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PMID: 17135193 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels.

Nucleic acids research ·Vol. 35 ·No. Database issue ·2007-01-00 ·Pages D274-9

Ren Q, Chen K, Paulsen IT

Abstract

TransportDB (http://www.membranetransport.org/) is a comprehensive database resource of information on cytoplasmic membrane transporters and outer membrane channels in organisms whose complete genome sequences are available. The complete set of membrane transport systems and outer membrane channels of each organism are annotated based on a series of experimental and bioinformatic evidence and classified into different types and families according to their mode of transport, bioenergetics, molecular phylogeny and substrate specificities. User-friendly web interfaces are designed for easy access, query and download of the data. Features of the TransportDB website include text-based and BLAST search tools against known transporter and outer membrane channel proteins; comparison of transporter and outer membrane channel contents from different organisms; known 3D structures of transporters, and phylogenetic trees of transporter families. On individual protein pages, users can find detailed functional annotation, supporting bioinformatic evidence, protein/DNA sequences, publications and cross-referenced external online resource links. TransportDB has now been in existence for over 10 years and continues to be regularly updated with new evidence and data from newly sequenced genomes, as well as having new features added periodically.

MeSH Terms
Bacterial Outer Membrane Proteins/chemistry,classification,genetics Cytoplasm/metabolism Databases, Protein Genomics Internet Membrane Transport Proteins/chemistry,classification,genetics Phylogeny User-Computer Interface
Chemicals
Bacterial Outer Membrane Proteins Membrane Transport Proteins
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Ren Qinghu
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA.
Chen Kaixi
Paulsen Ian T
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkl925
Published
2007-01-00
Epub
2006-00-28
Pages
D274-9
Language
English
Region
England
NLM ID
0411011
PMCID
PMC1747178
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/gkl925 PMC Full Text View journal details
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