YDJF - ECOLI - GREMLIN Contacts

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YDJF - Uncharacterized HTH-type transcriptional regulator YdjF

UniProt:	P77721	Sequences: MAAKDRIQAIKQMVANDKKVTVSNLSGIFQVTEETIRRDLEKLEDEGFLTRTYGGAVLNTAMLTENIHFYKRASSFYEEKQLIARKALPFIDNKTTMAADSSSTVMELLKLLQDRSGLTLLTNSAEAIHVLAQSEIKVVSTGGELNKNTLSLQGRITKEIIRRYHVDIMVMSCKGLDINSGALDSNEAEAEIKKTMIRQATEVALLVDHSKFDRKAFVQLADFSHINYIITDKSPGAEWIAFCKDNNIQLVW	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13482
Length:	252 (244)
Sequences:	7645 (5639)
Seq/√Len:	361.0

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

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
95_T	168_I	3.390	1.00
86_K	89_P	3.165	1.00
108_L	206_L	2.992	1.00
137_K	144_E	2.776	1.00
169_M	200_A	2.652	1.00
100_D	193_K	2.488	1.00
13_M	28_I	2.362	1.00
209_H	232_D	2.278	1.00
110_K	130_V	2.259	1.00
197_I	221_A	2.255	1.00
204_A	228_Y	2.137	1.00
92_D	95_T	2.100	1.00
162_R	195_T	2.080	1.00
168_I	204_A	2.069	1.00
9_A	12_Q	2.050	1.00
98_A	166_V	2.049	1.00
13_M	17_D	2.033	1.00
197_I	203_V	1.998	1.00
81_Q	107_E	1.995	1.00
85_R	111_L	1.986	1.00
219_Q	222_D	1.977	1.00
235_P	240_I	1.970	1.00
99_A	105_V	1.936	1.00
159_E	162_R	1.922	1.00
168_I	202_E	1.919	1.00
98_A	196_M	1.855	1.00
121_L	166_V	1.833	1.00
107_E	110_K	1.788	1.00
93_N	115_R	1.781	1.00
202_E	228_Y	1.758	1.00
240_I	244_K	1.752	1.00
87_A	170_V	1.729	1.00
222_D	225_H	1.718	1.00
166_V	196_M	1.707	1.00
159_E	163_R	1.660	1.00
87_A	206_L	1.629	1.00
158_K	191_E	1.599	1.00
140_S	152_L	1.597	1.00
195_T	198_R	1.593	1.00
167_D	201_T	1.569	1.00
108_L	170_V	1.569	1.00
141_T	160_I	1.567	1.00
182_A	226_I	1.559	1.00
76_F	210_S	1.554	1.00
128_I	140_S	1.547	1.00
241_A	245_D	1.527	1.00
88_L	111_L	1.514	1.00
162_R	198_R	1.514	1.00
31_V	36_I	1.505	1.00
25_L	36_I	1.505	1.00
182_A	205_L	1.503	1.00
19_K	57_V	1.500	1.00
7_I	46_E	1.468	1.00
10_I	25_L	1.460	1.00
84_A	111_L	1.458	1.00
13_M	20_V	1.439	1.00
141_T	152_L	1.437	1.00
157_T	192_I	1.435	1.00
40_L	56_A	1.428	1.00
17_D	24_N	1.425	1.00
81_Q	111_L	1.424	1.00
8_Q	12_Q	1.409	1.00
90_F	230_I	1.399	1.00
195_T	199_Q	1.396	1.00
9_A	13_M	1.394	1.00
76_F	79_E	1.388	1.00
120_L	131_L	1.386	1.00
90_F	204_A	1.381	1.00
15_A	58_L	1.374	1.00
101_S	151_S	1.366	1.00
145_L	152_L	1.363	1.00
50_T	59_N	1.358	1.00
205_L	226_I	1.357	1.00
209_H	234_S	1.350	1.00
23_S	33_E	1.348	1.00
