GLCR - BACSU - GREMLIN Contacts

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GLCR - HTH-type transcriptional repressor GlcR

UniProt:	P94591	Sequences: MYQEERLVAILDFLKQHNRITTEQICTLLQVSRDTARRDLVKLEEQNAIIRTRGGAILPTVHQKIQSYSGRLKTVSEEKNKIGRLAASLIHDGDRVILDASTTVQACAKHLNAVDCTVITNSINLADVLSDKEGIEIYLLGGKLEKEHRFLYGSSVIEKLSSYHVDKALIGVVGISEHGITIAHEEDGMVKRKMIQQAKQVIALADHSKLGSTSFYQYAELNEIDLLITDRLPNQAFCDLLDRNGVELLVTEQDEGKD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	258 (246)
Sequences:	7683 (5607)
Seq/√Len:	357.5

ECOLI - YGBI AGAR YIHW GLPR SGCR ULAR SRLR YDJF GATR DEOR YCIT FUCR
BACSU - GLCR YULB IOLR FRUR

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
94_D	167_K	3.296	1.00
85_L	88_S	3.054	1.00
107_C	204_L	2.974	1.00
136_E	143_K	2.709	1.00
168_A	198_A	2.565	1.00
13_F	28_L	2.344	1.00
99_D	191_K	2.326	1.00
207_H	230_D	2.228	1.00
109_K	128_V	2.221	1.00
195_I	219_A	2.217	1.00
226_L	249_L	2.199	1.00
91_H	94_D	2.114	1.00
161_S	193_K	2.080	1.00
167_K	202_I	2.057	1.00
202_I	226_L	2.053	1.00
13_F	17_H	2.045	1.00
9_A	12_D	2.019	1.00
97_I	165_V	1.982	1.00
84_R	110_H	1.981	1.00
80_N	106_A	1.978	1.00
195_I	201_V	1.974	1.00
217_Q	220_E	1.931	1.00
98_L	104_V	1.903	1.00
167_K	200_Q	1.897	1.00
158_E	161_S	1.893	1.00
233_P	238_C	1.847	1.00
97_I	194_M	1.834	1.00
106_A	109_K	1.777	1.00
92_D	114_V	1.769	1.00
238_C	242_D	1.759	1.00
119_I	165_V	1.757	1.00
200_Q	226_L	1.746	1.00
86_A	169_L	1.694	1.00
220_E	223_E	1.666	1.00
165_V	194_M	1.657	1.00
85_L	249_L	1.653	1.00
158_E	162_S	1.645	1.00
193_K	196_Q	1.592	1.00
86_A	204_L	1.591	1.00
157_I	189_M	1.581	1.00
139_L	151_L	1.564	1.00
140_L	159_K	1.560	1.00
126_A	139_L	1.553	1.00
166_D	199_K	1.518	1.00
75_V	208_S	1.518	1.00
107_C	169_L	1.513	1.00
180_I	203_A	1.498	1.00
180_I	224_I	1.497	1.00
31_V	36_A	1.491	1.00
25_I	36_A	1.489	1.00
161_S	196_Q	1.486	1.00
87_A	110_H	1.471	1.00
19_R	57_I	1.470	1.00
156_V	190_V	1.448	1.00
118_V	129_L	1.436	1.00
239_D	243_R	1.433	1.00
7_L	46_Q	1.429	1.00
80_N	110_H	1.420	1.00
10_I	25_I	1.418	1.00
83_G	110_H	1.410	1.00
140_L	151_L	1.406	1.00
50_I	59_P	1.403	1.00
40_L	56_A	1.396	1.00
9_A	13_F	1.394	1.00
75_V	78_E	1.394	1.00
92_D	115_D	1.389	1.00
13_F	20_I	1.388	1.00
15_K	58_L	1.382	1.00
234_N	237_F	1.378	1.00
8_V	12_D	1.377	1.00
193_K	197_Q	1.372	1.00
89_L	228_I	1.364	1.00
144_L	151_L	1.360	1.00
94_D	166_D	1.358	1.00
100_A	150_F	1.356	1.00
