LEXA - BACSU - GREMLIN Contacts

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LEXA - LexA repressor

UniProt:	P31080	Sequences: MTKLSKRQLDILRFIKAEVKSKGYPPSVREIGEAVGLASSSTVHGHLARLETKGLIRRDPTKPRAIEILDEEVDIPQSQVVNVPVIGKVTAGSPITAVENIEEYFPLPDRMVPPDEHVFMLEIMGDSMIDAGILDKDYVIVKQQNTANNGEIVVAMTEDDEATVKRFYKEDTHIRLQPENPTMEPIILQNVSILGKVIGVFRTVH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	205 (186)
Sequences:	4901 (3467)
Seq/√Len:	254.2

ECOLI - LEXA COHE UMUD
BACSU - LEXA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
19_V	47_L	4.039	1.00
166_R	179_E	3.839	1.00
89_V	154_V	3.000	1.00
126_D	183_M	2.778	1.00
139_V	164_V	2.677	1.00
18_E	22_K	2.649	1.00
91_A	123_I	2.583	1.00
134_L	137_D	2.466	1.00
130_D	181_P	2.370	1.00
173_H	187_I	2.355	1.00
151_E	196_K	2.295	1.00
120_M	138_Y	2.235	1.00
168_Y	177_Q	2.183	1.00
120_M	140_I	2.137	1.00
14_F	72_E	2.109	1.00
29_R	33_E	2.090	1.00
147_A	153_V	2.067	1.00
117_H	143_Q	2.051	1.00
11_I	15_I	2.038	1.00
29_R	40_S	2.032	1.00
170_E	175_R	2.023	1.00
82_N	106_P	1.991	1.00
83_V	120_M	1.961	1.00
88_K	124_M	1.950	1.00
131_A	179_E	1.883	1.00
46_H	53_K	1.879	1.00
156_M	192_S	1.844	1.00
168_Y	175_R	1.779	1.00
141_V	197_V	1.764	1.00
17_A	21_S	1.762	1.00
163_T	178_P	1.704	1.00
44_H	48_A	1.631	1.00
133_I	152_I	1.609	1.00
122_E	138_Y	1.603	1.00
177_Q	185_P	1.602	1.00
18_E	21_S	1.580	1.00
164_V	197_V	1.561	1.00
188_L	191_V	1.553	1.00
35_V	65_A	1.487	1.00
69_L	72_E	1.463	1.00
126_D	182_T	1.440	1.00
38_A	41_S	1.411	1.00
132_G	179_E	1.390	1.00
31_I	43_V	1.369	1.00
141_V	154_V	1.366	1.00
155_A	167_F	1.360	1.00
123_I	164_V	1.351	1.00
51_E	58_R	1.350	1.00
28_V	47_L	1.329	1.00
123_I	139_V	1.324	1.00
14_F	18_E	1.312	1.00
40_S	44_H	1.310	1.00
156_M	194_L	1.310	1.00
85_V	103_E	1.289	1.00
45_G	50_L	1.277	1.00
12_L	47_L	1.250	1.00
131_A	152_I	1.246	1.00
153_V	167_F	1.234	1.00
139_V	197_V	1.226	1.00
92_G	165_K	1.226	1.00
30_E	34_A	1.223	1.00
53_K	58_R	1.221	1.00
37_L	43_V	1.208	1.00
105_F	120_M	1.204	1.00
42_T	46_H	1.191	1.00
34_A	65_A	1.181	1.00
28_V	40_S	1.171	1.00
27_S	30_E	1.154	1.00
116_E	142_K	1.149	1.00
18_E	66_I	1.144	1.00
127_S	165_K	1.138	1.00
37_L	42_T	1.135	1.00
119_F	143_Q	1.124	1.00
32_G	40_S	1.124	1.00
28_V	44_H	1.120	1.00
32_G	35_V	1.114	1.00
51_E	57_R	1.114	1.00
152_I	166_R	1.111	1.00
30_E	33_E	1.107	1.00
175_R	185_P	1.104	1.00
43_V	46_H	1.098	1.00
57_R	67_E	1.095	1.00
118_V	198_I	1.087	1.00
41_S	44_H	1.084	1.00