95_T	167_D	1.347	1.00
93_N	116_S	1.337	1.00
52_T	55_G	1.335	1.00
144_E	188_A	1.331	1.00
236_G	239_W	1.331	1.00
79_E	232_D	1.329	1.00
7_I	42_K	1.297	1.00
77_Y	107_E	1.286	1.00
141_T	157_T	1.282	1.00
93_N	117_G	1.282	1.00
80_K	103_S	1.282	1.00
237_A	241_A	1.281	1.00
120_L	136_I	1.269	1.00
94_K	117_G	1.268	1.00
221_A	225_H	1.265	1.00
11_K	48_F	1.263	1.00
21_T	24_N	1.246	1.00
34_E	38_R	1.245	1.00
176_L	212_F	1.245	1.00
91_I	112_L	1.240	1.00
3_A	7_I	1.228	1.00
9_A	28_I	1.220	1.00
86_K	90_F	1.218	1.00
81_Q	110_K	1.212	1.00
241_A	244_K	1.209	1.00
202_E	227_N	1.203	1.00
119_T	139_V	1.196	1.00
109_L	131_L	1.177	1.00
78_E	81_Q	1.174	1.00
9_A	29_F	1.170	1.00
198_R	225_H	1.163	1.00
177_D	180_S	1.163	1.00
12_Q	16_N	1.152	1.00
14_V	49_L	1.152	1.00
98_A	199_Q	1.152	1.00
173_C	207_V	1.151	1.00
212_F	235_P	1.138	1.00
170_V	204_A	1.125	1.00
158_K	192_I	1.123	1.00
17_D	28_I	1.122	1.00
77_Y	81_Q	1.121	1.00
92_D	168_I	1.115	1.00
41_E	45_D	1.109	1.00
175_G	183_L	1.104	1.00
50_T	57_V	1.091	1.00
11_K	14_V	1.089	1.00
203_V	226_I	1.086	1.00
119_T	137_K	1.082	1.00
156_I	160_I	1.082	1.00
79_E	209_H	1.080	1.00
14_V	58_L	1.074	1.00
204_A	230_I	1.062	1.00
173_C	220_L	1.057	1.00
49_L	56_A	1.050	1.00
22_V	40_L	1.033	1.00
139_V	144_E	1.030	1.00
91_I	170_V	1.019	1.00
88_L	108_L	1.016	1.00
42_K	46_E	1.013	1.00
87_A	108_L	0.996	1.00
121_L	164_Y	0.994	1.00
3_A	42_K	0.993	1.00
90_F	228_Y	0.992	1.00
26_S	33_E	0.986	1.00
88_L	91_I	0.984	1.00
212_F	229_I	0.982	1.00
109_L	130_V	0.980	1.00
141_T	161_I	0.976	1.00
79_E	83_I	0.975	1.00
99_A	108_L	0.975	1.00
5_D	9_A	0.969	1.00
174_K	184_D	0.963	1.00
156_I	164_Y	0.961	1.00
239_W	242_F	0.957	1.00
69_F	103_S	0.952	1.00
176_L	207_V	0.949	1.00
80_K	104_T	0.944	1.00
84_A	88_L	0.943	1.00
105_V	127_A	0.937	1.00
169_M	196_M	0.936	1.00
104_T	208_D	0.935	1.00
13_M	16_N	0.932	1.00
224_S	246_N	0.924	1.00
41_E	44_E	0.924	1.00
24_N	28_I	0.922	1.00
80_K	211_K	0.919	1.00
108_L	111_L	0.918	1.00
190_A	218_V	0.918	1.00
102_S	105_V	0.917	1.00
81_Q	85_R	0.917	1.00
165_H	201_T	0.911	1.00
158_K	195_T	0.911	1.00
173_C	205_L	0.907	1.00
191_E	194_K	0.906	1.00
163_R	194_K	0.904	1.00
177_D	215_K	0.902	1.00
26_S	36_I	0.902	1.00
105_V	108_L	0.895	1.00
83_I	104_T	0.892	1.00
126_E	150_L	0.890	1.00
42_K	45_D	0.887	1.00
104_T	211_K	0.882	1.00
84_A	107_E	0.879	1.00
138_V	145_L	0.871	1.00
84_A	108_L	0.868	1.00
165_H	180_S	0.865	1.00
