OPENSEQ.org - DEF - ECOLI GREMLIN

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DEF - Peptide deformylase

UniProt:	P0A6K3	Sequence MSVLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIVIDVSENRDERLVLINPELLEKSGETGIEEGCLSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFMDYLSPLKQQRIRQKVEKLDRLKARA	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG11440
Length:	169 (165)
Sequences:	2848
Seq/Len:	17.26

DEF
Paralog alert: 0.44 [within 20: 0.01] - ratio of genomes with paralogs

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
57_R	139_V	4.426	1.00
111_A	119_F	3.35	1.00
113_D	117_K	3.32	1.00
110_R	118_P	2.931	1.00
77_E	110_R	2.929	1.00
33_D	114_R	2.685	1.00
15_R	145_D	2.681	1.00
59_I	135_M	2.677	1.00
108_K	120_E	2.616	1.00
36_F	70_R	2.569	1.00
110_R	120_E	2.407	1.00
24_V	28_I	2.177	1.00
123_A	131_I	2.12	1.00
32_V	114_R	2.096	1.00
45_I	126_L	1.999	1.00
32_V	72_V	1.928	1.00
6_V	42_E	1.887	1.00
4_L	52_V	1.869	1.00
40_Y	62_D	1.857	1.00
7_L	13_R	1.846	1.00
50_T	55_H	1.821	1.00
86_G	102_P	1.731	1.00
31_I	58_I	1.71	1.00
24_V	112_L	1.707	1.00
106_K	124_D	1.707	1.00
104_A	132_Q	1.688	1.00
87_I	129_I	1.649	1.00
108_K	122_E	1.649	1.00
59_I	73_L	1.645	1.00
112_L	118_P	1.629	1.00
7_L	11_D	1.623	1.00
113_D	119_F	1.611	1.00
80_E	108_K	1.607	1.00
123_A	127_L	1.606	1.00
26_A	29_Q	1.586	1.00
106_K	122_E	1.565	1.00
82_S	106_K	1.551	1.00
20_P	57_R	1.541	1.00
31_I	54_I	1.532	1.00
18_A	55_H	1.523	1.00
88_E	100_L	1.522	1.00
79_L	110_R	1.502	1.00
4_L	34_D	1.49	1.00
34_D	38_T	1.452	1.00
32_V	58_I	1.419	1.00
25_N	28_I	1.417	1.00
72_V	114_R	1.383	0.99
17_V	20_P	1.37	0.99
7_L	53_D	1.364	0.99
18_A	50_T	1.363	0.99
32_V	74_I	1.32	0.99
29_Q	114_R	1.313	0.99
105_E	125_G	1.31	0.99
13_R	55_H	1.304	0.99
73_L	111_A	1.283	0.99
31_I	52_V	1.283	0.99
135_M	139_V	1.262	0.99
30_R	34_D	1.259	0.99
29_Q	115_D	1.256	0.99
99_A	143_F	1.241	0.98
81_K	104_A	1.222	0.98
19_K	55_H	1.22	0.98
32_V	36_F	1.205	0.98
86_G	100_L	1.181	0.98
73_L	119_F	1.165	0.97
126_L	130_C	1.128	0.97
121_L	131_I	1.128	0.97
27_E	56_Q	1.125	0.97
40_Y	70_R	1.109	0.96
63_V	130_C	1.108	0.96
17_V	139_V	1.107	0.96
8_H	95_P	1.106	0.96
71_L	121_L	1.105	0.96
85_T	104_A	1.096	0.96
20_P	77_E	1.065	0.95
149_P	153_Q	1.063	0.95
45_I	130_C	1.059	0.95
131_I	135_M	1.059	0.95
36_F	60_V	1.058	0.95
73_L	131_I	1.052	0.95
61_I	71_L	1.036	0.94
21_V	58_I	1.033	0.94
79_L	108_K	1.019	0.93

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
3u04A	1	0.9941	100	-0.001	Contact Map	0.868
1n5nA	2	0.9882	100	0.009	Contact Map	0.821
3qu1A	2	0.9822	100	0.021	Contact Map	0.769
1rl4A	2	1	100	0.022	Contact Map	0.845
1xeoA	1	0.9882	100	0.026	Contact Map	0.836
4e9aA	1	0.9941	100	0.026	Contact Map	0.823
2w3tA	1	0.9941	100	0.027	Contact Map	0.905
1v3yA	2	0.9882	100	0.028	Contact Map	0.646
3e3uA	1	1	100	0.031	Contact Map	0.728
4dr8A	4	1	100	0.034	Contact Map	0.835

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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