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EffectiveDB specifications

Information


Unique identifier OMICS_03186
Name EffectiveDB
Alternative name Effective
Restrictions to use None
Maintained Yes

Maintainer


  • person_outline Thomas Rattei

Publications for EffectiveDB

EffectiveDB citations

 (7)
library_books

On Burkholderiales order microorganisms and cystic fibrosis in Russia

2018
BMC Genomics
PMCID: 5836817
PMID: 29504898
DOI: 10.1186/s12864-018-4472-9

[…] d that the presence of the T3SS Ysc family is an indicator of an extracellular pathogen.Our searching for effectors of T3SS included four steps (Table ): predicting secreted proteins with the help of EffectiveDB server; correction of data based PSORTb information, choosing only coiled-coil domain containing proteins, and data-sorting according to MxxY motif in protein sequence (Additional file : T […]

library_books

Gene and transcript abundances of bacterial type III secretion systems from the rumen microbiome are correlated with methane yield in sheep

2017
BMC Res Notes
PMCID: 5549432
PMID: 28789673
DOI: 10.1186/s13104-017-2671-0

[…] nslocation of Yersinia outer proteins into eukaryotic cells). Analysis of the amino acid sequences of the predicted protein coding sequences of S. dextrinosolvens strains H5, 22B and ACV-10 using the EffectiveDB suite of software, identified proteins predicted to be secreted by T3SSs, proteins containing conserved chaperone binding domains in their N-terminal regions, eukaryotic-like N-terminal si […]

library_books

The genome of the cotton bacterial blight pathogen Xanthomonas citri pv. malvacearum strain MSCT1

2017
Stand Genomic Sci
PMCID: 5525278
PMID: 28770027
DOI: 10.1186/s40793-017-0253-3

[…] nducible promoter sequences in the promoter region (both strands) of genes were identified with the regular expression ‘TTCGN [] TTCG’, where N is any nucleotide, as described by Lee et al. 2005 [–]. EffectiveDB was used to determine if MSCT1 contains functional T3SS, T4SS, and T6SS secretory systems. EffectiveDB also identified eukaryotic-like domains, potential T3SS, and potential T4SS secreted […]

library_books

Unexpected genomic features in widespread intracellular bacteria: evidence for motility of marine chlamydiae

2017
PMCID: 5604735
PMID: 28644443
DOI: 10.1038/ismej.2017.95

[…] f orthologous groups was determined by blast against the eggNOG database (as in December 2015) (). Prediction of potential effector proteins of the NF-T3SSs was performed using the respective tool at EffectiveDB (). […]

library_books

Interactions “Candidatus Liberibacter solanacearum”—Bactericera cockerelli: Haplotype Effect on Vector Fitness and Gene Expression Analyses

2016
PMCID: 4899927
PMID: 27376032
DOI: 10.3389/fcimb.2016.00062

[…] 5) based on RT-qPCR and transcriptomic analyses.The expression level of CKC_RS04230 and CKC_RS02605 was also determined by RT-qPCR. They were selected among the 92 predicted putative effectors in the EffectiveDB database. They encoded proteins with signal peptides and were predicted to have an ER localization. CKC_RS04230 is a hypothetical protein, and its relative expression was higher in LsoB ps […]

call_split

Host Associated Genomic Features of the Novel Uncultured Intracellular Pathogen Ca. Ichthyocystis Revealed by Direct Sequencing of Epitheliocysts

2016
Genome Biol Evol
PMCID: 4943182
PMID: 27190004
DOI: 10.1093/gbe/evw111
call_split See protocol

[…] Translated gene models from each genome draft were screened for the presence of functional type III and IV secretion systems using EffectiveDB () and T346Hunter (). Prediction of secreted proteins based on eukaryotic-like domains was performed using EffectiveDB with Z-score refinement. […]

Citations

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EffectiveDB institution(s)
Department of Genome Oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Freising, Germany; Department of Computational Systems Biology, Ecology Centre, University of Vienna, Vienna, Austria
EffectiveDB funding source(s)
Austrian Science Fund (FWF) [I 2191]

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