43_L	48_F	0.865	1.00
76_F	208_D	0.861	1.00
109_L	127_A	0.854	1.00
20_V	56_A	0.850	1.00
20_V	25_L	0.849	1.00
164_Y	187_E	0.840	1.00
113_Q	130_V	0.838	1.00
156_I	163_R	0.835	1.00
124_S	127_A	0.830	1.00
165_H	219_Q	0.827	1.00
149_T	174_K	0.827	1.00
184_D	190_A	0.823	1.00
132_A	150_L	0.819	1.00
201_T	215_K	0.818	1.00
11_K	15_A	0.817	1.00
5_D	8_Q	0.816	1.00
170_V	206_L	0.816	1.00
161_I	196_M	0.815	1.00
242_F	245_D	0.810	1.00
12_Q	15_A	0.802	1.00
165_H	215_K	0.802	1.00
87_A	230_I	0.798	1.00
203_V	227_N	0.797	1.00
113_Q	133_Q	0.791	1.00
72_R	174_K	0.789	1.00
98_A	161_I	0.778	1.00
76_F	209_H	0.775	1.00
82_L	85_R	0.768	1.00
41_E	51_R	0.767	1.00
180_S	215_K	0.766	1.00
187_E	218_V	0.765	1.00
176_L	182_A	0.764	1.00
24_N	27_G	0.761	1.00
5_D	19_K	0.761	1.00
105_V	206_L	0.761	1.00
117_G	135_E	0.759	1.00
183_L	215_K	0.758	1.00
99_A	120_L	0.756	1.00
161_I	195_T	0.755	1.00
146_N	189_E	0.753	1.00
165_H	199_Q	0.744	1.00
99_A	109_L	0.738	1.00
106_M	130_V	0.733	1.00
173_C	182_A	0.732	1.00
163_R	219_Q	0.732	1.00
103_S	211_K	0.728	1.00
107_E	111_L	0.721	0.99
235_P	239_W	0.718	0.99
142_G	157_T	0.718	0.99
128_I	152_L	0.716	0.99
129_H	150_L	0.713	0.99
66_N	72_R	0.711	0.99
184_D	189_E	0.711	0.99
78_E	82_L	0.711	0.99
68_H	71_K	0.698	0.99
18_K	58_L	0.698	0.99
197_I	220_L	0.698	0.99
169_M	203_V	0.697	0.99
101_S	149_T	0.696	0.99
166_V	200_A	0.694	0.99
7_I	11_K	0.694	0.99
128_I	145_L	0.693	0.99
184_D	220_L	0.692	0.99
146_N	153_Q	0.690	0.99
208_D	211_K	0.687	0.99
31_V	34_E	0.686	0.99
154_G	157_T	0.680	0.99
182_A	220_L	0.675	0.99
142_G	160_I	0.675	0.99
11_K	43_L	0.674	0.99
123_N	196_M	0.674	0.99
237_A	240_I	0.673	0.99
176_L	223_F	0.672	0.99
207_V	229_I	0.671	0.99
82_L	86_K	0.669	0.99
85_R	89_P	0.661	0.99
52_T	57_V	0.661	0.99
44_E	51_R	0.659	0.99
23_S	27_G	0.658	0.99
40_L	51_R	0.656	0.99
96_T	121_L	0.656	0.99
25_L	40_L	0.652	0.99
171_M	200_A	0.651	0.99
125_A	152_L	0.651	0.99
204_A	227_N	0.648	0.99
22_V	36_I	0.647	0.99
73_A	106_M	0.644	0.99
194_K	198_R	0.644	0.99
34_E	124_S	0.640	0.99
159_E	191_E	0.639	0.99
83_I	206_L	0.638	0.99
155_R	159_E	0.638	0.99
97_M	120_L	0.638	0.99
97_M	168_I	0.629	0.99
162_R	199_Q	0.628	0.99
122_T	128_I	0.628	0.99
238_E	242_F	0.626	0.99
14_V	20_V	0.625	0.99
174_K	216_A	0.623	0.99
106_M	126_E	0.620	0.98
155_R	191_E	0.619	0.98
242_F	246_N	0.616	0.98
44_E	49_L	0.614	0.98
200_A	203_V	0.613	0.98
