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TransportDB specifications

Information


Unique identifier OMICS_07178
Name TransportDB
Restrictions to use Academic or non-commercial use
Database management system MySQL
Community driven No
Data access File download, Browse
User data submission Allowed
Version 2.0
Maintained Yes

Documentation


Publications for TransportDB

TransportDB citations

 (36)
call_split

Insights into the Evolution of Host Association through the Isolation and Characterization of a Novel Human Periodontal Pathobiont, Desulfobulbus oralis

2018
MBio
PMCID: 5850319
PMID: 29535201
DOI: 10.1128/mBio.02061-17
call_split See protocol

[…] platforms, which included Pfam, COG, TIGRFam, knockout (KO), EC, secretion signal, and transmembrane domains, we also analyzed the predicted proteins and their functions through MetaCyc, eggNOG, and TransportDB. For metabolic reconstruction, we combined the use of the IMG networks, KEGG-BlastKOALA, and MetaCyc-Pathway Tools with individual gene searches (blast and hmmsearch), sequence alignments, […]

library_books

Transcriptional Response to Lactic Acid Stress in the Hybrid Yeast Zygosaccharomyces parabailii

2018
Appl Environ Microbiol
PMCID: 5812937
PMID: 29269498
DOI: 10.1128/AEM.02294-17

[…] ATCC 60483 amino acid sequences against the PFAM database () using HMMER v.3.0 (). A genome-wide annotation of transmembrane proteins was also made by comparing the Z. parabailii proteome against the TransportDB 2.0 () database using BLAST v.2.2.22 (). The sequences were then filtered based on identity (>35%) and coverage (>80%) and submitted to the TMHMM server v.2.0 () to determine a minimum of […]

library_books

Wholly Rickettsia! Reconstructed Metabolic Profile of the Quintessential Bacterial Parasite of Eukaryotic Cells

2017
MBio
PMCID: 5615194
PMID: 28951473
DOI: 10.1128/mBio.00859-17

[…] ted in an iterative process involving bioinformatics predictions, manual evaluation, and comparative genomics analyses. For the R. typhi strain Wilmington genome, 96 transporters were predicted using TransportDB (). The breakdown of these predictions was ATP-dependent systems (n = 38), ion channels (n = 3), secondary transporters (n = 48), and unclassified transporters (n = 7). Several Rickettsia […]

library_books

Network reconstruction and systems analysis of plant cell wall deconstruction by Neurospora crassa

2017
Biotechnol Biofuels
PMCID: 5609067
PMID: 28947916
DOI: 10.1186/s13068-017-0901-2

[…] rom two databases, the CAZY [, ] and the N. crassa e-Compendium [, ]. Following manual curation, we generated an updated list of predicted carbohydrate-active enzymes in N. crassa (Additional file ). TransportDB [, ] was used to obtain a list of predicted transporters in the N. crassa genome. Proteins destined for the secretory pathway are likely to have a signal peptide sequence in their N termin […]

call_split

Into the Wild: Parallel Transcriptomics of the Tsetse Wigglesworthia Mutualism within Kenyan Populations

2017
Genome Biol Evol
PMCID: 5601960
PMID: 28934375
DOI: 10.1093/gbe/evx175
call_split See protocol

[…] torBase annotation, NCBI blastx analyses to the nonredundant protein sequences (nr) database were performed with results filtered to retain only hits with an E-value of < 1e−10 and a BitScore of >50. TRANSPORTDB 2.0 () (http://www.membranetransport.org/transportDB2/index.html; last accessed June 15 2017) was used to describe the predicted cytoplasmic transport protein complement within the Wiggles […]

library_books

Analysis of complete genome sequence and major surface antigens of Neorickettsia helminthoeca, causative agent of salmon poisoning disease

2017
PMCID: 5481527
PMID: 28585301
DOI: 10.1111/1751-7915.12731

[…] scores of E < 10−10.Metabolic pathways and transporters were compared across genomes using (i) the orthologue clusters generated with reciprocal blastp, (ii) Genome Properties (Haft et al., ), (iii) TransportDB (Ren et al., ), (iv) Kyoto Encyclopedia of Genes and Genomes (KEGG, http://www.kegg.jp), and (v) Biocyc (Krieger et al., ). Signal peptides and membrane proteins were predicted using the p […]

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TransportDB institution(s)
Department of Chemistry and Biomolecular Sciences, Macquarie University, NSW, Australia
TransportDB funding source(s)
Macquarie University Research Development Grant (9201401563), Australian Research Council Fellowship Grant (DE150100009)

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