203_A	224_I	1.355	1.00
17_H	24_Q	1.344	1.00
78_E	230_D	1.337	1.00
143_K	186_E	1.337	1.00
89_L	202_I	1.334	1.00
207_H	232_L	1.320	1.00
52_T	55_G	1.319	1.00
23_E	33_R	1.317	1.00
7_L	42_K	1.298	1.00
118_V	135_I	1.298	1.00
76_S	106_A	1.296	1.00
112_N	132_K	1.290	1.00
219_A	223_E	1.286	1.00
21_T	24_Q	1.276	1.00
11_L	48_A	1.269	1.00
90_I	111_L	1.253	1.00
175_I	210_L	1.252	1.00
9_A	28_L	1.243	1.00
93_G	115_D	1.241	1.00
3_Q	7_L	1.239	1.00
34_D	38_R	1.237	1.00
79_K	102_T	1.237	1.00
140_L	156_V	1.234	1.00
200_Q	225_D	1.231	1.00
85_L	89_L	1.225	1.00
80_N	109_K	1.209	1.00
235_Q	239_D	1.208	1.00
117_T	138_Y	1.196	1.00
9_A	29_L	1.167	1.00
89_L	249_L	1.167	1.00
97_I	197_Q	1.154	1.00
172_V	205_A	1.149	1.00
108_A	129_L	1.146	1.00
239_D	242_D	1.144	1.00
196_Q	223_E	1.140	1.00
14_L	49_I	1.130	1.00
76_S	80_N	1.124	1.00
78_E	207_H	1.124	1.00
77_E	80_N	1.124	1.00
157_I	190_V	1.123	1.00
169_L	202_I	1.119	1.00
41_V	45_E	1.114	1.00
91_H	167_K	1.110	1.00
14_L	58_L	1.104	1.00
210_L	233_P	1.103	1.00
117_T	136_E	1.102	1.00
11_L	14_L	1.101	1.00
17_H	28_L	1.098	1.00
226_L	247_E	1.097	1.00
12_D	16_Q	1.096	1.00
172_V	218_Y	1.080	1.00
155_S	159_K	1.080	1.00
50_I	57_I	1.075	1.00
201_V	224_I	1.072	1.00
174_G	181_T	1.063	1.00
49_I	56_A	1.035	1.00
202_I	228_I	1.024	1.00
22_T	40_L	1.024	1.00
237_F	240_L	1.020	1.00
87_A	90_I	1.018	1.00
86_A	107_C	1.013	1.00
138_Y	143_K	1.011	1.00
68_Y	102_T	1.005	1.00
42_K	46_Q	1.004	1.00
83_G	87_A	1.004	1.00
119_I	163_Y	1.000	1.00
26_C	33_R	0.993	1.00
210_L	227_L	0.988	1.00
78_E	82_I	0.986	1.00
175_I	205_A	0.986	1.00
140_L	160_L	0.982	1.00
98_L	107_C	0.982	1.00
90_I	169_L	0.980	1.00
5_E	9_A	0.976	1.00
155_S	163_Y	0.974	1.00
89_L	226_L	0.951	1.00
104_V	125_L	0.943	1.00
3_Q	42_K	0.942	1.00
108_A	128_V	0.939	1.00
13_F	16_Q	0.939	1.00
157_I	193_K	0.938	1.00
87_A	107_C	0.938	1.00
189_M	192_R	0.936	1.00
173_V	182_I	0.933	1.00
80_N	84_R	0.932	1.00
176_S	213_T	0.929	1.00
222_N	244_N	0.928	1.00
172_V	203_A	0.927	1.00
164_H	178_H	0.922	1.00
168_A	194_M	0.917	1.00
101_S	104_V	0.916	1.00
162_S	192_R	0.915	1.00
42_K	45_E	0.904	1.00
107_C	110_H	0.901	1.00
41_V	44_E	0.900	1.00
82_I	103_T	0.896	1.00
103_T	206_D	0.896	1.00
75_V	206_D	0.890	1.00
188_G	216_Y	0.886	1.00
124_N	149_R	0.884	1.00
164_H	199_K	0.883	1.00
24_Q	28_L	0.882	1.00
83_G	107_C	0.879	1.00
238_C	248_L	0.879	1.00
20_I	56_A	0.878	1.00
79_K	103_T	0.876	1.00
83_G	106_A	0.873	1.00
