DGOR - ECOLI - GREMLIN Contacts

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DGOR - Galactonate operon transcriptional repressor

UniProt:	P31460	Sequences: MTLNKTDRIVITLGKQIVHGKYVPGSPLPAEAELCEEFATSRNIIREVFRSLMAKRLIEMKRYRGAFVAPRNQWNYLDTDVLQWVLENDYDPRLISAMSEVRNLVEPAIARWAAERATSSDLAQIESALNEMIANNQDREAFNEADIRYHEAVLQSVHNPVLQQLSIAISSLQRAVFERTWMGDEANMPQTLQEHKALFDAIRHQDGDAAEQAALTMIASSTRRLKEIT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11718
Length:	229 (199)
Sequences:	23400 (17284)
Seq/√Len:	1225.2

ECOLI - DGOR NANR YIEP LLDR PDHR EXUR CSIR GLCC YJJM FADR YDFH MCBR UXUR FRLR YIDP YEGW PHNF YIHL MNGR
BACSU - YDHC GNTR LUTR YCBG YVOA YMFC TRER YURK YYDK YBGA
SULSO - Q97YR4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
126_E	203_R	3.687	1.00
111_R	211_E	3.294	1.00
206_D	209_A	2.936	1.00
133_I	196_K	2.742	1.00
16_Q	21_K	2.713	1.00
23_V	26_S	2.641	1.00
16_Q	37_E	2.379	1.00
104_L	108_A	2.349	1.00
124_Q	152_A	2.226	1.00
97_A	160_P	2.147	1.00
103_N	219_A	2.091	1.00
10_V	51_S	2.056	1.00
59_E	69_A	2.026	1.00
100_E	112_W	1.963	1.00
115_E	207_G	1.947	1.00
14_G	55_K	1.945	1.00
9_I	40_T	1.943	1.00
155_Q	163_Q	1.835	1.00
121_D	158_H	1.814	1.00
122_L	203_R	1.810	1.00
9_I	38_F	1.806	1.00
201_A	209_A	1.776	1.00
152_A	155_Q	1.752	1.00
118_T	121_D	1.751	1.00
60_M	66_A	1.745	1.00
12_T	16_Q	1.721	1.00
107_P	215_L	1.704	1.00
111_R	207_G	1.655	1.00
129_L	199_F	1.646	1.00
138_D	141_A	1.640	1.00
101_V	165_L	1.610	1.00
194_E	220_S	1.592	1.00
30_A	42_R	1.591	1.00
107_P	211_E	1.571	1.00
211_E	215_L	1.563	1.00
15_K	19_H	1.562	1.00
209_A	213_A	1.552	1.00
108_A	111_R	1.546	1.00
150_H	195_H	1.520	1.00
197_A	213_A	1.484	1.00
131_E	145_A	1.434	1.00
121_D	156_S	1.431	1.00
154_L	166_S	1.421	1.00
161_V	172_L	1.417	1.00
110_A	210_A	1.416	1.00
164_Q	168_A	1.409	1.00
103_N	215_L	1.407	1.00
151_E	167_I	1.401	1.00
126_E	199_F	1.388	1.00
200_D	204_H	1.386	1.00
133_I	192_L	1.382	1.00
128_A	145_A	1.366	1.00
10_V	55_K	1.362	1.00
61_K	64_R	1.359	1.00
32_A	36_E	1.356	1.00
204_H	209_A	1.350	1.00
97_A	161_V	1.324	1.00
126_E	130_N	1.282	1.00
103_N	222_T	1.281	1.00
117_A	122_L	1.278	1.00
196_K	200_D	1.277	1.00
207_G	211_E	1.270	1.00
127_S	131_E	1.226	1.00
33_E	37_E	1.225	1.00
131_E	148_R	1.203	1.00
29_P	33_E	1.202	1.00
129_L	196_K	1.192	1.00
27_P	67_F	1.191	1.00
8_R	12_T	1.188	1.00
128_A	152_A	1.188	1.00
103_N	107_P	1.182	1.00
34_L	45_I	1.179	1.00
194_E	217_M	1.166	1.00
61_K	67_F	1.159	1.00
212_Q	216_T	1.154	1.00
148_R	152_A	1.147	1.00
151_E	155_Q	1.145	1.00
12_T	38_F	1.145	1.00
102_R	106_E	1.144	1.00
16_Q	38_F	1.143	1.00
117_A	205_Q	1.138	1.00
215_L	219_A	1.136	1.00
12_T	15_K	1.135	1.00
128_A	148_R	1.130	1.00
153_V	202_I	1.129	1.00
