YQJI - ECOLI - GREMLIN Contacts

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YQJI - Transcriptional regulator YqjI

UniProt:	P64588	Sequences: MSHHHEGCCKHEGQPRHEGCCKGEKSEHEHCGHGHQHEHGQCCGGRHGRGGGRRQRFFGHGELRLVILDILSRDDSHGYELIKAIENLTQGNYTPSPGVIYPTLDFLQEQSLITIREEEGGKKQIALTEQGAQWLEENREQVEMIEERIKARCVGAALRQNPQMKRALDNFKAVLDLRVNQSDISDAQIKKIIAVIDRAAFDITQLD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12954
Length:	207 (173)
Sequences:	752 (527)
Seq/√Len:	40.1

ECOLI - YQJI
SULSO - Q981A9 Q981A0 Q7LX63

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
198_R	202_D	6.520	1.00
67_I	81_L	4.624	1.00
192_I	203_I	4.538	1.00
129_E	132_A	4.061	1.00
105_D	109_E	3.334	1.00
114_T	126_A	3.299	1.00
195_V	206_L	3.280	1.00
195_V	199_A	3.194	1.00
73_R	88_L	2.790	1.00
166_R	197_D	2.707	1.00
118_E	121_G	2.474	1.00
39_H	43_C	2.459	1.00
115_I	125_I	2.223	1.00
139_R	143_E	2.147	0.99
74_D	80_E	2.078	0.99
170_N	197_D	1.968	0.99
194_A	201_F	1.936	0.99
84_A	87_N	1.764	0.97
103_T	107_L	1.687	0.97
134_W	137_E	1.654	0.96
175_L	203_I	1.568	0.95
35_H	38_E	1.515	0.94
134_W	138_N	1.478	0.93
67_I	100_I	1.471	0.93
58_F	148_R	1.470	0.93
166_R	170_N	1.467	0.93
199_A	203_I	1.428	0.92
89_T	174_V	1.403	0.91
103_T	106_F	1.392	0.91
99_V	103_T	1.391	0.91
138_N	141_Q	1.384	0.90
111_S	130_Q	1.366	0.90
38_E	44_G	1.362	0.90
185_S	188_Q	1.361	0.90
36_Q	39_H	1.360	0.90
58_F	93_Y	1.357	0.90
108_Q	115_I	1.347	0.89
71_L	127_L	1.341	0.89
167_A	193_I	1.335	0.89
133_Q	136_E	1.325	0.88
61_G	64_R	1.322	0.88
39_H	44_G	1.307	0.88
33_H	38_E	1.302	0.87
99_V	105_D	1.295	0.87
88_L	150_K	1.292	0.87
191_K	203_I	1.274	0.86
104_L	125_I	1.273	0.86
135_L	138_N	1.251	0.85
168_L	172_K	1.241	0.85
31_C	35_H	1.231	0.84
140_E	150_K	1.229	0.84
196_I	199_A	1.223	0.84
33_H	39_H	1.189	0.82
167_A	197_D	1.188	0.82
184_I	188_Q	1.180	0.82
164_M	179_V	1.175	0.81
43_C	119_E	1.167	0.81
108_Q	175_L	1.163	0.81
110_Q	127_L	1.159	0.81
77_H	106_F	1.158	0.80
76_S	81_L	1.157	0.80
112_L	172_K	1.149	0.80
57_F	60_H	1.138	0.79
94_T	100_I	1.130	0.79
30_H	33_H	1.119	0.78
30_H	187_A	1.119	0.78
45_G	49_R	1.102	0.77
63_L	204_T	1.096	0.77
35_H	39_H	1.081	0.76
103_T	200_A	1.077	0.75
120_G	124_Q	1.072	0.75
135_L	142_V	1.060	0.74
105_D	125_I	1.060	0.74
143_E	147_E	1.046	0.73
112_L	134_W	1.036	0.72
31_C	34_G	1.035	0.72
171_F	199_A	1.026	0.72