37_L	46_H	1.074	1.00
130_D	179_E	1.071	1.00
118_V	140_I	1.058	1.00
166_R	177_Q	1.057	1.00
178_P	185_P	1.041	1.00
12_L	19_V	1.041	1.00
154_V	164_V	1.037	1.00
42_T	45_G	1.033	1.00
12_L	49_R	1.026	1.00
133_I	164_V	1.010	1.00
45_G	51_E	1.003	1.00
121_L	154_V	1.002	1.00
123_I	133_I	1.000	1.00
90_T	94_P	1.000	1.00
94_P	163_T	0.992	1.00
16_K	47_L	0.990	1.00
83_V	118_V	0.985	1.00
22_K	66_I	0.982	1.00
22_K	67_E	0.970	1.00
89_V	121_L	0.969	1.00
130_D	134_L	0.958	1.00
169_K	174_I	0.943	1.00
10_D	13_R	0.943	1.00
28_V	43_V	0.943	1.00
149_N	169_K	0.932	1.00
175_R	187_I	0.930	1.00
68_I	72_E	0.928	1.00
131_A	166_R	0.924	1.00
125_G	135_D	0.923	1.00
89_V	164_V	0.922	1.00
154_V	197_V	0.922	1.00
92_G	125_G	0.919	1.00
63_P	68_I	0.916	1.00
148_N	151_E	0.904	1.00
45_G	49_R	0.888	1.00
125_G	165_K	0.888	1.00
29_R	32_G	0.883	1.00
90_T	95_I	0.881	1.00
31_I	62_K	0.881	1.00
13_R	17_A	0.877	1.00
55_L	59_D	0.868	1.00
118_V	143_Q	0.868	1.00
147_A	196_K	0.863	1.00
31_I	34_A	0.861	0.99
85_V	120_M	0.861	0.99
54_G	58_R	0.853	0.99
153_V	196_K	0.852	0.99
170_E	173_H	0.852	0.99
54_G	57_R	0.849	0.99
88_K	122_E	0.848	0.99
85_V	138_Y	0.837	0.99
102_E	122_E	0.834	0.99
152_I	164_V	0.834	0.99
157_T	161_E	0.831	0.99
156_M	160_D	0.827	0.99
32_G	43_V	0.821	0.99
28_V	45_G	0.816	0.99
155_A	176_L	0.813	0.99
157_T	188_L	0.811	0.99
51_E	56_I	0.810	0.99
51_E	54_G	0.806	0.99
117_H	144_Q	0.803	0.99
41_S	45_G	0.795	0.99
84_P	104_Y	0.794	0.99
176_L	186_I	0.791	0.99
40_S	46_H	0.790	0.99
18_E	68_I	0.783	0.99
159_D	190_N	0.781	0.99
46_H	54_G	0.779	0.99
101_I	104_Y	0.776	0.99
97_A	162_A	0.773	0.99
14_F	31_I	0.771	0.99
149_N	168_Y	0.769	0.99
37_L	41_S	0.767	0.99
57_R	60_P	0.761	0.99
178_P	183_M	0.757	0.99
118_V	142_K	0.745	0.99
11_I	46_H	0.738	0.98
140_I	199_G	0.734	0.98
87_G	121_L	0.733	0.98
56_I	66_I	0.728	0.98
89_V	92_G	0.726	0.98
82_N	104_Y	0.725	0.98
126_D	180_N	0.725	0.98
124_M	135_D	0.722	0.98
53_K	56_I	0.721	0.98
147_A	167_F	0.719	0.98
147_A	155_A	0.718	0.98
107_L	111_M	0.717	0.98
48_A	52_T	0.710	0.98
12_L	55_L	0.708	0.98
133_I	200_V	0.703	0.98
37_L	57_R	0.702	0.98
178_P	186_I	0.701	0.98
140_I	201_F	0.699	0.98
38_A	42_T	0.699	0.98
159_D	189_Q	0.694	0.98
121_L	162_A	0.693	0.98
126_D	135_D	0.683	0.97
14_F	17_A	0.681	0.97
145_N	192_S	0.678	0.97
27_S	31_I	0.676	0.97
81_V	109_D	0.673	0.97
38_A	45_G	0.672	0.97
46_H	51_E	0.671	0.97
108_P	111_M	0.668	0.97
24_Y	31_I	0.665	0.97
37_L	55_L	0.664	0.97
18_E	72_E	0.660	0.97
