GNTR - BACSU - GREMLIN Contacts

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GNTR - Gluconate operon transcriptional repressor

UniProt:	P10585	Sequences: MLDSKDLLYPAKWLSKASTGVRVAYELRMRIVSGLIESGTILSENTIAAEFSVSRSPVREALKILASEKIIRLERMGAVVIGLTEKKIAEIYDVRLLLETFVFERLVKIDIEPLVKDLSKILEMMKVSIKYEDADEFSFQDVLFHETIIRAIDHSYIQMIWNNLKPVMESFILLSMRVRLKEKYEDFTRILDNHELYIQAIKTKDRALMIQSLHQNFDDVQDKVEDLWLSQQMLAKGAEYNND	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	243 (205)
Sequences:	23427 (17318)
Seq/√Len:	1209.6

ECOLI - YDFH MCBR YJJM PDHR GLCC NANR CSIR EXUR YIEP UXUR LLDR DGOR FADR FRLR
BACSU - GNTR YDHC YCBG LUTR
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
119_S	202_K	3.844	1.00
104_E	210_I	3.331	1.00
205_D	208_L	2.954	1.00
126_K	195_E	2.819	1.00
30_R	35_L	2.730	1.00
37_E	40_T	2.719	1.00
30_R	50_E	2.420	1.00
97_L	101_F	2.319	1.00
90_E	155_S	2.281	1.00
44_E	55_R	2.234	1.00
117_D	147_T	2.207	1.00
96_L	218_D	2.107	1.00
24_A	64_I	2.073	1.00
72_R	81_I	2.026	1.00
28_R	68_E	1.979	1.00
23_V	53_V	1.962	1.00
108_K	206_R	1.953	1.00
93_D	105_R	1.939	1.00
73_L	78_A	1.820	1.00
115_V	202_K	1.809	1.00
200_A	208_L	1.804	1.00
150_R	158_Q	1.798	1.00
23_V	51_F	1.792	1.00
114_L	153_D	1.787	1.00
111_I	114_L	1.767	1.00
147_T	150_R	1.721	1.00
26_E	30_R	1.657	1.00
133_D	136_E	1.652	1.00
122_L	198_I	1.644	1.00
193_N	219_D	1.628	1.00
100_T	214_H	1.608	1.00
17_A	25_Y	1.600	1.00
104_E	206_R	1.598	1.00
208_L	212_S	1.590	1.00
94_V	160_I	1.581	1.00
29_M	33_S	1.565	1.00
100_T	210_I	1.563	1.00
210_I	214_H	1.560	1.00
145_H	194_H	1.558	1.00
101_F	104_E	1.525	1.00
196_L	212_S	1.463	1.00
199_Q	203_T	1.434	1.00
146_E	162_N	1.431	1.00
103_F	209_M	1.412	1.00
121_I	140_Q	1.409	1.00
124_M	140_Q	1.406	1.00
24_A	68_E	1.406	1.00
159_M	163_N	1.402	1.00
149_I	161_W	1.399	1.00
119_S	198_I	1.383	1.00
96_L	214_H	1.380	1.00
114_L	151_A	1.379	1.00
126_K	191_L	1.371	1.00
156_Y	167_V	1.367	1.00
203_T	208_L	1.349	1.00
45_N	49_A	1.338	1.00
96_L	221_Q	1.335	1.00
90_E	156_Y	1.330	1.00
195_E	199_Q	1.324	1.00
124_M	143_L	1.283	1.00
119_S	123_E	1.278	1.00
110_D	115_V	1.266	1.00
206_R	210_I	1.263	1.00
120_K	124_M	1.247	1.00
46_T	50_E	1.238	1.00
121_I	147_T	1.224	1.00
211_Q	215_Q	1.221	1.00
41_I	79_V	1.211	1.00
22_R	26_E	1.208	1.00
43_S	46_T	1.199	1.00
47_I	58_V	1.197	1.00
95_R	99_E	1.197	1.00
96_L	100_T	1.197	1.00
193_N	216_N	1.196	1.00
122_L	195_E	1.195	1.00
208_L	211_Q	1.193	1.00
26_E	29_M	1.188	1.00
30_R	51_F	1.185	1.00
89_A	225_E	1.160	1.00
146_E	150_R	1.150	1.00
100_T	104_E	1.146	1.00
26_E	51_F	1.144	1.00
66_A	73_L	1.143	1.00
143_L	147_T	1.139	1.00
136_E	139_F	1.130	1.00
90_E	154_H	1.128	1.00
89_A	221_Q	1.126	1.00
104_E	207_A	1.124	1.00
110_D	204_K	1.118	1.00
214_H	218_D	1.112	1.00
