DEOR - ECOLI - GREMLIN Contacts

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DEOR - Deoxyribose operon repressor

UniProt:	P0ACK5	Sequences: METRREERIGQLLQELKRSDKLHLKDAAALLGVSEMTIRRDLNNHSAPVVLLGGYIVLEPRSASHYLLSDQKSRLVEEKRRAAKLAATLVEPDQTLFFDCGTTTPWIIEAIDNEIPFTAVCYSLNTFLALKEKPHCRAFLCGGEFHASNAIFKPIDFQQTLNNFCPDIAFYSAAGVHVSKGATCFNLEELPVKHWAMSMAQKHVLVVDHSKFGKVRPARMGDLKRFDIVVSDCCPEDEYVKYAQTQRIKLMY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10223
Length:	252 (242)
Sequences:	7673 (5622)
Seq/√Len:	361.4

ECOLI - DEOR SGCR AGAR YIHW YDJF GATR YGBI GLPR SRLR ULAR YCIT FUCR
BACSU - YULB GLCR 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_Q	168_I	3.372	1.00
85_L	88_T	3.134	1.00
107_I	206_V	2.981	1.00
137_R	144_E	2.754	1.00
169_A	200_A	2.642	1.00
99_D	193_K	2.467	1.00
15_E	30_L	2.349	1.00
209_H	232_D	2.272	1.00
197_M	221_G	2.256	1.00
109_E	129_A	2.252	1.00
204_V	228_I	2.144	1.00
91_E	94_Q	2.114	1.00
162_N	195_W	2.078	1.00
168_I	204_V	2.073	1.00
15_E	19_S	2.042	1.00
11_Q	14_Q	2.041	1.00
97_F	166_P	2.019	1.00
197_M	203_H	2.011	1.00
84_K	110_A	1.984	1.00
80_R	106_W	1.969	1.00
219_R	222_D	1.948	1.00
235_P	240_V	1.941	1.00
159_Q	162_N	1.938	1.00
98_F	104_T	1.925	1.00
168_I	202_K	1.903	1.00
97_F	196_A	1.859	1.00
120_V	166_P	1.813	1.00
92_P	114_E	1.808	1.00
240_V	244_Q	1.780	1.00
106_W	109_E	1.770	1.00
202_K	228_I	1.758	1.00
222_D	225_R	1.705	1.00
86_A	170_F	1.700	1.00
166_P	196_A	1.689	1.00
159_Q	163_N	1.669	1.00
86_A	206_V	1.648	1.00
140_L	152_F	1.599	1.00
158_Q	191_P	1.584	1.00
107_I	170_F	1.580	1.00
195_W	198_S	1.580	1.00
167_D	201_Q	1.578	1.00
141_C	160_T	1.560	1.00
75_L	210_S	1.558	1.00
127_F	140_L	1.558	1.00
182_A	226_F	1.545	1.00
27_A	38_I	1.508	1.00
87_A	110_A	1.505	1.00
241_K	245_T	1.499	1.00
33_V	38_I	1.498	1.00
162_N	198_S	1.491	1.00
182_A	205_L	1.489	1.00
9_I	48_P	1.489	1.00
21_K	57_V	1.464	1.00
141_C	152_F	1.453	1.00
12_L	27_A	1.447	1.00
157_F	192_V	1.440	1.00
83_A	110_A	1.435	1.00
80_R	110_A	1.434	1.00
89_L	230_V	1.422	1.00
75_L	78_E	1.417	1.00
119_A	130_L	1.408	1.00
15_E	22_L	1.404	1.00
42_L	56_I	1.402	1.00
19_S	26_D	1.399	1.00
195_W	199_M	1.389	1.00
89_L	204_V	1.388	1.00
10_G	14_Q	1.387	1.00
100_C	151_I	1.385	1.00
11_Q	15_E	1.384	1.00
205_L	226_F	1.382	1.00
52_L	55_Y	1.377	1.00
209_H	234_C	1.362	1.00
145_F	152_F	1.357	1.00
17_K	58_L	1.353	1.00
25_K	35_E	1.343	1.00
