LRP - ECOLI - GREMLIN Contacts

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LRP - Leucine-responsive regulatory protein

UniProt:	P0ACJ0	Sequences: MVDSKKRPGKDLDRIDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQGFIQGYTALLNPHYLDASLLVFVEITLNRGAPDVFEQFNTAVQKLEEIQECHLVSGDFDYLLKTRVPDMSAYRKLLGETLLRLPGVNDTRTYVVMEEVKQSNRLVIKTR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10547
Length:	164 (141)
Sequences:	13551 (8650)
Seq/√Len:	728.5

ECOLI - LRP YBAO ASNC
BACSU - YWRC AZLB LRPB YUGG LRPC YEZC LRPA
HALSA - Q9HQ13 Q9HNI1 Q9HQ33 Q9HQB6 Q9HP41 Q9HQG1 Q9HP70 Q9HNW8
SULSO - Q7LXS6 Q97W90 Q7LX67 Q97XP7 LYSM Q97X78 Q980P3 Q97VN7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
53_E	61_Y	2.992	1.00
22_E	37_R	2.925	1.00
105_E	118_K	2.659	1.00
112_D	145_R	2.608	1.00
81_T	143_D	2.551	1.00
31_N	49_V	2.344	1.00
122_P	126_A	2.287	1.00
68_H	125_S	2.238	1.00
16_D	48_R	2.177	1.00
59_Q	66_N	2.098	1.00
22_E	29_I	2.066	1.00
51_R	55_Q	2.011	1.00
83_N	142_N	1.945	1.00
89_V	92_Q	1.935	1.00
77_F	107_H	1.874	1.00
59_Q	64_L	1.839	1.00
100_L	130_L	1.769	1.00
50_R	54_R	1.748	1.00
40_L	44_P	1.728	1.00
22_E	25_K	1.719	1.00
75_L	118_K	1.712	1.00
15_I	40_L	1.710	1.00
100_L	134_T	1.689	1.00
33_E	36_K	1.662	1.00
104_Q	120_R	1.653	1.00
126_A	129_K	1.580	1.00
123_D	126_A	1.579	1.00
19_I	34_L	1.573	1.00
29_I	37_R	1.558	1.00
32_V	36_K	1.551	1.00
79_E	147_Y	1.531	1.00
40_L	45_C	1.492	1.00
96_A	99_K	1.491	1.00
102_E	126_A	1.489	1.00
93_F	97_V	1.479	1.00
41_S	44_P	1.446	1.00
31_N	46_L	1.442	1.00
38_V	45_C	1.429	1.00
28_R	61_Y	1.418	1.00
94_N	98_Q	1.402	1.00
96_A	138_L	1.399	1.00
32_V	42_P	1.373	1.00
129_K	133_E	1.371	1.00
152_E	155_Q	1.358	1.00
78_V	119_T	1.344	1.00
80_I	117_L	1.344	1.00
91_E	95_T	1.314	1.00
81_T	112_D	1.294	1.00
128_R	151_E	1.289	1.00
33_E	37_R	1.274	1.00
14_R	18_N	1.271	1.00
23_L	49_V	1.256	1.00
25_K	37_R	1.256	1.00
29_I	34_L	1.253	1.00
79_E	113_F	1.249	1.00
102_E	134_T	1.236	1.00
94_N	151_E	1.232	1.00
74_L	124_M	1.227	1.00
30_S	33_E	1.225	1.00
13_D	48_R	1.224	1.00
82_L	93_F	1.202	1.00
72_A	122_P	1.199	1.00
15_I	18_N	1.189	1.00
50_R	53_E	1.173	1.00
81_T	142_N	1.165	1.00
15_I	38_V	1.148	1.00
26_D	37_R	1.145	1.00
22_E	34_L	1.123	1.00
79_E	145_R	1.122	1.00
18_N	21_N	1.043	1.00
75_L	120_R	1.033	1.00
31_N	35_S	1.017	1.00
106_C	117_L	1.013	1.00
73_S	123_D	1.008	1.00
66_N	69_Y	0.997	1.00
18_N	22_E	0.996	1.00
109_V	116_L	0.994	1.00
92_Q	96_A	0.987	1.00
28_R	53_E	0.980	1.00
21_N	25_K	0.979	1.00
77_F	116_L	0.970	1.00
27_G	61_Y	0.970	1.00
94_N	115_Y	0.968	1.00
29_I	33_E	0.967	1.00
60_G	64_L	0.966	1.00
31_N	42_P	0.959	1.00
95_T	99_K	0.955	1.00
35_S	45_C	0.942	1.00
103_I	119_T	0.929	1.00
121_V	126_A	0.929	1.00
42_P	46_L	0.928	1.00
119_T	130_L	0.923	1.00
121_V	127_Y	0.921	1.00
95_T	98_Q	0.916	1.00
107_H	118_K	0.898	1.00
77_F	118_K	0.897	1.00
121_V	130_L	0.894	1.00
35_S	40_L	0.881	1.00
34_L	49_V	0.866	1.00
46_L	50_R	0.851	1.00
97_V	106_C	0.841	1.00
32_V	46_L	0.830	1.00