110_D	114_L	1.110	1.00
199_Q	202_K	1.110	1.00
110_D	151_A	1.109	1.00
148_I	201_I	1.105	1.00
141_D	145_H	1.101	1.00
103_F	107_V	1.097	1.00
115_V	198_I	1.095	1.00
103_F	213_L	1.089	1.00
198_I	202_K	1.070	1.00
93_D	154_H	1.065	1.00
102_V	149_I	1.058	1.00
147_T	151_A	1.051	1.00
117_D	150_R	1.041	1.00
36_I	80_V	1.040	1.00
119_S	195_E	1.038	1.00
121_I	143_L	1.032	1.00
122_L	125_M	1.028	1.00
194_H	216_N	1.023	1.00
123_E	126_K	1.011	1.00
115_V	204_K	1.010	1.00
152_I	158_Q	1.001	1.00
17_A	22_R	0.995	1.00
122_L	126_K	0.993	1.00
107_V	206_R	0.991	1.00
145_H	216_N	0.989	1.00
221_Q	225_E	0.988	1.00
160_I	163_N	0.986	1.00
117_D	120_K	0.985	1.00
140_Q	143_L	0.979	1.00
66_A	71_I	0.979	1.00
200_A	205_D	0.972	1.00
99_E	145_H	0.971	1.00
196_L	215_Q	0.967	1.00
20_G	64_I	0.961	1.00
196_L	208_L	0.955	1.00
60_E	63_K	0.955	1.00
62_L	78_A	0.954	1.00
192_D	196_L	0.953	1.00
101_F	210_I	0.952	1.00
41_I	77_G	0.949	1.00
144_F	198_I	0.948	1.00
30_R	36_I	0.941	1.00
116_K	120_K	0.941	1.00
117_D	121_I	0.936	1.00
72_R	79_V	0.934	1.00
197_Y	213_L	0.934	1.00
105_R	109_I	0.933	1.00
31_I	80_V	0.928	1.00
107_V	201_I	0.927	1.00
139_F	143_L	0.922	1.00
44_E	59_R	0.916	1.00
87_K	156_Y	0.915	1.00
71_I	78_A	0.905	1.00
196_L	199_Q	0.893	1.00
158_Q	162_N	0.887	1.00
24_A	28_R	0.883	1.00
207_A	211_Q	0.880	1.00
95_R	217_F	0.873	1.00
94_V	156_Y	0.869	1.00
19_T	22_R	0.865	1.00
64_I	67_S	0.864	1.00
126_K	130_K	0.864	1.00
84_T	87_K	0.859	1.00
141_D	194_H	0.859	1.00
207_A	210_I	0.859	1.00
101_F	105_R	0.858	1.00
119_S	199_Q	0.854	1.00
121_I	124_M	0.850	1.00
115_V	119_S	0.849	1.00
46_T	49_A	0.847	1.00
54_S	57_P	0.844	1.00
28_R	70_I	0.842	1.00
109_I	153_D	0.842	1.00
112_E	116_K	0.841	1.00
191_L	195_E	0.840	1.00
48_A	58_V	0.834	1.00
76_M	79_V	0.833	1.00
63_K	66_A	0.833	1.00
110_D	201_I	0.830	1.00
86_K	153_D	0.828	1.00
107_V	204_K	0.817	1.00
53_V	58_V	0.808	1.00
123_E	127_V	0.807	1.00
28_R	32_V	0.805	1.00
118_L	198_I	0.804	1.00
47_I	62_L	0.803	1.00
197_Y	212_S	0.801	1.00
124_M	127_V	0.801	1.00
123_E	195_E	0.800	1.00
21_V	64_I	0.795	1.00
128_S	136_E	0.795	1.00
196_L	200_A	0.787	1.00
112_E	204_K	0.786	1.00
156_Y	160_I	0.784	1.00
19_T	57_P	0.783	1.00
118_L	147_T	0.782	1.00
114_L	117_D	0.778	1.00
93_D	221_Q	0.777	1.00
106_L	151_A	0.776	1.00
20_G	24_A	0.773	1.00
125_M	137_F	0.769	1.00
107_V	209_M	0.768	1.00
188_T	192_D	0.768	1.00
62_L	71_I	0.766	1.00
127_V	131_Y	0.764	1.00
218_D	222_D	0.756	1.00
200_A	212_S	0.754	1.00
86_K	90_E	0.754	1.00
156_Y	159_M	0.750	1.00
18_S	21_V	0.750	1.00
105_R	108_K	0.744	1.00
146_E	165_K	0.733	1.00
124_M	136_E	0.730	1.00
105_R	154_H	0.729	1.00
63_K	73_L	0.729	1.00
212_S	215_Q	0.727	1.00
94_V	157_I	0.719	1.00
117_D	143_L	0.718	1.00
211_Q	214_H	0.713	1.00
116_K	202_K	0.713	1.00