94_Q	167_D	1.331	1.00
92_P	115_I	1.329	1.00
78_E	232_D	1.327	1.00
9_I	44_N	1.319	1.00
13_L	50_V	1.316	1.00
144_E	188_E	1.308	1.00
76_V	106_W	1.300	1.00
92_P	116_P	1.299	1.00
79_K	102_T	1.296	1.00
141_C	157_F	1.293	1.00
236_E	239_Y	1.280	1.00
112_D	133_K	1.279	1.00
90_V	111_I	1.278	1.00
93_D	116_P	1.276	1.00
119_A	136_C	1.273	1.00
237_D	241_K	1.265	1.00
23_H	26_D	1.256	1.00
176_V	212_F	1.254	1.00
36_M	40_R	1.246	1.00
221_G	225_R	1.230	1.00
80_R	109_E	1.226	1.00
11_Q	30_L	1.220	1.00
85_L	89_L	1.219	1.00
202_K	227_D	1.217	1.00
241_K	244_Q	1.193	1.00
118_T	139_F	1.190	1.00
11_Q	31_L	1.188	1.00
198_S	225_R	1.183	1.00
97_F	199_M	1.168	1.00
108_I	130_L	1.168	1.00
173_A	207_V	1.159	1.00
16_L	51_L	1.157	1.00
14_Q	18_R	1.156	1.00
43_N	47_A	1.145	1.00
170_F	204_V	1.121	1.00
77_E	80_R	1.118	1.00
212_F	235_P	1.118	1.00
177_H	180_K	1.114	1.00
76_V	80_R	1.109	1.00
19_S	30_L	1.109	1.00
78_E	209_H	1.109	1.00
158_Q	192_V	1.107	1.00
156_D	160_T	1.099	1.00
91_E	168_I	1.095	1.00
203_H	226_F	1.091	1.00
118_T	137_R	1.086	1.00
13_L	16_L	1.083	1.00
204_V	230_V	1.080	1.00
173_A	220_M	1.065	1.00
175_G	183_T	1.061	1.00
24_L	42_L	1.056	1.00
16_L	58_L	1.054	1.00
51_L	56_I	1.044	1.00
139_F	144_E	1.036	1.00
44_N	48_P	1.029	1.00
87_A	90_V	1.027	1.00
120_V	164_F	1.009	1.00
90_V	170_F	1.000	1.00
28_A	35_E	0.997	1.00
7_E	11_Q	0.997	1.00
89_L	228_I	0.996	1.00
87_A	107_I	0.990	1.00
98_F	107_I	0.988	1.00
86_A	107_I	0.987	1.00
156_D	164_F	0.979	1.00
212_F	229_V	0.978	1.00
78_E	82_A	0.975	1.00
141_C	161_L	0.970	1.00
174_A	184_C	0.970	1.00
68_L	102_T	0.965	1.00
43_N	46_S	0.958	1.00
79_K	211_K	0.950	1.00
239_Y	242_Y	0.950	1.00
101_G	104_T	0.945	1.00
79_K	103_T	0.943	1.00
103_T	208_D	0.940	1.00
108_I	129_A	0.940	1.00
176_V	207_V	0.939	1.00
169_A	196_A	0.935	1.00
158_Q	195_W	0.930	1.00
83_A	87_A	0.929	1.00
80_R	84_K	0.925	1.00
191_P	194_H	0.923	1.00
15_E	18_R	0.920	1.00
44_N	47_A	0.918	1.00
224_K	246_Q	0.917	1.00
107_I	110_A	0.912	1.00
28_A	38_I	0.906	1.00
104_T	107_I	0.904	1.00
165_C	201_Q	0.902	1.00
125_N	150_A	0.902	1.00
104_T	126_T	0.901	1.00
103_T	211_K	0.899	1.00
163_N	194_H	0.899	1.00
173_A	205_L	0.894	1.00
190_L	218_A	0.893	1.00
83_A	107_I	0.891	1.00
83_A	106_W	0.890	1.00
26_D	30_L	0.888	1.00
82_A	103_T	0.887	1.00
177_H	215_V	0.878	1.00
75_L	208_D	0.875	1.00
138_A	145_F	0.873	1.00
165_C	180_K	0.872	1.00
