GADX - ECOLI - GREMLIN Contacts

Home
GREMLIN
- Submit - Monomer
- Submit - Complex
Contacts
Metagenomics
- Contacts
- Structures
Structures
- List
Old Projects
- Complexes (2014)
- PFAM (2013)

GADX - HTH-type transcriptional regulator GadX

UniProt:	P37639	Sequences: MQSLHGNCLIAYARHKYILTMVNGEYRYFNGGDLVFADASQIRVDKCVENFVFVSRDTLSLFLPMLKEEALNLHAHKKVSSLLVHHCSRDIPVFQEVAQLSQNKNLRYAEMLRKRALIFALLSVFLEDEHFIPLLLNVLQPNMRTRVCTVINNNIAHEWTLARIASELLMSPSLLKKKLREEETSYSQLLTECRMQRALQLIVIHGFSIKRVAVSCGYHSVSYFIYVFRNYYGMTPTEYQERSAQRLSNRDSAASIVAQGNFYGTDRSAEGIRL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12243
Length:	274 (235)
Sequences:	32914 (28853)
Seq/√Len:	1882.1

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

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
199_L	232_Y	3.390	1.00
184_T	192_E	3.272	1.00
152_N	193_C	3.052	1.00
207_F	215_S	3.035	1.00
195_M	232_Y	2.888	1.00
150_V	154_N	2.802	1.00
162_A	172_P	2.777	1.00
197_R	200_Q	2.687	1.00
154_N	157_H	2.636	1.00
192_E	231_Y	2.555	1.00
228_F	239_Y	2.546	1.00
147_V	175_L	2.465	1.00
201_L	215_S	2.360	1.00
198_A	224_F	2.355	1.00
179_L	189_L	2.182	1.00
201_L	216_C	2.124	1.00
160_T	163_R	2.034	1.00
207_F	211_R	1.989	1.00
19_L	26_Y	1.982	1.00
155_I	193_C	1.960	1.00
187_S	191_T	1.930	1.00
234_M	242_R	1.904	1.00
150_V	167_E	1.869	1.00
19_L	28_Y	1.866	1.00
147_V	168_L	1.866	1.00
151_I	190_L	1.837	1.00
201_L	207_F	1.818	1.00
195_M	231_Y	1.774	1.00
21_M	26_Y	1.762	1.00
208_S	211_R	1.751	1.00
221_V	225_I	1.747	1.00
199_L	239_Y	1.729	1.00
227_V	230_N	1.701	1.00
161_L	176_K	1.695	1.00
174_L	178_K	1.682	1.00
164_I	186_Y	1.658	1.00
9_L	43_R	1.646	1.00
30_N	33_D	1.622	1.00
117_L	120_A	1.616	1.00
17_Y	28_Y	1.603	1.00
116_A	120_A	1.586	1.00
184_T	188_Q	1.580	1.00
116_A	123_S	1.575	1.00
197_R	201_L	1.574	1.00
193_C	197_R	1.568	1.00
152_N	189_L	1.546	1.00
149_T	153_N	1.534	1.00
210_K	221_V	1.532	1.00
175_L	186_Y	1.530	1.00
202_I	209_I	1.521	1.00
172_P	176_K	1.517	1.00
155_I	197_R	1.510	1.00
150_V	159_W	1.508	1.00
234_M	238_E	1.500	1.00
120_A	124_V	1.465	1.00
211_R	215_S	1.454	1.00
186_Y	190_L	1.447	1.00
148_C	152_N	1.438	1.00
223_Y	227_V	1.428	1.00
237_T	241_E	1.406	1.00
210_K	214_V	1.403	1.00
156_A	215_S	1.403	1.00
174_L	177_K	1.403	1.00
170_M	174_L	1.402	1.00
211_R	214_V	1.394	1.00
198_A	216_C	1.393	1.00
141_P	182_E	1.392	1.00