164_Y	218_V	0.611	0.98
29_F	36_I	0.611	0.98
121_L	217_F	0.610	0.98
117_G	137_K	0.606	0.98
221_A	226_I	0.606	0.98
79_E	234_S	0.605	0.98
133_Q	136_I	0.602	0.98
125_A	140_S	0.602	0.98
4_K	7_I	0.601	0.98
6_R	39_D	0.600	0.98
102_S	172_S	0.599	0.98
174_K	189_E	0.590	0.98
185_S	216_A	0.586	0.98
88_L	115_R	0.584	0.98
72_R	189_E	0.583	0.98
100_D	105_V	0.582	0.98
146_N	186_N	0.580	0.98
73_A	107_E	0.580	0.98
124_S	189_E	0.579	0.98
190_A	220_L	0.579	0.98
171_M	220_L	0.577	0.98
125_A	129_H	0.576	0.98
70_Y	73_A	0.576	0.98
212_F	239_W	0.574	0.98
155_R	158_K	0.574	0.98
91_I	108_L	0.571	0.97
239_W	243_C	0.571	0.97
151_S	189_E	0.563	0.97
234_S	240_I	0.563	0.97
157_T	160_I	0.562	0.97
80_K	208_D	0.562	0.97
97_M	170_V	0.561	0.97
121_L	139_V	0.561	0.97
82_L	233_K	0.558	0.97
96_T	217_F	0.555	0.97
158_K	162_R	0.555	0.97
102_S	174_K	0.554	0.97
174_K	185_S	0.554	0.97
126_E	129_H	0.553	0.97
66_N	146_N	0.552	0.97
34_E	174_K	0.552	0.97
188_A	191_E	0.552	0.97
193_K	220_L	0.549	0.97
172_S	184_D	0.549	0.97
114_D	133_Q	0.548	0.97
177_D	183_L	0.544	0.97
184_D	193_K	0.543	0.97
192_I	195_T	0.539	0.96
131_L	136_I	0.536	0.96
203_V	225_H	0.536	0.96
116_S	135_E	0.534	0.96
209_H	235_P	0.532	0.96
212_F	231_T	0.531	0.96
174_K	193_K	0.529	0.96
102_S	124_S	0.528	0.96
38_R	176_L	0.527	0.96
98_A	169_M	0.526	0.96
171_M	197_I	0.523	0.96
97_M	108_L	0.522	0.96
175_G	214_R	0.522	0.96
98_A	121_L	0.522	0.96
101_S	189_E	0.520	0.96
178_I	242_F	0.517	0.95
171_M	203_V	0.513	0.95
182_A	221_A	0.512	0.95
178_I	239_W	0.512	0.95
99_A	127_A	0.511	0.95
79_E	82_L	0.511	0.95
159_E	194_K	0.507	0.95
152_L	160_I	0.506	0.95
114_D	135_E	0.506	0.95
10_I	29_F	0.506	0.95
237_A	244_K	0.504	0.95
175_G	216_A	0.504	0.95
155_R	188_A	0.503	0.95
149_T	184_D	0.503	0.95
156_I	159_E	0.503	0.95
20_V	52_T	0.502	0.95
137_K	147_K	0.501	0.95
29_F	35_T	0.500	0.95
27_G	30_Q	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
1stzA	3	0.9405	100	0.512	Contact Map
3rrlB	1	0.6627	100	0.535	Contact Map
2w48A	3	0.9286	100	0.57	Contact Map
3l7oA	2	0.5952	100	0.6	Contact Map
1o8bA	2	0.5833	100	0.603	Contact Map
1m0sA	2	0.6071	100	0.611	Contact Map
1uj6A	2	0.6032	100	0.613	Contact Map
1lk5A	4	0.6032	100	0.613	Contact Map
4io1A	2	0.6071	100	0.616	Contact Map
3uw1A	2	0.6151	100	0.617	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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