77_H	80_E	1.024	0.72
44_G	140_E	1.023	0.72
53_R	122_K	1.023	0.72
30_H	37_H	1.022	0.71
85_I	103_T	1.011	0.71
40_G	43_C	1.000	0.70
178_R	192_I	0.999	0.70
87_N	107_L	0.998	0.70
132_A	136_E	0.985	0.69
133_Q	137_E	0.972	0.68
48_G	129_E	0.960	0.67
30_H	34_G	0.958	0.66
184_I	192_I	0.944	0.65
109_E	112_L	0.941	0.65
69_D	73_R	0.941	0.65
164_M	176_D	0.936	0.65
72_S	139_R	0.930	0.64
189_I	193_I	0.927	0.64
170_N	200_A	0.924	0.64
32_G	35_H	0.922	0.63
30_H	35_H	0.921	0.63
36_Q	41_Q	0.914	0.63
30_H	147_E	0.914	0.63
71_L	76_S	0.913	0.63
195_V	198_R	0.912	0.63
33_H	36_Q	0.912	0.63
115_I	122_K	0.905	0.62
88_L	94_T	0.903	0.62
38_E	41_Q	0.903	0.62
59_G	67_I	0.899	0.61
57_F	94_T	0.899	0.61
32_G	39_H	0.895	0.61
37_H	41_Q	0.894	0.61
32_G	36_Q	0.894	0.61
106_F	134_W	0.887	0.60
164_M	184_I	0.883	0.60
76_S	83_K	0.881	0.60
130_Q	161_N	0.874	0.59
70_I	75_D	0.873	0.59
92_N	164_M	0.864	0.58
58_F	67_I	0.859	0.58
114_T	120_G	0.853	0.57
76_S	84_A	0.840	0.56
166_R	175_L	0.838	0.56
110_Q	146_E	0.834	0.56
61_G	128_T	0.830	0.55
87_N	133_Q	0.828	0.55
84_A	88_L	0.825	0.55
163_Q	166_R	0.823	0.55
74_D	81_L	0.819	0.54
41_Q	44_G	0.815	0.54
49_R	52_G	0.804	0.53
66_V	146_E	0.797	0.52
126_A	132_A	0.796	0.52
80_E	191_K	0.795	0.52
81_L	103_T	0.794	0.52
93_Y	148_R	0.793	0.52
112_L	135_L	0.793	0.52
64_R	89_T	0.790	0.52
66_V	164_M	0.787	0.51
191_K	202_D	0.784	0.51
168_L	196_I	0.779	0.51
55_Q	80_E	0.774	0.50
62_E	127_L	0.774	0.50
59_G	122_K	0.769	0.50
127_L	135_L	0.762	0.49
184_I	204_T	0.758	0.49
78_G	101_Y	0.758	0.49
129_E	133_Q	0.754	0.48
44_G	48_G	0.753	0.48
54_R	198_R	0.753	0.48
56_R	93_Y	0.744	0.47
72_S	132_A	0.740	0.47
62_E	190_K	0.739	0.47
40_G	44_G	0.738	0.47
34_G	188_Q	0.736	0.47
50_G	198_R	0.734	0.46
60_H	63_L	0.723	0.45
31_C	37_H	0.722	0.45
32_G	43_C	0.719	0.45
60_H	88_L	0.714	0.45
37_H	42_C	0.713	0.45
163_Q	193_I	0.711	0.44
53_R	159_R	0.711	0.44
39_H	138_N	0.708	0.44
113_I	125_I	0.691	0.43
90_Q	176_D	0.688	0.42
72_S	162_P	0.686	0.42
71_L	113_I	0.684	0.42
114_T	129_E	0.683	0.42
93_Y	127_L	0.680	0.42
136_E	139_R	0.678	0.41
76_S	80_E	0.674	0.41
198_R	201_F	0.671	0.41
178_R	184_I	0.670	0.41
66_V	93_Y	0.670	0.41
32_G	194_A	0.667	0.40
34_G	42_C	0.660	0.40
67_I	130_Q	0.656	0.39
93_Y	204_T	0.653	0.39
188_Q	191_K	0.652	0.39
180_N	196_I	0.648	0.39
146_E	156_A	0.647	0.39
178_R	203_I	0.647	0.39