176_K	186_Y	1.389	1.00
151_I	193_C	1.386	1.00
173_S	177_K	1.383	1.00
197_R	216_C	1.382	1.00
119_F	123_S	1.377	1.00
200_Q	204_I	1.364	1.00
21_M	44_V	1.362	1.00
147_V	164_I	1.360	1.00
212_V	216_C	1.356	1.00
163_R	167_E	1.346	1.00
17_Y	30_N	1.328	1.00
185_S	188_Q	1.325	1.00
123_S	127_E	1.318	1.00
19_L	46_K	1.318	1.00
218_Y	227_V	1.313	1.00
15_H	48_V	1.298	1.00
192_E	196_Q	1.292	1.00
23_N	41_Q	1.285	1.00
222_S	225_I	1.279	1.00
8_C	39_A	1.272	1.00
193_C	196_Q	1.269	1.00
191_T	227_V	1.247	1.00
170_M	175_L	1.229	1.00
14_R	50_N	1.228	1.00
143_M	170_M	1.206	1.00
162_A	166_S	1.198	1.00
38_D	41_Q	1.170	1.00
171_S	174_L	1.161	1.00
115_R	119_F	1.155	1.00
226_Y	230_N	1.153	1.00
157_H	163_R	1.149	1.00
56_R	59_L	1.149	1.00
116_A	119_F	1.139	1.00
95_Q	99_Q	1.130	1.00
225_I	235_T	1.129	1.00
225_I	237_T	1.124	1.00
161_L	186_Y	1.121	1.00
15_H	31_G	1.120	1.00
94_F	100_L	1.100	1.00
178_K	182_E	1.095	1.00
113_R	120_A	1.095	1.00
207_F	212_V	1.094	1.00
205_H	240_Q	1.091	1.00
199_L	203_V	1.088	1.00
150_V	168_L	1.078	1.00
158_E	219_H	1.071	1.00
238_E	241_E	1.062	1.00
156_A	197_R	1.052	1.00
178_K	181_E	1.051	1.00
191_T	230_N	1.051	1.00
142_N	146_R	1.039	1.00
237_T	240_Q	1.029	1.00
143_M	168_L	1.015	1.00
196_Q	199_L	1.012	1.00
165_A	172_P	1.001	1.00
145_T	149_T	1.001	1.00
13_A	18_I	0.994	1.00
235_T	238_E	0.988	1.00
96_E	100_L	0.988	1.00
159_W	164_I	0.984	1.00
113_R	117_L	0.980	1.00
209_I	212_V	0.978	1.00
225_I	229_R	0.977	1.00
143_M	178_K	0.976	1.00
188_Q	191_T	0.969	1.00
220_S	226_Y	0.969	1.00
173_S	176_K	0.968	1.00
91_I	95_Q	0.959	1.00
148_C	189_L	0.957	1.00
164_I	167_E	0.952	1.00
151_I	186_Y	0.951	1.00
50_N	56_R	0.949	1.00
161_L	172_P	0.949	1.00
146_R	167_E	0.947	1.00
201_L	212_V	0.943	1.00
120_A	123_S	0.935	1.00
22_V	25_E	0.929	1.00
194_R	216_C	0.925	1.00
14_R	48_V	0.925	1.00
163_R	166_S	0.916	1.00
150_V	164_I	0.905	1.00
227_V	231_Y	0.904	1.00
179_L	186_Y	0.898	1.00
188_Q	192_E	0.895	1.00
8_C	36_F	0.892	1.00
21_M	24_G	0.885	1.00
232_Y	239_Y	0.881	1.00
168_L	175_L	0.877	1.00
199_L	228_F	0.873	1.00
155_I	190_L	0.871	1.00
146_R	149_T	0.869	1.00
187_S	223_Y	0.868	1.00
238_E	242_R	0.866	1.00
100_L	104_K	0.858	1.00
145_T	148_C	0.858	1.00
223_Y	226_Y	0.853	1.00
202_I	212_V	0.851	1.00
191_T	231_Y	0.851	1.00
155_I	159_W	0.847	1.00
144_R	182_E	0.841	1.00
195_M	227_V	0.839	1.00
