OPENSEQ.org - LYSQ - ECOLI GREMLIN

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LYSQ - Probable lysozyme from lambdoid prophage Qin

UniProt:	P76159	Sequence MNTKIRYGLSAAVLALIGAGASAPQILDQFLDEKEGNHTMAYRDGSGIWTICRGATVVDGKTVFPNMKLSKEKCDQVNAIERDKALAWVERNIKVPLTEPQKAGIASFCPYNIGPGKCFPSTFYKRLNAGDRKGACEAIRWWIKDGGRDCRIRSNNCYGQVIRRDQESALTCWGIEQ	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG13829
Length:	177 (170)
Sequences:	463
Seq/Len:	2.72

LYSQ
Paralog alert: 0.50 [within 20: 0.03] - ratio of genomes with paralogs
Cluster includes: LYSD LYSQ

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Scaled Score	Prob
99_E	103_A	3.562	1.00
131_D	134_G	3.53	1.00
55_A	81_E	2.971	1.00
126_R	138_A	2.752	1.00
138_A	141_W	2.534	1.00
98_T	101_Q	2.264	1.00
136_C	171_T	2.238	1.00
49_W	65_P	2.142	1.00
52_C	74_C	2.087	1.00
37_N	53_R	2.032	1.00
123_F	138_A	1.896	0.99
143_I	149_D	1.783	0.99
71_K	75_D	1.75	0.98
88_W	115_P	1.697	0.98
92_N	119_F	1.69	0.98
62_T	67_M	1.672	0.98
164_R	167_E	1.654	0.97
143_I	161_V	1.632	0.97
41_A	51_I	1.599	0.97
168_S	172_C	1.569	0.96
46_S	145_D	1.532	0.95
152_I	156_N	1.529	0.95
121_S	142_W	1.509	0.95
69_L	74_C	1.505	0.95
108_F	113_I	1.482	0.94
107_S	167_E	1.462	0.94
43_R	49_W	1.446	0.93
32_D	75_D	1.441	0.93
118_C	124_Y	1.436	0.93
86_L	106_A	1.43	0.93
158_Y	162_I	1.428	0.93
34_K	162_I	1.426	0.93
126_R	134_G	1.423	0.93
52_C	69_L	1.42	0.92
48_I	56_T	1.391	0.91
126_R	131_D	1.388	0.91
137_E	168_S	1.367	0.91
99_E	102_K	1.36	0.90
41_A	70_S	1.344	0.89
140_R	168_S	1.339	0.89
85_A	110_P	1.339	0.89
51_I	69_L	1.332	0.89
41_A	67_M	1.291	0.87
13_V	26_I	1.283	0.86
97_L	127_L	1.275	0.86
153_R	156_N	1.253	0.85
108_F	118_C	1.25	0.84
36_G	78_N	1.247	0.84
34_K	166_Q	1.223	0.83
53_R	78_N	1.212	0.82
41_A	66_N	1.194	0.80
102_K	106_A	1.187	0.80
7_Y	10_S	1.185	0.80
42_Y	50_T	1.157	0.77
44_D	47_G	1.152	0.77
30_F	34_K	1.143	0.76
45_G	150_C	1.134	0.75
31_L	107_S	1.104	0.73
122_T	142_W	1.088	0.71
6_R	15_A	1.086	0.71
37_N	71_K	1.082	0.71
24_P	27_L	1.081	0.70
6_R	10_S	1.081	0.70
97_L	101_Q	1.079	0.70
93_I	128_N	1.036	0.66
8_G	11_A	1.032	0.65
18_G	24_P	1.022	0.64
108_F	124_Y	1.017	0.64
90_E	102_K	1.012	0.63
53_R	71_K	1.008	0.63
135_A	171_T	1.001	0.62

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Scaled Score = (raw_score/average(raw_scores)) > 1 are listed. For all 3L/2 predictions, click on one of the links below.

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling

HHsearch Results: GREMLIN results overlayed on top 10 PDB hits:

Legend: Blue filled circles are GREMLIN results (Scaled_score >1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 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	P(%)	HHΔ		Acc
3hdeA	4	0.9322	100	0.15	Contact Map	0.76
1xjtA	1	0.9322	100	0.216	Contact Map	0.726
3hdfA	2	0.791	100	0.225	Contact Map	0.624
2anvA	2	0.8136	100	0.232	Contact Map	0.771
1xjuA	2	0.8136	100	0.238	Contact Map	0.559
4httA	2	0.8701	100	0.334	Contact Map
1swyA	1	0.791	100	0.347	Contact Map	0.658
4e97A	2	0.904	100	0.356	Contact Map	0.663
4epiA	1	0.904	100	0.366	Contact Map	0.67
1wthA	1	0.8927	100	0.367	Contact Map	0.713

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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