74_D	113_I	0.645	0.39
172_K	193_I	0.642	0.38
62_E	144_M	0.639	0.38
200_A	204_T	0.636	0.38
113_I	118_E	0.633	0.37
37_H	147_E	0.632	0.37
99_V	106_F	0.630	0.37
58_F	63_L	0.630	0.37
44_G	129_E	0.629	0.37
34_G	37_H	0.622	0.37
34_G	38_E	0.622	0.37
129_E	147_E	0.620	0.36
64_R	103_T	0.618	0.36
67_I	145_I	0.616	0.36
97_P	120_G	0.615	0.36
55_Q	111_S	0.610	0.36
36_Q	129_E	0.609	0.35
103_T	170_N	0.607	0.35
64_R	184_I	0.606	0.35
133_Q	185_S	0.605	0.35
85_I	196_I	0.604	0.35
84_A	114_T	0.604	0.35
86_E	91_G	0.599	0.35
58_F	205_Q	0.599	0.35
64_R	110_Q	0.598	0.35
83_K	170_N	0.594	0.34
60_H	99_V	0.589	0.34
94_T	150_K	0.589	0.34
45_G	48_G	0.589	0.34
35_H	43_C	0.588	0.34
93_Y	178_R	0.588	0.34
177_L	204_T	0.586	0.34
80_E	122_K	0.584	0.33
167_A	196_I	0.584	0.33
94_T	204_T	0.583	0.33
125_I	135_L	0.582	0.33
82_I	93_Y	0.580	0.33
34_G	169_D	0.578	0.33
195_V	202_D	0.575	0.33
77_H	165_K	0.574	0.33
65_L	135_L	0.573	0.32
74_D	191_K	0.566	0.32
82_I	100_I	0.564	0.32
161_N	164_M	0.563	0.32
163_Q	197_D	0.561	0.32
60_H	121_G	0.560	0.31
121_G	184_I	0.559	0.31
166_R	205_Q	0.556	0.31
117_E	124_Q	0.553	0.31
194_A	203_I	0.546	0.30
183_D	192_I	0.544	0.30
34_G	39_H	0.544	0.30
130_Q	193_I	0.542	0.30
66_V	163_Q	0.540	0.30
65_L	93_Y	0.539	0.30
94_T	123_K	0.539	0.30
61_G	87_N	0.536	0.30
114_T	147_E	0.535	0.30
89_T	124_Q	0.535	0.30
115_I	123_K	0.534	0.29
71_L	144_M	0.533	0.29
72_S	129_E	0.533	0.29
106_F	110_Q	0.527	0.29
101_Y	104_L	0.527	0.29
85_I	193_I	0.526	0.29
80_E	99_V	0.526	0.29
83_K	112_L	0.522	0.29
31_C	41_Q	0.522	0.29
147_E	150_K	0.520	0.28
93_Y	110_Q	0.520	0.28
38_E	43_C	0.518	0.28
59_G	168_L	0.517	0.28
86_E	104_L	0.516	0.28
77_H	167_A	0.511	0.28
30_H	136_E	0.504	0.27
178_R	204_T	0.503	0.27
80_E	104_L	0.501	0.27
63_L	81_L	0.500	0.27
112_L	128_T	0.500	0.27

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
1bm9A	2	0.5459	99.8	0.694	Contact Map
2rkhA	2	0.5942	99.8	0.702	Contact Map
3l9fA	2	0.6329	99.8	0.714	Contact Map
1yg2A	2	0.6522	99.7	0.733	Contact Map
1xmaA	2	0.4879	99.6	0.752	Contact Map
2eshA	2	0.5314	99.6	0.754	Contact Map
2e1nA	2	0.5169	99.6	0.755	Contact Map
2zfwA	2	0.5169	99.6	0.761	Contact Map
2dqlA	2	0.5314	99.5	0.763	Contact Map
3f8bA	2	0.4879	99.5	0.771	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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