67_P	120_R	0.827	1.00
27_G	63_A	0.825	1.00
52_L	57_F	0.824	1.00
77_F	149_V	0.824	1.00
107_H	152_E	0.823	1.00
103_I	106_C	0.815	1.00
112_D	143_D	0.810	1.00
18_N	38_V	0.807	1.00
107_H	149_V	0.804	1.00
103_I	117_L	0.803	1.00
92_Q	95_T	0.799	1.00
12_L	17_R	0.795	1.00
80_I	93_F	0.790	1.00
129_K	134_T	0.768	1.00
16_D	51_R	0.762	1.00
17_R	21_N	0.760	1.00
34_L	45_C	0.743	1.00
79_E	116_L	0.743	1.00
90_F	115_Y	0.738	1.00
131_L	146_T	0.732	1.00
19_I	29_I	0.729	1.00
110_S	148_V	0.722	1.00
96_A	100_L	0.713	1.00
57_F	69_Y	0.712	1.00
91_E	94_N	0.711	1.00
83_N	140_G	0.711	1.00
27_G	33_E	0.709	1.00
113_F	145_R	0.707	1.00
13_D	16_D	0.696	1.00
93_F	115_Y	0.695	1.00
76_V	127_Y	0.694	1.00
125_S	128_R	0.688	1.00
124_M	148_V	0.686	1.00
83_N	89_V	0.684	1.00
76_V	146_T	0.678	1.00
22_E	26_D	0.676	1.00
94_N	153_V	0.675	1.00
26_D	29_I	0.671	1.00
14_R	17_R	0.670	1.00
78_V	144_T	0.670	1.00
108_L	115_Y	0.670	1.00
43_T	47_E	0.669	1.00
81_T	113_F	0.666	1.00
75_L	149_V	0.662	1.00
47_E	51_R	0.662	1.00
19_I	22_E	0.661	1.00
136_L	144_T	0.656	1.00
27_G	60_G	0.654	1.00
97_V	117_L	0.650	1.00
72_A	120_R	0.648	1.00
19_I	45_C	0.642	1.00
19_I	48_R	0.639	1.00
47_E	50_R	0.634	1.00
12_L	57_F	0.634	1.00
65_L	70_L	0.632	1.00
130_L	135_L	0.631	1.00
31_N	45_C	0.624	1.00
100_L	138_L	0.617	1.00
66_N	70_L	0.616	1.00
80_I	141_V	0.616	1.00
19_I	52_L	0.616	1.00
102_E	130_L	0.609	1.00
78_V	117_L	0.608	1.00
79_E	112_D	0.602	1.00
56_G	59_Q	0.600	1.00
48_R	52_L	0.596	1.00
43_T	46_L	0.595	1.00
35_S	42_P	0.592	1.00
109_V	113_F	0.591	1.00
79_E	109_V	0.585	1.00
131_L	144_T	0.584	1.00
130_L	134_T	0.580	1.00
76_V	148_V	0.579	1.00
125_S	129_K	0.578	1.00
124_M	150_M	0.576	1.00
58_I	61_Y	0.572	1.00
16_D	52_L	0.569	1.00
109_V	149_V	0.569	1.00
126_A	130_L	0.567	1.00
80_I	144_T	0.566	1.00
20_L	52_L	0.561	1.00
92_Q	140_G	0.554	1.00
38_V	44_P	0.551	1.00
26_D	33_E	0.551	1.00
24_Q	62_T	0.546	1.00
19_I	49_V	0.545	1.00
127_Y	148_V	0.545	1.00
112_D	147_Y	0.544	1.00
72_A	102_E	0.543	1.00
17_R	24_Q	0.542	1.00
75_L	107_H	0.542	1.00
134_T	138_L	0.534	1.00
30_S	35_S	0.530	1.00
15_I	44_P	0.526	1.00
92_Q	139_P	0.526	1.00
100_L	103_I	0.523	1.00
96_A	139_P	0.519	1.00
131_L	150_M	0.519	1.00
108_L	114_D	0.519	1.00
82_L	114_D	0.516	1.00
104_Q	118_K	0.511	1.00
75_L	152_E	0.511	1.00
88_D	92_Q	0.511	1.00
110_S	150_M	0.508	1.00
91_E	137_R	0.505	1.00
32_V	35_S	0.504	0.99
105_E	155_Q	0.502	0.99
90_F	136_L	0.501	0.99
102_E	122_P	0.501	0.99
136_L	143_D	0.500	0.99

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
4ch7A	1	0.8293	100	0.199	Contact Map
4un1A	1	0.8659	100	0.221	Contact Map
4un1B	1	0.9146	100	0.222	Contact Map
2e1cA	1	0.8963	100	0.227	Contact Map
4pcqA	2	0.9207	100	0.232	Contact Map
2p5vA	5	0.9573	100	0.237	Contact Map
3i4pA	5	0.9268	100	0.25	Contact Map
2ia0A	2	0.8963	100	0.261	Contact Map
2pn6A	5	0.8963	100	0.271	Contact Map
2cg4A	6	0.9085	100	0.271	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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