LEXA - ECOLI - GREMLIN Contacts

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LEXA - LexA repressor

UniProt:	P0A7C2	Sequences: MKALTARQQEVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLKALARKGVIEIVSGASRGIRLLQEEEEGLPLVGRVAAGEPLLAQQHIEGHYQVDPSLFKPNADFLLRVSGMSMKDIGIMDGDLLAVHKTQDVRNGQVVVARIDDEVTVKRLKKQGNKVELLPENSEFKPIVVDLRQQSFTIEGLAVGVIRNGDWL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10533
Length:	202 (181)
Sequences:	4858 (3424)
Seq/√Len:	254.5

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_I	47_L	3.992	1.00
157_R	170_E	3.824	1.00
18_H	22_T	2.799	1.00
82_V	146_V	2.768	1.00
131_L	155_V	2.659	1.00
118_M	174_F	2.590	1.00
84_A	115_V	2.577	1.00
126_M	129_D	2.398	1.00
164_K	178_V	2.384	1.00
122_D	172_S	2.295	1.00
112_L	130_L	2.287	1.00
11_V	15_I	2.198	1.00
159_K	168_L	2.154	1.00
29_A	40_P	2.121	1.00
143_Q	191_L	2.107	1.00
29_A	33_Q	2.070	1.00
112_L	132_A	2.042	1.00
46_H	53_K	2.007	1.00
75_G	99_Q	1.954	1.00
109_A	135_K	1.951	1.00
139_V	145_V	1.935	1.00
81_R	116_S	1.932	1.00
123_I	170_E	1.897	1.00
76_L	112_L	1.855	1.00
148_R	187_T	1.846	1.00
161_Q	166_E	1.762	1.00
9_Q	13_D	1.754	1.00
133_V	192_A	1.751	1.00
159_K	166_E	1.747	1.00
168_L	176_P	1.696	1.00
154_T	169_P	1.661	1.00
17_D	21_Q	1.642	1.00
114_R	130_L	1.604	1.00
155_V	192_A	1.598	1.00
179_V	186_F	1.572	1.00
44_E	48_K	1.564	1.00
18_H	21_Q	1.549	1.00
150_D	185_S	1.533	1.00
14_L	18_H	1.520	1.00
38_R	41_N	1.502	1.00
125_I	144_V	1.469	1.00
118_M	173_E	1.450	1.00
31_I	43_A	1.436	1.00
124_G	170_E	1.412	1.00
133_V	146_V	1.386	1.00
147_A	158_L	1.381	1.00
115_V	155_V	1.371	1.00
78_L	96_G	1.367	1.00
45_E	50_L	1.357	1.00
12_F	47_L	1.346	1.00
115_V	131_L	1.343	1.00
40_P	44_E	1.320	1.00
37_F	43_A	1.318	1.00
28_R	47_L	1.317	1.00
164_K	180_D	1.257	1.00
30_E	34_R	1.251	1.00
144_V	157_R	1.249	1.00
53_K	56_I	1.235	1.00
131_L	192_A	1.215	1.00
37_F	42_A	1.194	1.00
123_I	144_V	1.187	1.00
148_R	189_E	1.185	1.00
27_T	30_E	1.178	1.00
28_R	40_P	1.168	1.00
145_V	158_L	1.163	1.00
150_D	184_Q	1.159	1.00
62_A	66_I	1.158	1.00
12_F	19_I	1.151	1.00
59_V	63_S	1.148	1.00
45_E	51_A	1.146	1.00
28_R	44_E	1.143	1.00
98_Y	112_L	1.139	1.00
16_R	47_L	1.127	1.00
37_F	46_H	1.126	1.00
32_A	35_L	1.122	1.00
85_G	156_K	1.113	1.00
129_D	197_R	1.102	1.00
12_F	49_A	1.092	1.00
51_A	56_I	1.080	1.00
59_V	62_A	1.078	1.00
110_D	193_V	1.075	1.00
42_A	46_H	1.066	1.00
