0.562	1.00
151_V	182_K	0.560	1.00
117_R	131_D	0.559	1.00
202_A	216_V	0.559	1.00
22_V	38_L	0.557	1.00
90_L	93_L	0.557	1.00
155_I	163_W	0.556	1.00
156_E	201_Y	0.555	1.00
165_L	177_S	0.555	1.00
123_F	129_F	0.555	1.00
144_R	178_L	0.555	1.00
110_E	113_S	0.554	1.00
146_C	186_E	0.554	1.00
151_V	155_I	0.554	1.00
232_F	236_Y	0.553	1.00
153_Q	156_E	0.549	1.00
19_W	48_S	0.549	1.00
204_N	207_M	0.548	1.00
52_N	55_V	0.547	1.00
200_R	235_F	0.545	1.00
206_L	243_Y	0.544	1.00
203_V	238_M	0.542	1.00
208_M	211_K	0.541	1.00
194_I	197_C	0.540	1.00
163_W	194_I	0.539	1.00
170_S	173_C	0.538	1.00
192_Q	234_D	0.538	1.00
231_V	236_Y	0.537	1.00
94_T	108_P	0.537	1.00
103_Q	121_L	0.535	1.00
125_V	129_F	0.534	1.00
10_I	35_M	0.534	1.00
118_T	129_F	0.532	1.00
168_V	198_R	0.531	1.00
20_I	44_I	0.531	1.00
35_M	38_L	0.524	1.00
53_T	57_H	0.519	1.00
21_R	24_G	0.519	1.00
13_L	34_H	0.517	1.00
117_R	127_S	0.516	1.00
100_V	108_P	0.512	1.00
149_D	186_E	0.508	1.00
154_I	159_I	0.506	1.00
10_I	37_L	0.506	1.00
195_T	222_Y	0.504	1.00
201_Y	219_S	0.503	1.00
9_C	38_L	0.501	1.00
21_R	46_D	0.500	1.00
124_T	131_D	0.500	1.00

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
3gbgA	1	0.9249	100	0.201	Contact Map
3mklA	1	0.4387	100	0.433	Contact Map
1bl0A	1	0.4348	100	0.438	Contact Map
3oouA	1	0.4111	100	0.438	Contact Map
3oioA	1	0.4387	100	0.442	Contact Map
3mn2A	1	0.415	100	0.445	Contact Map
2k9sA	1	0.415	99.9	0.453	Contact Map
3w6vA	1	0.4308	99.9	0.454	Contact Map
3lsgA	2	0.3992	99.9	0.461	Contact Map
1d5yA	1	0.4348	99.9	0.47	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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