79_K	209_K	0.871	1.00
104_V	107_C	0.871	1.00
26_C	36_A	0.869	1.00
20_I	25_I	0.865	1.00
122_S	125_L	0.859	1.00
137_I	144_L	0.853	1.00
43_L	48_A	0.847	1.00
108_A	125_L	0.846	1.00
169_L	204_L	0.844	1.00
199_K	213_T	0.844	1.00
130_S	149_R	0.843	1.00
11_L	15_K	0.842	1.00
240_L	243_R	0.840	1.00
103_T	209_K	0.834	1.00
155_S	162_S	0.823	1.00
115_D	134_G	0.820	1.00
148_H	173_V	0.818	1.00
160_L	194_M	0.817	1.00
5_E	8_V	0.812	1.00
160_L	193_K	0.804	1.00
163_Y	185_E	0.802	1.00
164_H	217_Q	0.798	1.00
12_D	15_K	0.798	1.00
81_K	84_R	0.797	1.00
182_I	188_G	0.794	1.00
201_V	225_D	0.784	1.00
185_E	216_Y	0.783	1.00
104_V	204_L	0.778	1.00
164_H	213_T	0.776	1.00
233_P	248_L	0.774	1.00
175_I	180_I	0.773	1.00
71_R	173_V	0.764	1.00
178_H	213_T	0.762	1.00
41_V	51_R	0.762	1.00
86_A	228_I	0.760	1.00
127_D	149_R	0.756	1.00
97_I	160_L	0.752	1.00
164_H	197_Q	0.752	1.00
105_Q	128_V	0.747	1.00
132_K	135_I	0.747	1.00
145_E	187_D	0.743	1.00
75_V	207_H	0.742	1.00
181_T	213_T	0.742	1.00
98_L	108_A	0.738	1.00
162_S	217_Q	0.737	1.00
195_I	218_Y	0.733	1.00
18_N	58_L	0.732	1.00
24_Q	27_T	0.731	1.00
128_V	131_D	0.730	1.00
233_P	237_F	0.727	1.00
40_L	51_R	0.725	1.00
5_E	19_R	0.724	0.99
98_L	118_V	0.717	0.99
77_E	81_K	0.711	0.99
172_V	180_I	0.711	0.99
102_T	209_K	0.708	0.99
7_L	11_L	0.706	0.99
67_S	70_G	0.704	0.99
165_V	198_A	0.704	0.99
112_N	128_V	0.703	0.99
180_I	218_Y	0.698	0.99
65_I	71_R	0.694	0.99
100_A	148_H	0.693	0.99
145_E	152_Y	0.691	0.99
182_I	218_Y	0.690	0.99
192_R	196_Q	0.690	0.99
126_A	144_L	0.687	0.99
23_E	27_T	0.683	0.99
205_A	227_L	0.681	0.99
106_A	110_H	0.680	0.99
168_A	201_V	0.678	0.99
141_G	156_V	0.676	0.99
84_R	88_S	0.675	0.99
72_L	105_Q	0.673	0.99
126_A	151_L	0.673	0.99
175_I	221_L	0.672	0.99
11_L	43_L	0.669	0.99
52_T	57_I	0.669	0.99
141_G	159_K	0.667	0.99
235_Q	238_C	0.667	0.99
182_I	187_D	0.666	0.99
240_L	244_N	0.666	0.99
96_V	118_V	0.662	0.99
31_V	34_D	0.662	0.99
95_R	119_I	0.662	0.99
158_E	189_M	0.659	0.99
153_G	156_V	0.659	0.99
25_I	40_L	0.654	0.99
44_E	51_R	0.653	0.99
131_D	149_R	0.651	0.99
82_I	204_L	0.650	0.99
81_K	85_L	0.649	0.99
44_E	49_I	0.649	0.99
236_A	240_L	0.648	0.99
154_S	189_M	0.648	0.99
206_D	209_K	0.647	0.99
161_S	197_Q	0.638	0.99
113_A	132_K	0.638	0.99
154_S	158_E	0.633	0.99
96_V	167_K	0.632	0.99
22_T	36_A	0.629	0.99
123_I	151_L	0.628	0.99
121_N	194_M	0.626	0.99
114_V	134_G	0.622	0.98
14_L	20_I	0.622	0.98
202_I	225_D	0.618	0.98