43_A	46_H	1.064	1.00
41_N	44_E	1.061	1.00
32_A	40_P	1.055	1.00
108_N	134_H	1.050	1.00
126_M	197_R	1.044	1.00
83_A	87_P	1.041	1.00
42_A	45_E	1.023	1.00
111_F	135_K	1.021	1.00
166_E	176_P	1.020	1.00
119_S	156_K	1.016	1.00
146_V	155_V	1.005	1.00
110_D	132_A	1.001	1.00
125_I	155_V	1.001	1.00
30_E	33_Q	0.995	1.00
115_V	125_I	0.988	1.00
122_D	170_E	0.987	1.00
169_P	176_P	0.978	1.00
87_P	154_T	0.971	1.00
157_R	168_L	0.955	1.00
57_E	67_R	0.952	1.00
147_A	167_L	0.932	1.00
82_V	155_V	0.932	1.00
10_E	13_D	0.928	1.00
123_I	157_R	0.922	1.00
51_A	54_G	0.920	1.00
146_V	192_A	0.916	1.00
28_R	45_E	0.912	1.00
76_L	110_D	0.910	1.00
139_V	191_L	0.910	1.00
117_G	127_D	0.902	1.00
28_R	43_A	0.900	1.00
113_L	146_V	0.899	1.00
80_G	113_L	0.893	1.00
45_E	49_A	0.888	1.00
78_L	112_L	0.877	1.00
132_A	194_G	0.877	1.00
37_F	41_N	0.870	1.00
82_V	113_L	0.868	1.00
63_S	68_L	0.863	1.00
166_E	178_V	0.863	1.00
50_L	54_G	0.862	1.00
31_I	34_R	0.862	1.00
63_S	66_I	0.861	0.99
62_A	65_G	0.854	0.99
140_R	143_Q	0.841	0.99
85_G	117_G	0.839	0.99
160_K	165_V	0.834	0.99
13_D	17_D	0.833	0.99
107_P	134_H	0.832	0.99
145_V	191_L	0.831	0.99
81_R	114_R	0.829	0.99
83_A	88_L	0.828	0.99
110_D	135_K	0.827	0.99
46_H	51_A	0.827	0.99
122_D	126_M	0.823	0.99
117_G	156_K	0.823	0.99
60_S	63_S	0.816	0.99
41_N	45_E	0.814	0.99
29_A	32_A	0.811	0.99
11_V	46_H	0.811	0.99
161_Q	164_K	0.810	0.99
10_E	14_L	0.809	0.99
38_R	42_A	0.797	0.99
66_I	69_L	0.793	0.99
134_H	137_Q	0.787	0.99
109_A	136_T	0.785	0.99
57_E	61_G	0.785	0.99
38_R	45_E	0.780	0.99
149_I	179_V	0.779	0.99
65_G	68_L	0.779	0.99
18_H	66_I	0.775	0.99
48_K	52_R	0.770	0.99
82_V	85_G	0.768	0.99
180_D	184_Q	0.767	0.99
144_V	155_V	0.763	0.99
40_P	46_H	0.761	0.99
14_L	17_D	0.759	0.99
141_N	160_K	0.758	0.99
32_A	43_A	0.757	0.99
51_A	55_V	0.756	0.99
149_I	152_E	0.756	0.99
77_P	97_H	0.753	0.99
78_L	130_L	0.750	0.99
125_I	195_V	0.744	0.99
94_I	97_H	0.744	0.99
16_R	20_S	0.741	0.98
141_N	159_K	0.739	0.98
148_R	151_D	0.737	0.98
14_L	31_I	0.724	0.98
27_T	31_I	0.722	0.98
37_F	55_V	0.720	0.98
163_N	180_D	0.713	0.98
95_E	114_R	0.707	0.98
35_L	65_G	0.705	0.98
46_H	54_G	0.704	0.98
139_V	147_A	0.702	0.98
167_L	177_I	0.700	0.98
62_A	69_L	0.700	0.98
12_F	55_V	0.696	0.98
132_A	196_I	0.693	0.98
19_I	27_T	0.688	0.98
110_D	134_H	0.674	0.97
60_S	64_R	0.673	0.97
42_A	51_A	0.672	0.97
28_R	53_K	0.665	0.97
116_S	127_D	0.664	0.97