146_R	168_L	0.838	1.00
96_E	99_Q	0.838	1.00
18_I	29_F	0.837	1.00
188_Q	231_Y	0.834	1.00
202_I	240_Q	0.833	1.00
144_R	178_K	0.833	1.00
144_R	147_V	0.826	1.00
195_M	224_F	0.820	1.00
101_S	104_K	0.816	1.00
158_E	163_R	0.816	1.00
154_N	167_E	0.811	1.00
170_M	178_K	0.810	1.00
148_C	179_L	0.808	1.00
92_P	96_E	0.805	1.00
189_L	193_C	0.801	1.00
205_H	212_V	0.798	1.00
92_P	95_Q	0.798	1.00
144_R	148_C	0.792	1.00
56_R	60_S	0.788	1.00
229_R	235_T	0.783	1.00
90_D	100_L	0.782	1.00
50_N	53_F	0.778	1.00
176_K	180_R	0.776	1.00
155_I	216_C	0.774	1.00
20_T	35_V	0.773	1.00
113_R	116_A	0.772	1.00
33_D	83_L	0.770	1.00
112_L	116_A	0.768	1.00
124_V	128_D	0.764	1.00
140_Q	181_E	0.761	1.00
187_S	190_L	0.758	1.00
177_K	181_E	0.758	1.00
176_K	187_S	0.747	1.00
154_N	163_R	0.746	1.00
214_V	219_H	0.743	1.00
12_Y	34_L	0.739	1.00
159_W	163_R	0.739	1.00
82_L	85_H	0.738	1.00
18_I	28_Y	0.736	1.00
234_M	239_Y	0.736	1.00
99_Q	103_N	0.730	1.00
155_I	194_R	0.727	1.00
229_R	238_E	0.723	1.00
213_A	221_V	0.723	1.00
203_V	239_Y	0.723	1.00
37_A	43_R	0.721	1.00
198_A	201_L	0.717	1.00
52_V	56_R	0.716	1.00
164_I	175_L	0.716	1.00
112_L	115_R	0.708	1.00
219_H	223_Y	0.706	1.00
11_A	37_A	0.705	1.00
29_F	35_V	0.704	1.00
151_I	189_L	0.704	1.00
143_M	146_R	0.704	1.00
111_M	115_R	0.704	1.00
93_V	101_S	0.693	1.00
100_L	103_N	0.692	1.00
147_V	150_V	0.688	1.00
104_K	108_Y	0.684	1.00
220_S	223_Y	0.681	1.00
147_V	186_Y	0.680	1.00
79_V	82_L	0.676	1.00
60_S	64_P	0.674	1.00
80_S	83_L	0.672	1.00
176_K	185_S	0.669	1.00
81_S	85_H	0.656	1.00
221_V	224_F	0.656	1.00
222_S	226_Y	0.655	1.00
98_A	104_K	0.654	1.00
184_T	189_L	0.650	1.00
141_P	178_K	0.648	1.00
180_R	185_S	0.648	1.00
110_E	114_K	0.647	1.00
191_T	223_Y	0.638	1.00
120_A	125_F	0.636	1.00
93_V	100_L	0.634	1.00
13_A	29_F	0.633	1.00
11_A	20_T	0.632	1.00
140_Q	143_M	0.632	1.00
206_G	212_V	0.629	1.00
93_V	96_E	0.627	1.00
147_V	179_L	0.627	1.00
61_L	64_P	0.627	1.00
79_V	84_V	0.626	1.00
222_S	235_T	0.625	1.00
112_L	123_S	0.624	1.00
195_M	218_Y	0.624	1.00
113_R	123_S	0.624	1.00
61_L	65_M	0.621	1.00
104_K	107_R	0.617	1.00
212_V	240_Q	0.615	1.00
74_H	77_K	0.615	1.00
116_A	124_V	0.615	1.00
93_V	98_A	0.612	1.00
9_L	53_F	0.612	1.00
198_A	212_V	0.612	1.00
83_L	86_H	0.611	1.00
228_F	234_M	0.610	1.00
11_A	35_V	0.610	1.00
94_F	97_V	0.609	1.00
110_E	127_E	0.608	1.00
161_L	187_S	0.608	1.00