146_D	150_H	1.115	1.00
141_A	144_E	1.115	1.00
209_A	212_Q	1.114	1.00
53_M	60_M	1.112	1.00
110_A	214_A	1.107	1.00
107_P	111_R	1.107	1.00
111_R	208_D	1.100	1.00
129_L	132_M	1.097	1.00
110_A	114_A	1.096	1.00
117_A	121_D	1.095	1.00
117_A	156_S	1.081	1.00
129_L	133_I	1.080	1.00
152_A	156_S	1.079	1.00
97_A	159_N	1.078	1.00
199_F	203_R	1.060	1.00
22_Y	68_V	1.060	1.00
109_I	154_L	1.057	1.00
200_D	203_R	1.053	1.00
122_L	199_F	1.045	1.00
100_E	159_N	1.043	1.00
59_E	67_F	1.039	1.00
126_E	196_K	1.037	1.00
96_S	222_T	1.032	1.00
145_A	148_R	1.030	1.00
124_Q	155_Q	1.021	1.00
122_L	205_Q	1.018	1.00
47_E	50_R	1.005	1.00
165_L	168_A	1.003	1.00
124_Q	127_S	0.994	1.00
201_A	206_D	0.988	1.00
130_N	133_I	0.983	1.00
53_M	58_I	0.982	1.00
112_W	116_R	0.968	1.00
49_F	66_A	0.963	1.00
114_A	207_G	0.959	1.00
124_Q	128_A	0.954	1.00
16_Q	22_Y	0.949	1.00
17_I	68_V	0.945	1.00
108_A	211_E	0.944	1.00
150_H	217_M	0.938	1.00
149_Y	199_F	0.936	1.00
197_A	216_T	0.934	1.00
195_H	217_M	0.931	1.00
193_Q	197_A	0.929	1.00
197_A	209_A	0.921	1.00
144_E	148_R	0.914	1.00
51_S	54_A	0.905	1.00
61_K	65_G	0.904	1.00
163_Q	167_I	0.901	1.00
106_E	150_H	0.899	1.00
197_A	200_D	0.898	1.00
114_A	202_I	0.896	1.00
27_P	65_G	0.896	1.00
116_R	158_H	0.894	1.00
123_A	127_S	0.892	1.00
94_L	161_V	0.890	1.00
198_L	214_A	0.889	1.00
157_V	163_Q	0.887	1.00
208_D	212_Q	0.886	1.00
6_T	51_S	0.871	1.00
10_V	14_G	0.868	1.00
208_D	211_E	0.866	1.00
101_V	161_V	0.865	1.00
108_A	112_W	0.864	1.00
58_I	66_A	0.862	1.00
128_A	131_E	0.860	1.00
41_S	44_I	0.850	1.00
64_R	67_F	0.850	1.00
131_E	134_A	0.849	1.00
192_L	196_K	0.847	1.00
29_P	32_A	0.846	1.00
122_L	126_E	0.840	1.00
35_C	45_I	0.837	1.00
126_E	200_D	0.834	1.00
50_R	53_M	0.829	1.00
14_G	57_L	0.827	1.00
146_D	195_H	0.826	1.00
119_S	123_A	0.824	1.00
197_A	201_A	0.823	1.00
114_A	205_Q	0.819	1.00
117_A	202_I	0.818	1.00
113_A	156_S	0.817	1.00
114_A	210_A	0.815	1.00
121_D	124_Q	0.814	1.00
7_D	51_S	0.813	1.00
102_R	218_I	0.811	1.00
14_G	18_V	0.810	1.00
49_F	58_I	0.806	1.00
33_E	36_E	0.806	1.00
161_V	165_L	0.804	1.00
198_L	213_A	0.789	1.00
119_S	205_Q	0.784	1.00
113_A	117_A	0.776	1.00
130_N	196_K	0.774	1.00
161_V	164_Q	0.774	1.00
40_T	45_I	0.772	1.00
201_A	213_A	0.771	1.00
135_N	141_A	0.771	1.00
125_I	152_A	0.770	1.00
100_E	222_T	0.769	1.00
130_N	134_A	0.766	1.00
34_L	49_F	0.765	1.00
112_W	115_E	0.757	1.00
112_W	159_N	0.753	1.00
151_E	170_S	0.752	1.00
132_M	142_F	0.750	1.00
189_P	193_Q	0.741	1.00
213_A	216_T	0.739	1.00
111_R	115_E	0.738	1.00
101_V	162_L	0.728	1.00
198_L	210_A	0.727	1.00
5_K	44_I	0.723	1.00
123_A	203_R	0.723	1.00
50_R	60_M	0.722	1.00
99_S	221_S	0.720	1.00
100_E	116_R	0.711	1.00
212_Q	215_L	0.709	1.00
123_A	126_E	0.709	1.00
