Deducing Transport Protein Evolution Based on Sequence, Structure, and Function

Wakabayashi, Steven T.; Shlykov, Maksim A.; Kumar, Ujjwal; Reddy, Vamsee S.; Malhotra, Ankur; Clarke, Erik L.; Chen, Jonathan S.; Castillo, Rostislav; Mare, Russell de La; Sun, Eric I.; Saier, Milton H.

doi:10.1002/9781118743089.ch12

Cited by 1 publication

(4 citation statements)

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“…For example, the browse tab for viewing the TC System ( http://www.tcdb.org/browse.php ) has been entirely redesigned using jQuery. For a more detailed description of the capabilities available to the user, see Wakabayashi et al ( 10 ).…”

Section: Database Content and Accessmentioning

confidence: 99%

“…We have: Incorporated an improved administration page, built-in semi-automatic machine learning tools ( 11 ) and user contributions, allowing protein history tracking, see Wakabayashi et al ( 10 ). Updated software to BLAST 2.2.27.…”

Section: Recent Technical Improvements (2011–13)mentioning

confidence: 99%

“…Affiliation with a family requires satisfying rigorous statistical criteria of homology. Superfamily status is based on the superfamily principle ( 44 , 45 ), stating that if protein A is homologous to protein B, and protein B is homologous to protein C, then protein A must be homologous to protein C, regardless of the degree of sequence similarity observed between proteins A and C. To avoid the concern of convergent evolution, the minimal length of aligned sequences to establish homology is 60 residues, and the comparison score must be at least 12 standard deviations using the GSAT program [see also Wakabayashi et al ( 10 )]. As the protein databases grow, this value must be increased ( 44–46 ).…”

Section: Establishing Homology Between Proteins Using Tcdb-related Somentioning

confidence: 99%

“…These programs can be found in the ‘BioTools’ link of TCDB. A reference resource providing detailed information on these programs can be found in our Wiki ( http://132.239.144.24 ) and in a chapter of a recent book edited by Christine A. Orengo ( 10 ).…”

Section: Establishing Homology Between Proteins Using Tcdb-related Somentioning

confidence: 99%

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The Transporter Classification Database

et al. 2013

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The Transporter Classification Database (TCDB; http://www.tcdb.org) serves as a common reference point for transport protein research. The database contains more than 10 000 non-redundant proteins that represent all currently recognized families of transmembrane molecular transport systems. Proteins in TCDB are organized in a five level hierarchical system, where the first two levels are the class and subclass, the second two are the family and subfamily, and the last one is the transport system. Superfamilies that contain multiple families are included as hyperlinks to the five tier TC hierarchy. TCDB includes proteins from all types of living organisms and is the only transporter classification system that is both universal and recognized by the International Union of Biochemistry and Molecular Biology. It has been expanded by manual curation, contains extensive text descriptions providing structural, functional, mechanistic and evolutionary information, is supported by unique software and is interconnected to many other relevant databases. TCDB is of increasing usefulness to the international scientific community and can serve as a model for the expansion of database technologies. This manuscript describes an update of the database descriptions previously featured in NAR database issues.

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Section: Database Content and Accessmentioning

confidence: 99%