22_L	56_I	0.870	1.00
22_L	27_A	0.864	1.00
123_S	126_T	0.832	1.00
45_H	50_V	0.831	1.00
164_F	187_L	0.829	1.00
156_D	163_N	0.825	1.00
108_I	126_T	0.825	1.00
149_N	174_A	0.825	1.00
13_L	17_K	0.821	1.00
131_K	150_A	0.821	1.00
201_Q	215_V	0.817	1.00
161_L	196_A	0.815	1.00
165_C	215_V	0.810	1.00
184_C	190_L	0.808	1.00
203_H	227_D	0.806	1.00
165_C	219_R	0.806	1.00
86_A	230_V	0.806	1.00
7_E	10_G	0.804	1.00
112_D	129_A	0.801	1.00
242_Y	245_T	0.801	1.00
170_F	206_V	0.796	1.00
26_D	29_A	0.786	1.00
71_Q	174_A	0.783	1.00
81_R	84_K	0.780	1.00
14_Q	17_K	0.778	1.00
75_L	209_H	0.774	1.00
176_V	182_A	0.767	1.00
187_L	218_A	0.766	1.00
7_E	21_K	0.761	1.00
129_A	132_E	0.760	1.00
180_K	215_V	0.756	1.00
98_F	108_I	0.756	1.00
97_F	161_L	0.754	1.00
173_A	182_A	0.753	1.00
105_P	129_A	0.751	1.00
183_T	215_V	0.750	1.00
104_T	206_V	0.748	1.00
161_L	195_W	0.747	1.00
102_T	211_K	0.746	1.00
178_V	181_G	0.742	1.00
67_L	70_D	0.741	1.00
98_F	119_A	0.737	1.00
133_K	136_C	0.737	1.00
116_P	135_H	0.737	1.00
165_C	199_M	0.727	1.00
77_E	81_R	0.725	1.00
146_H	189_E	0.723	1.00
9_I	13_L	0.723	1.00
100_C	149_N	0.719	0.99
235_P	239_Y	0.716	0.99
163_N	219_R	0.715	0.99
128_L	150_A	0.713	0.99
142_G	157_F	0.711	0.99
184_C	220_M	0.711	0.99
197_M	220_M	0.708	0.99
127_F	145_F	0.707	0.99
127_F	152_F	0.706	0.99
182_A	220_M	0.704	0.99
166_P	200_A	0.701	0.99
33_V	36_M	0.698	0.99
46_S	51_L	0.697	0.99
178_V	242_Y	0.696	0.99
20_D	58_L	0.695	0.99
146_H	153_K	0.694	0.99
169_A	203_H	0.693	0.99
208_D	211_K	0.692	0.99
106_W	110_A	0.683	0.99
142_G	160_T	0.682	0.99
176_V	223_L	0.680	0.99
154_P	157_F	0.680	0.99
25_K	29_A	0.679	0.99
52_L	57_V	0.676	0.99
65_H	71_Q	0.672	0.99
207_V	229_V	0.672	0.99
204_V	227_D	0.672	0.99
237_D	240_V	0.668	0.99
84_K	88_T	0.668	0.99
132_E	150_A	0.665	0.99
72_K	105_P	0.660	0.99
96_L	168_I	0.658	0.99
13_L	45_H	0.658	0.99
36_M	123_S	0.656	0.99
95_T	120_V	0.655	0.99
124_L	152_F	0.655	0.99
96_L	119_A	0.653	0.99
27_A	42_L	0.651	0.99
184_C	189_E	0.649	0.99
122_Y	196_A	0.646	0.99
171_Y	200_A	0.646	0.99
238_E	242_Y	0.643	0.99
81_R	85_L	0.641	0.99
174_A	216_R	0.641	0.99
24_L	38_I	0.640	0.99
194_H	198_S	0.638	0.99
105_P	125_N	0.634	0.99
155_I	159_Q	0.629	0.99
87_A	114_E	0.629	0.99
164_F	218_A	0.629	0.99
82_A	206_V	0.629	0.99
162_N	199_M	0.626	0.99
124_L	140_L	0.622	0.99
113_N	133_K	0.622	0.99
116_P	137_R	0.621	0.99
6_E	9_I	0.620	0.98