75_G	97_H	0.660	0.97
63_S	69_L	0.658	0.97
76_L	132_A	0.658	0.97
113_L	153_V	0.655	0.97
169_P	174_F	0.652	0.97
19_I	31_I	0.651	0.97
46_H	49_A	0.644	0.96
79_V	94_I	0.642	0.96
139_V	158_L	0.641	0.96
100_V	104_L	0.641	0.96
144_V	170_E	0.635	0.96
22_T	67_R	0.633	0.96
19_I	24_M	0.631	0.96
133_V	155_V	0.630	0.96
10_E	49_A	0.628	0.96
165_V	186_F	0.623	0.96
51_A	57_E	0.623	0.96
101_D	104_L	0.622	0.96
83_A	86_E	0.620	0.95
118_M	171_N	0.617	0.95
192_A	195_V	0.614	0.95
41_N	48_K	0.610	0.95
118_M	127_D	0.609	0.95
24_M	31_I	0.605	0.95
14_L	34_R	0.605	0.95
37_F	54_G	0.602	0.95
131_L	146_V	0.599	0.95
41_N	54_G	0.593	0.94
45_E	53_K	0.592	0.94
59_V	68_L	0.590	0.94
90_A	153_V	0.589	0.94
50_L	56_I	0.587	0.94
169_P	177_I	0.586	0.94
11_V	53_K	0.586	0.94
13_D	16_R	0.585	0.94
147_A	188_I	0.583	0.94
19_I	28_R	0.582	0.94
46_H	52_R	0.582	0.94
35_L	53_K	0.579	0.94
45_E	55_V	0.578	0.93
47_L	51_A	0.578	0.93
193_V	196_I	0.576	0.93
137_Q	187_T	0.576	0.93
142_G	159_K	0.574	0.93
124_G	129_D	0.567	0.93
156_K	169_P	0.563	0.93
59_V	66_I	0.563	0.93
148_R	153_V	0.563	0.93
24_M	47_L	0.561	0.92
83_A	154_T	0.558	0.92
29_A	50_L	0.557	0.92
35_L	41_N	0.556	0.92
35_L	46_H	0.556	0.92
83_A	127_D	0.552	0.92
18_H	24_M	0.552	0.92
45_E	54_G	0.551	0.92
62_A	68_L	0.551	0.92
61_G	64_R	0.551	0.92
100_V	105_F	0.551	0.92
40_P	45_E	0.551	0.92
78_L	114_R	0.550	0.92
11_V	31_I	0.547	0.92
62_A	67_R	0.547	0.92
144_V	174_F	0.545	0.91
11_V	14_L	0.544	0.91
123_I	171_N	0.539	0.91
90_A	148_R	0.538	0.91
73_E	99_Q	0.533	0.90
35_L	42_A	0.530	0.90
28_R	32_A	0.529	0.90
154_T	177_I	0.529	0.90
129_D	195_V	0.528	0.90
158_L	165_V	0.526	0.90
43_A	47_L	0.525	0.90
28_R	38_R	0.519	0.89
46_H	56_I	0.518	0.89
44_E	53_K	0.516	0.89
44_E	51_A	0.514	0.89
37_F	51_A	0.510	0.88
169_P	175_K	0.509	0.88
35_L	55_V	0.508	0.88
46_H	55_V	0.504	0.88
41_N	55_V	0.500	0.87
87_P	169_P	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
1jhfA	2	0.9802	100	0.24	Contact Map
3bdnA	2	0.9406	100	0.29	Contact Map
3k2zA	2	0.9604	100	0.31	Contact Map
2fjrA	4	0.8416	100	0.419	Contact Map
2hnfA	1	0.599	99.9	0.496	Contact Map
1umuA	2	0.5149	99.9	0.511	Contact Map
1kcaA	6	0.4604	99.9	0.57	Contact Map
2bnmA	3	0.8713	99.8	0.623	Contact Map
1dw9A	6	0.6881	99.6	0.668	Contact Map
4y42A	6	0.6832	99.4	0.706	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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