81_V	112_V	0.660	0.97
142_K	145_N	0.657	0.97
16_K	20_K	0.656	0.97
73_V	77_Q	0.654	0.97
141_V	164_V	0.653	0.97
59_D	63_P	0.651	0.97
50_L	54_G	0.650	0.97
83_V	140_I	0.646	0.96
74_D	77_Q	0.645	0.96
150_G	168_Y	0.642	0.96
57_R	61_T	0.630	0.96
42_T	51_E	0.629	0.96
40_S	45_G	0.625	0.96
132_G	137_D	0.623	0.96
41_S	48_A	0.623	0.96
19_V	31_I	0.619	0.95
60_P	64_R	0.617	0.95
16_K	70_D	0.617	0.95
79_Q	109_D	0.616	0.95
197_V	200_V	0.614	0.95
174_I	191_V	0.610	0.95
10_D	49_R	0.608	0.95
14_F	34_A	0.608	0.95
19_V	24_Y	0.606	0.95
11_I	31_I	0.604	0.95
54_G	59_D	0.604	0.95
173_H	189_Q	0.603	0.95
29_R	50_L	0.598	0.95
119_F	154_V	0.597	0.94
90_T	135_D	0.597	0.94
51_E	55_L	0.594	0.94
107_L	112_V	0.593	0.94
46_H	61_T	0.592	0.94
43_V	47_L	0.585	0.94
116_E	143_Q	0.583	0.94
46_H	62_K	0.582	0.94
178_P	184_E	0.580	0.94
139_V	154_V	0.580	0.94
11_I	53_K	0.578	0.93
131_A	180_N	0.578	0.93
152_I	183_M	0.577	0.93
80_V	106_P	0.574	0.93
14_F	68_I	0.574	0.93
41_S	54_G	0.573	0.93
46_H	49_R	0.569	0.93
46_H	55_L	0.567	0.93
46_H	52_T	0.566	0.93
156_M	162_A	0.565	0.93
94_P	178_P	0.565	0.93
12_L	15_I	0.564	0.93
24_Y	65_A	0.561	0.92
91_A	165_K	0.560	0.92
19_V	27_S	0.557	0.92
133_I	137_D	0.557	0.92
152_I	179_E	0.557	0.92
198_I	201_F	0.556	0.92
167_F	174_I	0.555	0.92
19_V	28_V	0.553	0.92
10_D	14_F	0.552	0.92
56_I	59_D	0.551	0.92
92_G	127_S	0.550	0.92
165_K	178_P	0.548	0.92
37_L	54_G	0.546	0.91
149_N	167_F	0.541	0.91
137_D	200_V	0.539	0.91
35_V	41_S	0.538	0.91
22_K	34_A	0.537	0.91
28_V	53_K	0.534	0.91
60_P	63_P	0.534	0.91
85_V	105_F	0.532	0.90
53_K	61_T	0.530	0.90
47_L	51_E	0.527	0.90
18_E	24_Y	0.525	0.90
45_G	53_K	0.524	0.90
144_Q	196_K	0.523	0.90
32_G	37_L	0.518	0.89
170_E	177_Q	0.518	0.89
13_R	16_K	0.518	0.89
19_V	22_K	0.516	0.89
28_V	32_G	0.515	0.89
177_Q	186_I	0.513	0.89
45_G	52_T	0.506	0.88
139_V	200_V	0.506	0.88
163_T	186_I	0.504	0.88
51_E	70_D	0.502	0.88
55_L	58_R	0.500	0.87

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
3bdnA	2	0.9561	100	0.271	Contact Map
1jhfA	2	0.9463	100	0.287	Contact Map
3k2zA	2	0.9415	100	0.319	Contact Map
2fjrA	4	0.8634	100	0.399	Contact Map
2hnfA	1	0.5902	99.9	0.506	Contact Map
1umuA	2	0.4976	99.9	0.51	Contact Map
1kcaA	6	0.4439	99.9	0.584	Contact Map
2bnmA	3	0.8585	99.8	0.612	Contact Map
1dw9A	6	0.6976	99.6	0.669	Contact Map
4y42A	6	0.6927	99.5	0.703	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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