104_E	108_K	0.710	1.00
93_D	109_I	0.706	1.00
92_Y	220_V	0.706	1.00
116_K	119_S	0.701	1.00
122_L	191_L	0.696	1.00
136_E	140_Q	0.691	1.00
35_L	50_E	0.690	1.00
197_Y	209_M	0.687	1.00
115_V	201_I	0.685	1.00
57_P	61_A	0.683	1.00
142_V	169_E	0.680	1.00
94_V	102_V	0.678	1.00
146_E	158_Q	0.675	1.00
114_L	150_R	0.667	1.00
64_I	68_E	0.663	1.00
17_A	21_V	0.659	1.00
215_Q	219_D	0.654	1.00
20_G	60_E	0.652	1.00
218_D	221_Q	0.650	1.00
75_R	78_A	0.648	1.00
120_K	123_E	0.647	1.00
219_D	223_K	0.645	1.00
103_F	206_R	0.645	1.00
197_Y	216_N	0.644	1.00
94_V	98_L	0.643	1.00
106_L	110_D	0.642	1.00
142_V	165_K	0.642	1.00
114_L	147_T	0.642	1.00
143_L	146_E	0.639	1.00
87_K	155_S	0.638	1.00
99_E	194_H	0.637	1.00
106_L	152_I	0.637	1.00
124_M	128_S	0.626	1.00
193_N	196_L	0.623	1.00
96_L	217_F	0.623	1.00
93_D	101_F	0.622	1.00
128_S	140_Q	0.613	1.00
97_L	157_I	0.611	1.00
36_I	40_T	0.609	1.00
137_F	190_I	0.608	1.00
102_V	152_I	0.605	1.00
100_T	213_L	0.599	1.00
102_V	157_I	0.598	1.00
30_R	34_G	0.598	1.00
39_G	82_G	0.594	1.00
74_E	77_G	0.590	1.00
113_P	117_D	0.583	1.00
100_T	206_R	0.580	1.00
97_L	100_T	0.578	1.00
127_V	130_K	0.575	1.00
222_D	225_E	0.574	1.00
128_S	132_E	0.570	1.00
85_E	89_A	0.567	1.00
125_M	191_L	0.566	1.00
16_K	22_R	0.565	1.00
106_L	148_I	0.563	1.00
118_L	151_A	0.562	1.00
45_N	48_A	0.561	1.00
104_E	214_H	0.560	1.00
98_L	161_W	0.559	1.00
51_F	58_V	0.557	1.00
159_M	167_V	0.557	1.00
49_A	52_S	0.554	1.00
38_S	82_G	0.553	1.00
112_E	202_K	0.548	1.00
128_S	133_D	0.548	1.00
185_E	188_T	0.544	1.00
21_V	25_Y	0.543	1.00
42_L	71_I	0.542	1.00
79_V	82_G	0.538	1.00
118_L	122_L	0.537	1.00
149_I	165_K	0.536	1.00
126_K	192_D	0.534	1.00
186_D	189_R	0.532	1.00
32_V	70_I	0.530	1.00
130_K	188_T	0.530	1.00
63_K	67_S	0.522	1.00
103_F	148_I	0.521	1.00
87_K	90_E	0.520	1.00
94_V	97_L	0.520	1.00
105_R	152_I	0.519	1.00
192_D	195_E	0.519	1.00
197_Y	200_A	0.515	1.00
209_M	213_L	0.513	1.00
36_I	42_L	0.512	1.00
159_M	162_N	0.512	1.00
101_F	157_I	0.512	1.00
186_D	223_K	0.511	1.00
45_N	55_R	0.511	1.00
27_L	47_I	0.511	1.00
215_Q	218_D	0.509	1.00
81_I	170_S	0.509	1.00
44_E	78_A	0.509	1.00
99_E	217_F	0.509	1.00
139_F	169_E	0.508	1.00
107_V	210_I	0.505	1.00
135_D	173_L	0.504	1.00
88_I	171_F	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
3sxyA	2	0.8189	100	0.205	Contact Map
3ihuA	1	0.8354	100	0.207	Contact Map
2hs5A	1	0.8477	100	0.213	Contact Map
3c7jA	4	0.9383	100	0.213	Contact Map
4p9fA	1	0.8642	100	0.219	Contact Map
4p96A	2	0.9177	100	0.241	Contact Map
2di3A	2	0.8642	100	0.257	Contact Map
1hw1A	2	0.8436	100	0.268	Contact Map
3ic7A	2	0.4486	99.8	0.587	Contact Map
3by6A	2	0.5021	99.8	0.591	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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