170_I	198_A	0.617	0.98
105_Q	124_N	0.617	0.98
34_D	122_S	0.614	0.98
6_R	39_D	0.611	0.98
90_I	107_C	0.611	0.98
115_D	136_E	0.610	0.98
237_F	241_L	0.608	0.98
173_V	214_S	0.605	0.98
163_Y	216_Y	0.605	0.98
29_L	36_A	0.599	0.98
123_I	139_L	0.598	0.98
101_S	171_G	0.597	0.98
95_R	215_F	0.595	0.98
198_A	201_V	0.595	0.98
123_I	127_D	0.592	0.98
186_E	189_M	0.590	0.98
154_S	157_I	0.589	0.98
4_E	7_L	0.588	0.98
120_T	126_A	0.586	0.98
119_I	215_F	0.586	0.98
156_V	159_K	0.584	0.98
176_S	181_T	0.584	0.98
200_Q	247_E	0.584	0.98
78_E	232_L	0.582	0.98
145_E	184_H	0.580	0.98
188_G	218_Y	0.579	0.98
219_A	224_I	0.579	0.98
124_N	127_D	0.578	0.98
150_F	187_D	0.576	0.97
38_R	175_I	0.575	0.97
232_L	238_C	0.574	0.97
157_I	161_S	0.570	0.97
190_V	193_K	0.568	0.97
170_I	218_Y	0.565	0.97
210_L	237_F	0.564	0.97
119_I	138_Y	0.562	0.97
170_I	195_I	0.562	0.97
207_H	233_P	0.562	0.97
99_D	104_V	0.557	0.97
173_V	187_D	0.555	0.97
180_I	219_A	0.550	0.97
96_V	169_L	0.550	0.97
81_K	231_R	0.549	0.97
173_V	183_A	0.548	0.97
170_I	201_V	0.548	0.97
171_G	182_I	0.547	0.97
72_L	106_A	0.546	0.97
183_A	214_S	0.544	0.96
191_K	218_Y	0.541	0.96
154_S	186_E	0.540	0.96
155_S	158_E	0.540	0.96
201_V	223_E	0.538	0.96
34_D	173_V	0.537	0.96
122_S	187_D	0.536	0.96
69_S	72_L	0.533	0.96
71_R	102_T	0.530	0.96
97_I	168_A	0.529	0.96
22_T	26_C	0.529	0.96
101_S	173_V	0.528	0.96
79_K	206_D	0.526	0.96
71_R	187_D	0.524	0.96
174_G	212_S	0.522	0.96
211_G	237_F	0.522	0.96
65_I	145_E	0.521	0.96
100_A	187_D	0.521	0.96
96_V	107_C	0.519	0.95
78_E	81_K	0.517	0.95
113_A	134_G	0.516	0.95
71_R	99_D	0.514	0.95
182_I	191_K	0.513	0.95
158_E	192_R	0.511	0.95
68_Y	149_R	0.509	0.95
27_T	30_Q	0.509	0.95
210_L	229_T	0.508	0.95
97_I	119_I	0.504	0.95
65_I	183_A	0.504	0.95
174_G	214_S	0.504	0.95
238_C	241_L	0.503	0.95
138_Y	155_S	0.502	0.95
155_S	185_E	0.501	0.94
10_I	29_L	0.500	0.94

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
1stzA	3	0.9457	100	0.524	Contact Map
3rrlB	1	0.6783	100	0.544	Contact Map
2w48A	3	0.907	100	0.577	Contact Map
2o0mA	1	0.6822	100	0.616	Contact Map
3l7oA	2	0.6008	100	0.627	Contact Map
1uj6A	2	0.6008	100	0.636	Contact Map
1o8bA	2	0.593	99.9	0.639	Contact Map
4l5jA	4	0.9031	99.9	0.639	Contact Map
1lk5A	4	0.6124	99.9	0.639	Contact Map
3ixqA	4	0.6085	99.9	0.641	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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