224_F	236_P	0.607	1.00
95_Q	98_A	0.607	1.00
22_V	37_A	0.606	1.00
196_Q	232_Y	0.605	1.00
49_E	53_F	0.602	1.00
50_N	55_S	0.601	1.00
93_V	97_V	0.599	1.00
11_A	51_F	0.599	1.00
165_A	168_L	0.598	1.00
159_W	194_R	0.597	1.00
224_F	228_F	0.595	1.00
150_V	163_R	0.593	1.00
21_M	46_K	0.593	1.00
58_T	61_L	0.593	1.00
98_A	102_Q	0.591	1.00
113_R	127_E	0.590	1.00
141_P	145_T	0.590	1.00
59_L	66_L	0.589	1.00
112_L	119_F	0.585	1.00
124_V	127_E	0.580	1.00
164_I	168_L	0.580	1.00
94_F	98_A	0.577	1.00
147_V	151_I	0.575	1.00
140_Q	182_E	0.573	1.00
105_N	108_Y	0.572	1.00
114_K	118_I	0.572	1.00
191_T	195_M	0.571	1.00
92_P	99_Q	0.571	1.00
105_N	109_A	0.566	1.00
159_W	190_L	0.564	1.00
142_N	182_E	0.563	1.00
190_L	194_R	0.563	1.00
90_D	104_K	0.562	1.00
208_S	212_V	0.561	1.00
147_V	167_E	0.559	1.00
196_Q	231_Y	0.557	1.00
33_D	85_H	0.557	1.00
20_T	37_A	0.555	1.00
218_Y	223_Y	0.554	1.00
144_R	175_L	0.553	1.00
209_I	237_T	0.551	1.00
82_L	86_H	0.551	1.00
107_R	110_E	0.550	1.00
122_L	125_F	0.550	1.00
149_T	152_N	0.550	1.00
138_V	141_P	0.549	1.00
81_S	84_V	0.548	1.00
114_K	117_L	0.548	1.00
166_S	169_L	0.547	1.00
13_A	16_K	0.541	1.00
114_K	125_F	0.541	1.00
51_F	55_S	0.537	1.00
116_A	125_F	0.536	1.00
144_R	168_L	0.531	1.00
97_V	100_L	0.530	1.00
80_S	84_V	0.529	1.00
78_K	81_S	0.528	1.00
220_S	230_N	0.527	1.00
227_V	232_Y	0.526	1.00
191_T	218_Y	0.526	1.00
161_L	173_S	0.524	1.00
55_S	59_L	0.524	1.00
228_F	232_Y	0.521	1.00
147_V	178_K	0.521	1.00
202_I	239_Y	0.519	1.00
152_N	197_R	0.517	1.00
168_L	172_P	0.516	1.00
118_I	122_L	0.516	1.00
97_V	101_S	0.514	1.00
90_D	93_V	0.513	1.00
98_A	101_S	0.513	1.00
79_V	86_H	0.512	1.00
22_V	27_R	0.511	1.00
218_Y	224_F	0.511	1.00
200_Q	203_V	0.507	1.00
23_N	42_I	0.507	1.00
57_D	60_S	0.506	1.00
20_T	43_R	0.505	1.00
151_I	159_W	0.504	1.00
196_Q	200_Q	0.501	1.00
110_E	113_R	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	0.8431	100	0.27	Contact Map
3mklA	1	0.4051	100	0.491	Contact Map
3oioA	1	0.4051	100	0.501	Contact Map
3oouA	1	0.3796	100	0.502	Contact Map
1bl0A	1	0.4197	100	0.502	Contact Map
3mn2A	1	0.3832	100	0.508	Contact Map
3w6vA	1	0.4015	100	0.508	Contact Map
2k9sA	1	0.3832	99.9	0.513	Contact Map
3lsgA	2	0.3686	99.9	0.52	Contact Map
4fe7A	2	0.8066	99.9	0.533	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.

Page generated in 0.0093 seconds.