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AromaDeg specifications

Information


Unique identifier OMICS_06783
Name AromaDeg
Restrictions to use Academic or non-commercial use
Maintained Yes

Maintainer


  • person_outline Dietmar H. Pieper

Publication for AromaDeg

AromaDeg citations

 (6)
library_books

Draft Genome Sequence of Monaibacterium marinum C7T, Isolated from Seawater from the Menai Straits, UK, UK

2018
Genome Announc
PMCID: 5794935
PMID: 29437088
DOI: 10.1128/genomeA.01444-17

[…] , 42; other RNA genes 3). Moreover, annotation revealed 3,558 protein-coding genes, with 2,915 having functional predictions. Analysis of the draft genome sequence of Monaibacterium marinum C7T using AromaDeg () and BLASTP against an in-house database (), which contains experimentally characterized enzymes involved in the catabolism of aliphatic and aromatic compounds, predicted genes encoding two […]

library_books

Comparative Genomics of Thalassobius Including the Description of Thalassobius activus sp. nov., and Thalassobius autumnalis sp. nov.

2018
Front Microbiol
PMCID: 5770400
PMID: 29375512
DOI: 10.3389/fmicb.2017.02645

[…] fatase is exclusive of the Shimia spp.-T. aestuarii group.It is interesting to highlight that T. aestuarii shares with T. gelatinovorus the ability to degrade aromatic compounds, as confirmed through Aromadeg (Duarte et al., ) showing a complete that both type strains contain genes coding for extradiol dioxygenases of Viccinal Chelate superfamily and Lig B superfamily (for degrading monocyclic sub […]

library_books

Complete Genome Sequence of a Bacterium Representing a Deep Uncultivated Lineage within the Gammaproteobacteria Associated with the Degradation of Polycyclic Aromatic Hydrocarbons

2016
Genome Announc
PMCID: 5054325
PMID: 27795254
DOI: 10.1128/genomeA.01086-16

[…] most closely related to two environmental clones recovered during SIP experiments with PAHs in our lab (99.8% similarity). The mol% G+C of the genome was 67.79%.The genome of TR3.2 was analyzed using AromaDeg () to detect genes putatively associated with degradation of aromatic compounds. Two novel genes were identified likely to encode for the large subunit of ring-hydroxylating dioxygenases (RHD […]

call_split

Comparative Genomics and Metabolic Analysis Reveals Peculiar Characteristics of Rhodococcus opacus Strain M213 Particularly for Naphthalene Degradation

2016
PLoS One
PMCID: 4988695
PMID: 27532207
DOI: 10.1371/journal.pone.0161032
call_split See protocol

[…] ces for the large subunits of naphthalene dioxygenase (narAa), phthalate 3,4 dioxygenase (phtAa) were mined from the whole genome sequence of strain M213 and phylogenetic trees were constructed using AromaDeg []. AromaDeg is a web-based repository of catabolic protein families such that when queried using a protein sequence of choice, AromaDeg builds a phylogenetic tree revealing clustering of the […]

library_books

Bacterial population and biodegradation potential in chronically crude oil contaminated marine sediments are strongly linked to temperature

2015
Sci Rep
PMCID: 4484246
PMID: 26119183
DOI: 10.1038/srep11651

[…] functional classification of key genes, particularly those encoding proteins of aromatic degradation. In brief, each query sequence from a genome or metagenome that matches a given protein family of AromaDeg is associated with a key catabolic enzyme for an aromatic degradation reaction. Individual reactions, and thus the corresponding substrate pollutants and intermediate degradation products (se […]

library_books

Complete Genome Sequence of a Novel Bacterium within the Family Rhodocyclaceae That Degrades Polycyclic Aromatic Hydrocarbons

2015
Genome Announc
PMCID: 4392151
PMID: 25858839
DOI: 10.1128/genomeA.00251-15

[…] A genes. The G+C content of the chromosome is 55.14%. The closest described relative is Sulfuritalea hydrogenivorans strain sk43H (94% 16S rRNA gene identity).The predicted proteins were submitted to AromaDeg, a database for the identification of genes associated with the degradation of aromatic compounds (). All eight RHD genes previously detected in a metagenome were present in the genome of Ca6 […]

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AromaDeg institution(s)
Microbial Interactions and Processes Research Group, HZI—Helmholtz Centre for Infection Research, Braunschweig, Germany
AromaDeg funding source(s)
European Community Project MAGICPAH (FP7-KBBE-2009-245226)

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