147_I	174_R	0.707	1.00
101_V	109_I	0.704	1.00
124_Q	148_R	0.700	1.00
141_A	145_A	0.699	1.00
219_A	223_R	0.696	1.00
5_K	8_R	0.691	1.00
125_I	199_F	0.690	1.00
131_E	141_A	0.687	1.00
6_T	10_V	0.686	1.00
129_L	192_L	0.684	1.00
51_S	55_K	0.677	1.00
21_K	37_E	0.676	1.00
100_E	108_A	0.672	1.00
74_W	158_H	0.672	1.00
151_E	163_Q	0.669	1.00
216_T	220_S	0.668	1.00
127_S	130_N	0.665	1.00
147_I	170_S	0.660	1.00
121_D	155_Q	0.658	1.00
194_E	197_A	0.656	1.00
94_L	160_P	0.655	1.00
22_Y	26_S	0.654	1.00
44_I	48_V	0.650	1.00
72_N	94_L	0.649	1.00
198_L	217_M	0.647	1.00
148_R	151_E	0.646	1.00
104_L	162_L	0.645	1.00
113_A	157_V	0.644	1.00
121_D	152_A	0.642	1.00
131_E	135_N	0.638	1.00
219_A	222_T	0.635	1.00
135_N	138_D	0.634	1.00
220_S	224_R	0.625	1.00
122_L	202_I	0.619	1.00
110_A	207_G	0.618	1.00
135_N	145_A	0.617	1.00
101_V	105_V	0.614	1.00
109_I	157_V	0.614	1.00
103_N	218_I	0.613	1.00
16_Q	20_G	0.608	1.00
24_P	70_P	0.606	1.00
6_T	47_E	0.603	1.00
74_W	97_A	0.592	1.00
106_E	195_H	0.592	1.00
109_I	162_L	0.591	1.00
25_G	70_P	0.590	1.00
107_P	207_G	0.587	1.00
107_P	214_A	0.585	1.00
63_Y	66_A	0.581	1.00
38_F	45_I	0.578	1.00
142_F	191_T	0.578	1.00
125_I	156_S	0.578	1.00
28_L	58_I	0.577	1.00
32_A	35_C	0.576	1.00
104_L	107_P	0.571	1.00
164_Q	172_L	0.571	1.00
120_S	124_Q	0.570	1.00
111_R	215_L	0.563	1.00
113_A	153_V	0.561	1.00
119_S	203_R	0.561	1.00
13_L	34_L	0.558	1.00
132_M	192_L	0.551	1.00
125_I	128_A	0.550	1.00
112_W	157_V	0.546	1.00
101_V	104_L	0.544	1.00
16_Q	19_H	0.543	1.00
50_R	54_A	0.543	1.00
96_S	100_E	0.540	1.00
136_N	139_R	0.539	1.00
110_A	153_V	0.538	1.00
198_L	201_A	0.536	1.00
175_A	179_R	0.536	1.00
36_E	39_A	0.536	1.00
160_P	163_Q	0.534	1.00
62_R	65_G	0.533	1.00
100_E	103_N	0.530	1.00
147_I	151_E	0.529	1.00
125_I	129_L	0.526	1.00
187_N	190_Q	0.525	1.00
22_Y	28_L	0.524	1.00
140_E	178_E	0.522	1.00
193_Q	196_K	0.521	1.00
164_Q	167_I	0.521	1.00
67_F	70_P	0.520	1.00
177_F	180_T	0.519	1.00
106_E	218_I	0.518	1.00
108_A	162_L	0.513	1.00
22_Y	37_E	0.511	1.00
214_A	218_I	0.509	1.00
12_T	37_E	0.505	1.00
187_N	224_R	0.503	1.00
144_E	174_R	0.501	1.00
69_A	175_A	0.501	1.00
194_E	216_T	0.500	1.00
56_R	164_Q	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
3c7jA	4	0.9039	100	0.153	Contact Map
2di3A	2	0.9694	100	0.155	Contact Map
4p96A	2	0.9956	100	0.155	Contact Map
3sxyA	2	0.8646	100	0.166	Contact Map
2hs5A	1	0.8908	100	0.175	Contact Map
3ihuA	1	0.8821	100	0.18	Contact Map
4p9fA	1	0.9039	100	0.18	Contact Map
1hw1A	2	0.9738	100	0.192	Contact Map
3by6A	2	0.5109	99.9	0.535	Contact Map
3ic7A	2	0.4847	99.9	0.536	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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