221_G	226_F	0.618	0.98
242_Y	246_Q	0.617	0.98
159_Q	191_P	0.616	0.98
239_Y	243_A	0.615	0.98
121_C	127_F	0.615	0.98
155_I	191_P	0.612	0.98
16_L	22_L	0.611	0.98
31_L	38_I	0.610	0.98
8_R	41_D	0.606	0.98
101_G	172_S	0.605	0.98
200_A	203_H	0.603	0.98
120_V	217_P	0.601	0.98
71_Q	189_E	0.595	0.98
190_L	220_M	0.594	0.98
78_E	234_C	0.590	0.98
65_H	146_H	0.588	0.98
185_F	216_R	0.588	0.98
146_H	186_N	0.587	0.98
99_D	104_T	0.586	0.98
123_S	189_E	0.580	0.98
124_L	128_L	0.577	0.98
155_I	158_Q	0.576	0.98
174_A	189_E	0.574	0.98
172_S	184_C	0.570	0.97
90_V	107_I	0.570	0.97
79_K	208_D	0.570	0.97
171_Y	220_M	0.567	0.97
69_S	72_K	0.565	0.97
125_N	128_L	0.565	0.97
36_M	174_A	0.564	0.97
96_L	170_F	0.564	0.97
72_K	106_W	0.562	0.97
95_T	217_P	0.561	0.97
188_E	191_P	0.559	0.97
158_Q	162_N	0.558	0.97
155_I	188_E	0.558	0.97
193_K	220_M	0.557	0.97
97_F	169_A	0.556	0.97
96_L	107_I	0.555	0.97
114_E	133_K	0.554	0.97
101_G	174_A	0.552	0.97
234_C	240_V	0.552	0.97
174_A	185_F	0.551	0.97
12_L	31_L	0.550	0.97
81_R	233_C	0.549	0.97
174_A	193_K	0.549	0.97
151_I	189_E	0.547	0.97
184_C	193_K	0.545	0.97
120_V	139_F	0.543	0.97
171_Y	197_M	0.543	0.97
42_L	46_S	0.539	0.96
212_F	231_S	0.539	0.96
31_L	37_T	0.539	0.96
192_V	195_W	0.537	0.96
212_F	239_Y	0.536	0.96
175_G	216_R	0.534	0.96
157_F	160_T	0.534	0.96
171_Y	203_H	0.532	0.96
152_F	160_T	0.531	0.96
177_H	183_T	0.531	0.96
40_R	176_V	0.526	0.96
97_F	120_V	0.523	0.96
209_H	235_P	0.522	0.96
101_G	123_S	0.522	0.96
22_L	52_L	0.521	0.96
175_G	214_K	0.520	0.96
130_L	136_C	0.517	0.95
203_H	225_R	0.517	0.95
182_A	221_G	0.515	0.95
113_N	135_H	0.514	0.95
178_V	239_Y	0.513	0.95
24_L	28_A	0.511	0.95
112_D	115_I	0.509	0.95
29_A	32_G	0.508	0.95
115_I	135_H	0.507	0.95
36_M	52_L	0.503	0.95
68_L	150_A	0.501	0.95
159_Q	194_H	0.501	0.95
237_D	244_Q	0.500	0.95
71_Q	99_D	0.500	0.95

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
3rrlB	1	0.6667	100	0.526	Contact Map
1stzA	3	0.9405	100	0.532	Contact Map
2w48A	3	0.9286	100	0.589	Contact Map
3l7oA	2	0.5952	100	0.604	Contact Map
1o8bA	2	0.5833	100	0.608	Contact Map
1m0sA	2	0.6071	100	0.614	Contact Map
1uj6A	2	0.6032	100	0.617	Contact Map
1lk5A	4	0.6032	100	0.617	Contact Map
3uw1A	2	0.6151	100	0.622	Contact Map
4io1A	2	0.6071	100	0.622	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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